diff --git a/NEWS.md b/NEWS.md index 8c5ca3c555..a4bce3f6be 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,12 @@ # ggplot2 (development version) +* The `summary()` method for ggplots is now more terse about facets + (@teunbrand, #5989). +* `guide_bins()`, `guide_colourbar()` and `guide_coloursteps()` gain an `angle` + argument to overrule theme settings, similar to `guide_axis(angle)` + (@teunbrand, #4594). +* `coord_*(expand)` can now take a logical vector to control expansion at any + side of the panel (top, right, bottom, left) (@teunbrand, #6020) * (Breaking) The defaults for all geoms can be set at one in the theme. (@teunbrand based on pioneering work by @dpseidel, #2239) * A new `theme(geom)` argument is used to track these defaults. @@ -22,7 +29,7 @@ class through new `Coord$draw_panel()` method. * `theme(strip.clip)` now defaults to `"on"` and is independent of Coord clipping (@teunbrand, 5952). -* (internal) rearranged the code of `Facet$draw_paensl()` method (@teunbrand). +* (internal) rearranged the code of `Facet$draw_panels()` method (@teunbrand). * Axis labels are now justified across facet panels (@teunbrand, #5820) * Fixed bug in `stat_function()` so x-axis title now produced automatically when no data added. (@phispu, #5647). @@ -168,6 +175,9 @@ * `theme_classic()` now has black ticks and text instead of dark gray. In addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978). * {tibble} is now suggested instead of imported (@teunbrand, #5986) +* The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, + `labs()` and several guides (@teunbrand, #3196). +* `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647). # ggplot2 3.5.1 diff --git a/R/coord-.R b/R/coord-.R index a57abc7691..64163a772f 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -184,10 +184,11 @@ Coord <- ggproto("Coord", # Will generally have to return FALSE for coordinate systems that enforce a fixed aspect ratio. is_free = function() FALSE, - setup_params = function(data) { + setup_params = function(self, data) { list( guide_default = guide_axis(), - guide_missing = guide_none() + guide_missing = guide_none(), + expand = parse_coord_expand(self$expand %||% TRUE) ) }, @@ -250,6 +251,26 @@ render_axis <- function(panel_params, axis, scale, position, theme) { } } +# Elaborates an 'expand' argument for every side (top, right, bottom or left) +parse_coord_expand <- function(expand) { + check_logical(expand) + if (anyNA(expand)) { + cli::cli_abort("{.arg expand} cannot contain missing values.") + } + + if (!is_named(expand)) { + return(rep_len(expand, 4)) + } + + # Match by top/right/bottom/left + out <- rep(TRUE, 4) + i <- match(names(expand), .trbl) + if (sum(!is.na(i)) > 0) { + out[i] <- unname(expand)[!is.na(i)] + } + out +} + # Utility function to check coord limits check_coord_limits <- function( limits, arg = caller_arg(limits), call = caller_env() diff --git a/R/coord-cartesian-.R b/R/coord-cartesian-.R index bcae23877d..1b13d9c6c0 100644 --- a/R/coord-cartesian-.R +++ b/R/coord-cartesian-.R @@ -9,6 +9,10 @@ #' @param expand If `TRUE`, the default, adds a small expansion factor to #' the limits to ensure that data and axes don't overlap. If `FALSE`, #' limits are taken exactly from the data or `xlim`/`ylim`. +#' Giving a logical vector will separately control the expansion for the four +#' directions (top, left, bottom and right). The `expand` argument will be +#' recycled to length 4 if necessary. Alternatively, can be a named logical +#' vector to control a single direction, e.g. `expand = c(bottom = FALSE)`. #' @param default Is this the default coordinate system? If `FALSE` (the default), #' then replacing this coordinate system with another one creates a message alerting #' the user that the coordinate system is being replaced. If `TRUE`, that warning @@ -100,8 +104,8 @@ CoordCartesian <- ggproto("CoordCartesian", Coord, setup_panel_params = function(self, scale_x, scale_y, params = list()) { c( - view_scales_from_scale(scale_x, self$limits$x, self$expand), - view_scales_from_scale(scale_y, self$limits$y, self$expand) + view_scales_from_scale(scale_x, self$limits$x, params$expand[c(4, 2)]), + view_scales_from_scale(scale_y, self$limits$y, params$expand[c(3, 1)]) ) }, diff --git a/R/coord-flip.R b/R/coord-flip.R index eb46d12669..502ff56f88 100644 --- a/R/coord-flip.R +++ b/R/coord-flip.R @@ -89,6 +89,7 @@ CoordFlip <- ggproto("CoordFlip", CoordCartesian, }, setup_panel_params = function(self, scale_x, scale_y, params = list()) { + params$expand <- params$expand[c(2, 1, 4, 3)] parent <- ggproto_parent(CoordCartesian, self) panel_params <- parent$setup_panel_params(scale_x, scale_y, params) flip_axis_labels(panel_params) diff --git a/R/coord-radial.R b/R/coord-radial.R index 2f44e1ae4b..3a5ccf1ee2 100644 --- a/R/coord-radial.R +++ b/R/coord-radial.R @@ -66,7 +66,6 @@ coord_radial <- function(theta = "x", check_bool(r.axis.inside, allow_null = TRUE) } - check_bool(expand) check_bool(rotate.angle) check_number_decimal(start, allow_infinite = FALSE) check_number_decimal(end, allow_infinite = FALSE, allow_null = TRUE) @@ -139,8 +138,8 @@ CoordRadial <- ggproto("CoordRadial", Coord, setup_panel_params = function(self, scale_x, scale_y, params = list()) { params <- c( - view_scales_polar(scale_x, self$theta, expand = self$expand), - view_scales_polar(scale_y, self$theta, expand = self$expand), + view_scales_polar(scale_x, self$theta, expand = params$expand[c(4, 2)]), + view_scales_polar(scale_y, self$theta, expand = params$expand[c(3, 1)]), list(bbox = polar_bbox(self$arc, inner_radius = self$inner_radius), arc = self$arc, inner_radius = self$inner_radius) ) @@ -469,27 +468,27 @@ CoordRadial <- ggproto("CoordRadial", Coord, }, setup_params = function(self, data) { - if (isFALSE(self$r_axis_inside)) { - place <- in_arc(c(0, 0.5, 1, 1.5) * pi, self$arc) - if (place[1]) { - return(list(r_axis = "left", fake_arc = c(0, 2) * pi)) - } - if (place[3]) { - return(list(r_axis = "left", fake_arc = c(1, 3)* pi)) - } - if (place[2]) { - return(list(r_axis = "bottom", fake_arc = c(0.5, 2.5) * pi)) - } - if (place[4]) { - return(list(r_axis = "bottom", fake_arc = c(1.5, 3.5) * pi)) - } + params <- ggproto_parent(Coord, self)$setup_params(data) + if (!isFALSE(self$r_axis_inside)) { + return(params) + } + + place <- in_arc(c(0, 0.5, 1, 1.5) * pi, self$arc) + if (!any(place)) { cli::cli_warn(c( "No appropriate placement found for {.arg r_axis_inside}.", i = "Axis will be placed at panel edge." )) - self$r_axis_inside <- TRUE + params$r_axis_inside <- TRUE + return(params) } - return(NULL) + + params$r_axis <- if (any(place[c(1, 3)])) "left" else "bottom" + params$fake_arc <- switch( + which(place[c(1, 3, 2, 4)])[1], + c(0, 2), c(1, 3), c(0.5, 2.5), c(1.5, 3.5) + ) * pi + params } ) diff --git a/R/coord-sf.R b/R/coord-sf.R index 118d1e678e..c31af6d393 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -18,12 +18,10 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, }, setup_params = function(self, data) { - crs <- self$determine_crs(data) + params <- ggproto_parent(Coord, self)$setup_params(data) - params <- list( - crs = crs, - default_crs = self$default_crs - ) + params$crs <- self$determine_crs(data) + params$default_crs <- self$default_crs self$params <- params params @@ -170,8 +168,8 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, setup_panel_params = function(self, scale_x, scale_y, params = list()) { # expansion factors for scale limits - expansion_x <- default_expansion(scale_x, expand = self$expand) - expansion_y <- default_expansion(scale_y, expand = self$expand) + expansion_x <- default_expansion(scale_x, expand = params$expand[c(4, 2)]) + expansion_y <- default_expansion(scale_y, expand = params$expand[c(3, 1)]) # get scale limits and coord limits and merge together # coord limits take precedence over scale limits diff --git a/R/coord-transform.R b/R/coord-transform.R index 83ffd7b9ee..1253529fdd 100644 --- a/R/coord-transform.R +++ b/R/coord-transform.R @@ -153,8 +153,8 @@ CoordTrans <- ggproto("CoordTrans", Coord, setup_panel_params = function(self, scale_x, scale_y, params = list()) { c( - view_scales_from_scale_with_coord_trans(scale_x, self$limits$x, self$trans$x, self$expand), - view_scales_from_scale_with_coord_trans(scale_y, self$limits$y, self$trans$y, self$expand) + view_scales_from_scale_with_coord_trans(scale_x, self$limits$x, self$trans$x, params$expand[c(4, 2)]), + view_scales_from_scale_with_coord_trans(scale_y, self$limits$y, self$trans$y, params$expand[c(3, 1)]) ) }, diff --git a/R/fortify.R b/R/fortify.R index 23166ffa99..da4bcf7892 100644 --- a/R/fortify.R +++ b/R/fortify.R @@ -8,9 +8,12 @@ #' @seealso [fortify.lm()] #' @param model model or other R object to convert to data frame #' @param data original dataset, if needed -#' @param ... other arguments passed to methods +#' @inheritParams rlang::args_dots_used #' @export -fortify <- function(model, data, ...) UseMethod("fortify") +fortify <- function(model, data, ...) { + warn_dots_used() + UseMethod("fortify") +} #' @export fortify.data.frame <- function(model, data, ...) model diff --git a/R/geom-hex.R b/R/geom-hex.R index 2e8174e5d8..152227a40b 100644 --- a/R/geom-hex.R +++ b/R/geom-hex.R @@ -6,6 +6,7 @@ #' the very regular alignment of [geom_bin_2d()]. #' #' @eval rd_aesthetics("geom", "hex") +#' @eval rd_aesthetics("stat", "binhex") #' @seealso [stat_bin_2d()] for rectangular binning #' @param geom,stat Override the default connection between `geom_hex()` and #' `stat_bin_hex()`. For more information about overriding these connections, diff --git a/R/geom-ribbon.R b/R/geom-ribbon.R index 470c013eee..a8f6b1be42 100644 --- a/R/geom-ribbon.R +++ b/R/geom-ribbon.R @@ -98,7 +98,7 @@ geom_ribbon <- function(mapping = NULL, data = NULL, GeomRibbon <- ggproto("GeomRibbon", Geom, default_aes = aes( colour = NA, - fill = from_theme(col_mix(ink, paper, 0.799)), + fill = from_theme(col_mix(ink, paper, 0.2)), linewidth = from_theme(borderwidth), linetype = from_theme(bordertype), alpha = NA), diff --git a/R/geom-text.R b/R/geom-text.R index b7f0d3f320..ed378734ba 100644 --- a/R/geom-text.R +++ b/R/geom-text.R @@ -31,8 +31,8 @@ #' #' @section Alignment: #' You can modify text alignment with the `vjust` and `hjust` -#' aesthetics. These can either be a number between 0 (right/bottom) and -#' 1 (top/left) or a character (`"left"`, `"middle"`, `"right"`, `"bottom"`, +#' aesthetics. These can either be a number between 0 (left/bottom) and +#' 1 (right/top) or a character (`"left"`, `"middle"`, `"right"`, `"bottom"`, #' `"center"`, `"top"`). There are two special alignments: `"inward"` and #' `"outward"`. Inward always aligns text towards the center, and outward #' aligns it away from the center. diff --git a/R/guide-axis.R b/R/guide-axis.R index 8280219f3d..bc2a2e1596 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -254,21 +254,8 @@ GuideAxis <- ggproto( }, override_elements = function(params, elements, theme) { - label <- elements$text - if (!inherits(label, "element_text")) { - return(elements) - } - label_overrides <- axis_label_element_overrides( - params$position, params$angle - ) - # label_overrides is an element_text, but label_element may not be; - # to merge the two elements, we just copy angle, hjust, and vjust - # unless their values are NULL - label$angle <- label_overrides$angle %||% label$angle - label$hjust <- label_overrides$hjust %||% label$hjust - label$vjust <- label_overrides$vjust %||% label$vjust - - elements$text <- label + elements$text <- + label_angle_heuristic(elements$text, params$position, params$angle) return(elements) }, @@ -584,49 +571,40 @@ axis_label_priority_between <- function(x, y) { ) } -#' Override axis text angle and alignment +#' Override text angle and alignment #' +#' @param element An `element_text()` #' @param axis_position One of bottom, left, top, or right #' @param angle The text angle, or NULL to override nothing #' #' @return An [element_text()] that contains parameters that should be #' overridden from the user- or theme-supplied element. #' @noRd -#' -axis_label_element_overrides <- function(axis_position, angle = NULL) { - - if (is.null(angle) || is.waive(angle)) { - return(element_text(angle = NULL, hjust = NULL, vjust = NULL)) +label_angle_heuristic <- function(element, position, angle) { + if (!inherits(element, "element_text") + || is.null(position) + || is.null(angle %|W|% NULL)) { + return(element) } + arg_match0(position, .trbl) check_number_decimal(angle) - angle <- angle %% 360 - arg_match0( - axis_position, - c("bottom", "left", "top", "right") - ) - - if (axis_position == "bottom") { - - hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 - vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 - - } else if (axis_position == "left") { - - hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 0 else 1 - vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 - - } else if (axis_position == "top") { - - hjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 0 else 1 - vjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 - - } else if (axis_position == "right") { - - hjust <- if (angle %in% c(90, 270)) 0.5 else if (angle > 90 & angle < 270) 1 else 0 - vjust <- if (angle %in% c(0, 180)) 0.5 else if (angle < 180) 1 else 0 - - } - - element_text(angle = angle, hjust = hjust, vjust = vjust) + radian <- deg2rad(angle) + digits <- 3 + + # Taking the sign of the (co)sine snaps the value to c(-1, 0, 1) + # Doing `x / 2 + 0.5` rescales it to c(0, 0.5, 1), which are good values for justification + # The rounding step ensures we can get (co)sine to exact 0 so it can become 0.5 + # which we need for center-justifications + cosine <- sign(round(cos(radian), digits)) / 2 + 0.5 + sine <- sign(round(sin(radian), digits)) / 2 + 0.5 + + # Depending on position, we might need to swap or flip justification values + hjust <- switch(position, left = cosine, right = 1 - cosine, top = 1 - sine, sine) + vjust <- switch(position, left = 1 - sine, right = sine, top = 1 - cosine, cosine) + + element$angle <- angle %||% element$angle + element$hjust <- hjust %||% element$hjust + element$vjust <- vjust %||% element$vjust + element } diff --git a/R/guide-bins.R b/R/guide-bins.R index 518655cbba..0124ea6052 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -11,6 +11,10 @@ NULL #' guide if they are mapped in the same way. #' #' @inheritParams guide_legend +#' @param angle Overrules the theme settings to automatically apply appropriate +#' `hjust` and `vjust` for angled legend text. Can be a single number +#' representing the text angle in degrees, or `NULL` to not overrule the +#' settings (default). #' @param show.limits Logical. Should the limits of the scale be shown with #' labels and ticks. Default is `NULL` meaning it will take the value from the #' scale. This argument is ignored if `labels` is given as a vector of @@ -65,6 +69,7 @@ guide_bins <- function( theme = NULL, # general + angle = NULL, position = NULL, direction = NULL, override.aes = list(), @@ -85,6 +90,7 @@ guide_bins <- function( theme = theme, # general + angle = angle, position = position, direction = direction, override.aes = rename_aes(override.aes), @@ -115,6 +121,7 @@ GuideBins <- ggproto( default_axis = element_line("black", linewidth = (0.5 / .pt)), default_ticks = element_line(inherit.blank = TRUE), + angle = NULL, direction = NULL, override.aes = list(), reverse = FALSE, diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index d03484edae..586caee124 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -32,6 +32,10 @@ NULL #' @param alpha A numeric between 0 and 1 setting the colour transparency of #' the bar. Use `NA` to preserve the alpha encoded in the colour itself #' (default). +#' @param angle Overrules the theme settings to automatically apply appropriate +#' `hjust` and `vjust` for angled legend text. Can be a single number +#' representing the text angle in degrees, or `NULL` to not overrule the +#' settings (default). #' @param draw.ulim A logical specifying if the upper limit tick marks should #' be visible. #' @param draw.llim A logical specifying if the lower limit tick marks should @@ -124,6 +128,7 @@ guide_colourbar <- function( alpha = NA, draw.ulim = TRUE, draw.llim = TRUE, + angle = NULL, position = NULL, direction = NULL, reverse = FALSE, @@ -151,6 +156,7 @@ guide_colourbar <- function( nbin = nbin, display = display, alpha = alpha, + angle = angle, draw_lim = c(isTRUE(draw.llim), isTRUE(draw.ulim)), position = position, direction = direction, @@ -193,6 +199,7 @@ GuideColourbar <- ggproto( direction = NULL, reverse = FALSE, order = 0, + angle = NULL, # parameter name = "colourbar", diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R index 52b6e1809d..54cd89a948 100644 --- a/R/guide-colorsteps.R +++ b/R/guide-colorsteps.R @@ -49,6 +49,7 @@ guide_coloursteps <- function( title = waiver(), theme = NULL, alpha = NA, + angle = NULL, even.steps = TRUE, show.limits = NULL, direction = NULL, @@ -66,6 +67,7 @@ guide_coloursteps <- function( title = title, theme = theme, alpha = alpha, + angle = angle, even.steps = even.steps, show.limits = show.limits, position = position, diff --git a/R/guide-legend.R b/R/guide-legend.R index 6f0b98ac33..671acf1a1c 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -374,6 +374,9 @@ GuideLegend <- ggproto( ggname("legend.key", element_grob(elements$key)) } + elements$text <- + label_angle_heuristic(elements$text, elements$text_position, params$angle) + elements }, @@ -688,6 +691,7 @@ deprecated_guide_args <- function( default.unit = "line", ..., .call = caller_call()) { + warn_dots_used(call = .call) args <- names(formals(deprecated_guide_args)) args <- setdiff(args, c("theme", "default.unit", "...", ".call")) diff --git a/R/labels.R b/R/labels.R index 7662153e91..20cc929d37 100644 --- a/R/labels.R +++ b/R/labels.R @@ -18,8 +18,8 @@ update_labels <- function(p, labels) { # Called in `ggplot_build()` to set default labels not specified by user. setup_plot_labels <- function(plot, layers, data) { - # Initiate from user-defined labels - labels <- plot$labels + # Initiate empty labels + labels <- list() # Find labels from every layer for (i in seq_along(layers)) { @@ -65,7 +65,26 @@ setup_plot_labels <- function(plot, layers, data) { labels <- defaults(labels, current) } } - labels + + # Warn for spurious labels that don't have a mapping. + # Note: sometimes, 'x' and 'y' might not have a mapping, like in + # `geom_function()`. We can display these labels anyway, so we include them. + plot_labels <- plot$labels + known_labels <- c(names(labels), fn_fmls_names(labs), "x", "y") + extra_labels <- setdiff(names(plot_labels), known_labels) + + if (length(extra_labels) > 0) { + extra_labels <- paste0( + "{.code ", extra_labels, " = \"", plot_labels[extra_labels], "\"}" + ) + names(extra_labels) <- rep("*", length(extra_labels)) + cli::cli_warn(c( + "Ignoring unknown labels:", + extra_labels + )) + } + + defaults(plot_labels, labels) } #' Modify axis, legend, and plot labels @@ -168,7 +187,7 @@ ggtitle <- function(label, subtitle = waiver()) { #' text from the information stored in the plot. #' #' @param p a ggplot object -#' @param ... Currently ignored +#' @inheritParams rlang::args_dots_used #' #' @return A text string #' @@ -191,6 +210,7 @@ ggtitle <- function(label, subtitle = waiver()) { #' get_alt_text(p) #' get_alt_text <- function(p, ...) { + warn_dots_used() UseMethod("get_alt_text") } #' @export diff --git a/R/scale-expansion.R b/R/scale-expansion.R index e3392fc5bf..0edb01f1b8 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -98,11 +98,24 @@ expand_range4 <- function(limits, expand) { #' default_expansion <- function(scale, discrete = expansion(add = 0.6), continuous = expansion(mult = 0.05), expand = TRUE) { - if (!expand) { - return(expansion(0, 0)) + out <- expansion() + if (!any(expand)) { + return(out) } + scale_expand <- scale$expand %|W|% + if (scale$is_discrete()) discrete else continuous - scale$expand %|W|% if (scale$is_discrete()) discrete else continuous + # for backward compatibility, we ensure expansions have expected length + expand <- rep_len(expand, 2L) + scale_expand <- rep_len(scale_expand, 4) + + if (expand[1]) { + out[1:2] <- scale_expand[1:2] + } + if (expand[2]) { + out[3:4] <- scale_expand[3:4] + } + out } #' Expand limits in (possibly) transformed space diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R index d76a22c442..a56bea189e 100644 --- a/R/stat-summary-bin.R +++ b/R/stat-summary-bin.R @@ -79,7 +79,7 @@ StatSummaryBin <- ggproto("StatSummaryBin", Stat, compute_group = function(data, scales, fun = NULL, bins = 30, binwidth = NULL, breaks = NULL, origin = NULL, right = FALSE, na.rm = FALSE, - flipped_aes = FALSE) { + flipped_aes = FALSE, width = NULL) { data <- flip_data(data, flipped_aes) x <- flipped_names(flipped_aes)$x breaks <- bin2d_breaks(scales[[x]], breaks, origin, binwidth, bins, @@ -90,7 +90,7 @@ StatSummaryBin <- ggproto("StatSummaryBin", Stat, locs <- bin_loc(breaks, out$bin) out$x <- locs$mid - out$width <- if (scales[[x]]$is_discrete()) 0.9 else locs$length + out$width <- width %||% if (scales[[x]]$is_discrete()) 0.9 else locs$length out$flipped_aes <- flipped_aes flip_data(out, flipped_aes) } diff --git a/R/summary.R b/R/summary.R index e5422f8ad4..4a227a3599 100644 --- a/R/summary.R +++ b/R/summary.R @@ -29,8 +29,9 @@ summary.ggplot <- function(object, ...) { cat("scales: ", paste(object$scales$input(), collapse = ", "), "\n") } - cat("faceting: ") - print(object$facet) + vars <- object$facet$vars() + vars <- if (length(vars) > 0) paste0("~", vars) else "" + cat("faceting: ", paste0(vars, collapse = ", "), "\n") if (length(object$layers) > 0) cat("-----------------------------------\n") diff --git a/R/utilities.R b/R/utilities.R index ccfb7e94e8..8772ed771b 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -777,6 +777,18 @@ as_unordered_factor <- function(x) { x } +warn_dots_used <- function(env = caller_env(), call = caller_env()) { + check_dots_used( + env = env, call = call, + # Demote from error to warning + error = function(cnd) { + # cli uses \f as newlines, not \n + msg <- gsub("\n", "\f", cnd_message(cnd)) + cli::cli_warn(msg, call = call) + } + ) +} + # Shim for scales/#424 col_mix <- function(a, b, amount = 0.5) { input <- vec_recycle_common(a = a, b = b, amount = amount) diff --git a/README.Rmd b/README.Rmd index 693181ebae..337aa50b45 100644 --- a/README.Rmd +++ b/README.Rmd @@ -47,7 +47,7 @@ pak::pak("tidyverse/ggplot2") It's hard to succinctly describe how ggplot2 works because it embodies a deep philosophy of visualisation. However, in most cases you start with `ggplot()`, supply a dataset and aesthetic mapping (with `aes()`). You then add on layers (like `geom_point()` or `geom_histogram()`), scales (like `scale_colour_brewer()`), faceting specifications (like `facet_wrap()`) and coordinate systems (like `coord_flip()`). ```{r example} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars coloured by 7 'types' of car. The displacement and miles #| per gallon are inversely correlated." library(ggplot2) diff --git a/man/coord_cartesian.Rd b/man/coord_cartesian.Rd index 5c39f4d288..20987083a5 100644 --- a/man/coord_cartesian.Rd +++ b/man/coord_cartesian.Rd @@ -17,7 +17,11 @@ coord_cartesian( \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{default}{Is this the default coordinate system? If \code{FALSE} (the default), then replacing this coordinate system with another one creates a message alerting diff --git a/man/coord_fixed.Rd b/man/coord_fixed.Rd index fc8c052506..8877019a91 100644 --- a/man/coord_fixed.Rd +++ b/man/coord_fixed.Rd @@ -14,7 +14,11 @@ coord_fixed(ratio = 1, xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{clip}{Should drawing be clipped to the extent of the plot panel? A setting of \code{"on"} (the default) means yes, and a setting of \code{"off"} diff --git a/man/coord_flip.Rd b/man/coord_flip.Rd index be69644cf0..48ea2e1dba 100644 --- a/man/coord_flip.Rd +++ b/man/coord_flip.Rd @@ -11,7 +11,11 @@ coord_flip(xlim = NULL, ylim = NULL, expand = TRUE, clip = "on") \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{clip}{Should drawing be clipped to the extent of the plot panel? A setting of \code{"on"} (the default) means yes, and a setting of \code{"off"} diff --git a/man/coord_map.Rd b/man/coord_map.Rd index 3aacd167d7..913768f29e 100644 --- a/man/coord_map.Rd +++ b/man/coord_map.Rd @@ -40,7 +40,11 @@ means no. For details, please see \code{\link[=coord_cartesian]{coord_cartesian( \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#superseded}{\figure{lifecycle-superseded.svg}{options: alt='[Superseded]'}}}{\strong{[Superseded]}} diff --git a/man/coord_trans.Rd b/man/coord_trans.Rd index bea5b54716..d1f46dc1ee 100644 --- a/man/coord_trans.Rd +++ b/man/coord_trans.Rd @@ -33,7 +33,11 @@ legend, the plot title, or the plot margins.} \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} } \description{ \code{coord_trans()} is different to scale transformations in that it occurs after diff --git a/man/fortify.Rd b/man/fortify.Rd index 59dcfea9ec..36d1837025 100644 --- a/man/fortify.Rd +++ b/man/fortify.Rd @@ -11,7 +11,7 @@ fortify(model, data, ...) \item{data}{original dataset, if needed} -\item{...}{other arguments passed to methods} +\item{...}{Arguments passed to methods.} } \description{ Rather than using this function, I now recommend using the \pkg{broom} diff --git a/man/geom_hex.Rd b/man/geom_hex.Rd index 11dbdb1f87..553787761b 100644 --- a/man/geom_hex.Rd +++ b/man/geom_hex.Rd @@ -138,6 +138,17 @@ the very regular alignment of \code{\link[=geom_bin_2d]{geom_bin_2d()}}. \item \code{\link[=aes_linetype_size_shape]{linewidth}} } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. + + +\code{stat_binhex()} understands the following aesthetics (required aesthetics are in bold): +\itemize{ +\item \strong{\code{\link[=aes_position]{x}}} +\item \strong{\code{\link[=aes_position]{y}}} +\item \code{\link[=aes_colour_fill_alpha]{fill}} +\item \code{\link[=aes_group_order]{group}} +\item \code{weight} +} +Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } \section{Computed variables}{ diff --git a/man/geom_text.Rd b/man/geom_text.Rd index 91c241ab4b..1b06e73ae1 100644 --- a/man/geom_text.Rd +++ b/man/geom_text.Rd @@ -209,8 +209,8 @@ the background colour of the label. \section{Alignment}{ You can modify text alignment with the \code{vjust} and \code{hjust} -aesthetics. These can either be a number between 0 (right/bottom) and -1 (top/left) or a character (\code{"left"}, \code{"middle"}, \code{"right"}, \code{"bottom"}, +aesthetics. These can either be a number between 0 (left/bottom) and +1 (right/top) or a character (\code{"left"}, \code{"middle"}, \code{"right"}, \code{"bottom"}, \code{"center"}, \code{"top"}). There are two special alignments: \code{"inward"} and \code{"outward"}. Inward always aligns text towards the center, and outward aligns it away from the center. diff --git a/man/get_alt_text.Rd b/man/get_alt_text.Rd index b0da28a783..c9f6bdeb1e 100644 --- a/man/get_alt_text.Rd +++ b/man/get_alt_text.Rd @@ -10,7 +10,7 @@ get_alt_text(p, ...) \arguments{ \item{p}{a ggplot object} -\item{...}{Currently ignored} +\item{...}{Arguments passed to methods.} } \value{ A text string diff --git a/man/ggsf.Rd b/man/ggsf.Rd index c4ec76bed1..7424d4107f 100644 --- a/man/ggsf.Rd +++ b/man/ggsf.Rd @@ -99,7 +99,11 @@ though they would be visible in the final plot region.} \item{expand}{If \code{TRUE}, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If \code{FALSE}, -limits are taken exactly from the data or \code{xlim}/\code{ylim}.} +limits are taken exactly from the data or \code{xlim}/\code{ylim}. +Giving a logical vector will separately control the expansion for the four +directions (top, left, bottom and right). The \code{expand} argument will be +recycled to length 4 if necessary. Alternatively, can be a named logical +vector to control a single direction, e.g. \code{expand = c(bottom = FALSE)}.} \item{crs}{The coordinate reference system (CRS) into which all data should be projected before plotting. If not specified, will use the CRS defined diff --git a/man/guide_bins.Rd b/man/guide_bins.Rd index ead7b8a099..8ee5311445 100644 --- a/man/guide_bins.Rd +++ b/man/guide_bins.Rd @@ -7,6 +7,7 @@ guide_bins( title = waiver(), theme = NULL, + angle = NULL, position = NULL, direction = NULL, override.aes = list(), @@ -26,6 +27,11 @@ specified in \code{\link[=labs]{labs()}} is used for the title.} differently from the plot's theme settings. The \code{theme} argument in the guide overrides, and is combined with, the plot's theme.} +\item{angle}{Overrules the theme settings to automatically apply appropriate +\code{hjust} and \code{vjust} for angled legend text. Can be a single number +representing the text angle in degrees, or \code{NULL} to not overrule the +settings (default).} + \item{position}{A character string indicating where the legend should be placed relative to the plot panels.} diff --git a/man/guide_colourbar.Rd b/man/guide_colourbar.Rd index 8e29943a44..9a441f39cc 100644 --- a/man/guide_colourbar.Rd +++ b/man/guide_colourbar.Rd @@ -14,6 +14,7 @@ guide_colourbar( alpha = NA, draw.ulim = TRUE, draw.llim = TRUE, + angle = NULL, position = NULL, direction = NULL, reverse = FALSE, @@ -31,6 +32,7 @@ guide_colorbar( alpha = NA, draw.ulim = TRUE, draw.llim = TRUE, + angle = NULL, position = NULL, direction = NULL, reverse = FALSE, @@ -77,6 +79,11 @@ be visible.} \item{draw.llim}{A logical specifying if the lower limit tick marks should be visible.} +\item{angle}{Overrules the theme settings to automatically apply appropriate +\code{hjust} and \code{vjust} for angled legend text. Can be a single number +representing the text angle in degrees, or \code{NULL} to not overrule the +settings (default).} + \item{position}{A character string indicating where the legend should be placed relative to the plot panels.} diff --git a/man/guide_coloursteps.Rd b/man/guide_coloursteps.Rd index a2938df745..5bec4a8d73 100644 --- a/man/guide_coloursteps.Rd +++ b/man/guide_coloursteps.Rd @@ -9,6 +9,7 @@ guide_coloursteps( title = waiver(), theme = NULL, alpha = NA, + angle = NULL, even.steps = TRUE, show.limits = NULL, direction = NULL, @@ -23,6 +24,7 @@ guide_colorsteps( title = waiver(), theme = NULL, alpha = NA, + angle = NULL, even.steps = TRUE, show.limits = NULL, direction = NULL, @@ -47,6 +49,11 @@ guide overrides, and is combined with, the plot's theme.} the bar. Use \code{NA} to preserve the alpha encoded in the colour itself (default).} +\item{angle}{Overrules the theme settings to automatically apply appropriate +\code{hjust} and \code{vjust} for angled legend text. Can be a single number +representing the text angle in degrees, or \code{NULL} to not overrule the +settings (default).} + \item{even.steps}{Should the rendered size of the bins be equal, or should they be proportional to their length in the data space? Defaults to \code{TRUE}} diff --git a/revdep/README.md b/revdep/README.md index 8976e81c90..498c024ad2 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,386 +1,646 @@ # Revdeps -## Failed to check (132) +## Failed to check (165) -|package |version |error |warning |note | -|:----------------------|:----------|:------|:-------|:----| -|abctools |1.1.7 |1 | | | -|animalEKF |1.2 |1 | | | -|ANOM |0.5 |1 | | | -|atRisk |0.1.0 |1 | | | -|AutoScore |1.0.0 |1 | | | -|bayesdfa |1.3.3 |1 | | | -|bayesDP |1.3.6 |1 | | | -|BayesianFactorZoo |0.0.0.2 |1 | | | -|BayesSurvive |0.0.2 |1 | | | -|BCClong |1.0.3 |1 | | | -|BGGM |2.1.3 |1 | | | -|binsreg |1.0 |1 | | | -|bmstdr |0.7.9 |1 | | | -|bspcov |1.0.0 |1 | | | -|BuyseTest |3.0.4 |1 | | | -|CalibrationCurves |2.0.3 |1 | | | -|CARBayesST |4.0 |1 | | | -|CaseBasedReasoning |0.3 |1 | | | -|CGPfunctions |0.6.3 |1 | | | -|cmprskcoxmsm |0.2.1 |1 | | | -|contrast |0.24.2 |1 | | | -|coxed |0.3.3 |1 | | | -|CRMetrics |0.3.0 |1 | | | -|csmpv |1.0.3 |1 | | | -|ctsem |3.10.0 |1 | | | -|DepthProc |2.1.5 |1 | | | -|DR.SC |3.4 |1 | | | -|DynNom |5.1 |1 | | | -|easybgm |0.1.2 |1 | | | -|ecolottery |1.0.0 |1 | | | -|EpiEstim |2.2-4 |1 | | | -|evolqg |0.3-4 |1 | | | -|ForecastComb |1.3.1 |1 | | | -|gapfill |0.9.6-1 |1 | |1 | -|GeomComb |1.0 |1 | | | -|ggrcs |0.4.0 |1 | | | -|ggrisk |1.3 |1 | | | -|gJLS2 |0.2.0 |1 | | | -|Greg |2.0.2 |1 | | | -|greport |0.7-4 |1 | | | -|hettx |0.1.3 |1 | | | -|hIRT |0.3.0 |1 | | | -|Hmsc |3.0-13 |1 | | | -|[inventorize](failures.md#inventorize)|1.1.1 |__+1__ | | | -|iNZightPlots |2.15.3 |1 | | | -|iNZightRegression |1.3.4 |1 | | | -|IRexamples |0.0.4 |1 | | | -|jmBIG |0.1.2 |1 | | | -|joineRML |0.4.6 |1 | | | -|JWileymisc |1.4.1 |1 | | | -|kmc |0.4-2 |1 | | | -|L2E |2.0 |1 | | | -|llbayesireg |1.0.0 |1 | | | -|LorenzRegression |1.0.0 |1 | | | -|lsirm12pl |1.3.1 |1 | | | -|mbsts |3.0 |1 | | | -|MendelianRandomization |0.10.0 |1 | | | -|MetabolicSurv |1.1.2 |1 | | | -|miWQS |0.4.4 |1 | | | -|MRZero |0.2.0 |1 | | | -|Multiaovbay |0.1.0 |1 | | | -|multilevelTools |0.1.1 |1 | | | -|multinma |0.7.1 |1 | | | -|NCA |4.0.1 |1 | | | -|netcmc |1.0.2 |1 | | | -|NetworkChange |0.8 |1 | | | -|nlmeVPC |2.6 |1 | | | -|NMADiagT |0.1.2 |1 | | | -|optweight |0.2.5 |1 | | | -|OVtool |1.0.3 |1 | | | -|paths |0.1.1 |1 | | | -|PLMIX |2.1.1 |1 | | | -|popstudy |1.0.1 |1 | | | -|pould |1.0.1 |1 | | | -|powerly |1.8.6 |1 | | | -|pre |1.0.7 |1 | | | -|ProFAST |? | | | | -|psbcSpeedUp |2.0.7 |1 | | | -|pscore |0.4.0 |1 | | | -|psfmi |1.4.0 |1 | | | -|qPCRtools |1.0.1 |1 | | | -|qreport |1.0-1 |1 | | | -|qris |1.1.1 |1 | | | -|qte |1.3.1 |1 | | | -|quid |0.0.1 |1 | | | -|RATest |0.1.10 |1 | | | -|RcmdrPlugin.RiskDemo |3.2 |1 | | | -|rddtools |1.6.0 |1 | | | -|riskRegression |2023.12.21 |1 | | | -|rms |6.8-1 |1 | |1 | -|rmsb |1.1-1 |1 | | | -|robmed |1.0.2 |1 | | | -|robmedExtra |0.1.0 |1 | | | -|RPPanalyzer |1.4.9 |1 | | | -|RQdeltaCT |1.3.0 |1 | | | -|scCustomize |2.1.2 |1 | |1 | -|SCdeconR |1.0.0 |1 | | | -|scGate |1.6.2 |1 | | | -|SCIntRuler |0.99.6 |1 | | | -|scMappR |1.0.11 |1 | | | -|scpi |2.2.5 |1 | | | -|scRNAstat |0.1.1 |1 | | | -|sectorgap |0.1.0 |1 | | | -|SEERaBomb |2019.2 |1 | | | -|semicmprskcoxmsm |0.2.0 |1 | | | -|SensMap |0.7 |1 | | | -|Seurat |5.1.0 |1 | | | -|shinyTempSignal |0.0.8 |1 | | | -|sievePH |1.1 |1 | | | -|Signac |1.13.0 |1 | | | -|SimplyAgree |0.2.0 |1 | | | -|sMSROC |0.1.2 |1 | | | -|SNPassoc |2.1-0 |1 | | | -|snplinkage |? | | | | -|SoupX |1.6.2 |1 | | | -|sparsereg |1.2 |1 | | | -|spikeSlabGAM |1.1-19 |1 | | | -|statsr |0.3.0 |1 | | | -|streamDAG |? | | | | -|survHE |2.0.1 |1 | |1 | -|survidm |1.3.2 |1 | | | -|tempted |0.1.1 |1 | | | -|[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | -|tidyEdSurvey |0.1.3 |1 | | | -|tidyseurat |0.8.0 |1 | | | -|tidyvpc |1.5.1 |1 | | | -|TriDimRegression |1.0.2 |1 | | | -|TSrepr |1.1.0 |1 | | | -|twang |2.6 |1 | | | -|vdg |1.2.3 |1 | | | -|visa |0.1.0 |1 | | | -|WRTDStidal |1.1.4 |1 | | | +|package |version |error |warning |note | +|:-----------------------|:-------|:------|:-------|:----| +|abctools |1.1.7 |1 | | | +|adjclust |? | | | | +|animalEKF |1.2 |1 | | | +|ANOM |0.5 |1 | | | +|atRisk |0.1.0 |1 | | | +|AutoScore |? | | | | +|baRulho |? | | | | +|bayesDP |1.3.6 |1 | | | +|BayesianFactorZoo |0.0.0.2 |1 | | | +|BayesSurvive |0.0.2 |1 | | | +|BCClong |1.0.3 |1 | | | +|BGGM |2.1.3 |1 | | | +|binsreg |1.1 |1 | | | +|bspcov |1.0.0 |1 | | | +|bsub |1.1.0 |1 | | | +|BuyseTest |3.0.4 |1 | | | +|CARBayesST |4.0 |1 | | | +|CGPfunctions |0.6.3 |1 | | | +|chemodiv |? | | | | +|cinaR |? | | | | +|cmprskcoxmsm |0.2.1 |1 | | | +|CNVScope |? | | | | +|COMMA |1.0.0 |1 | | | +|conos |? | | | | +|counterfactuals |? | | | | +|CRMetrics |? | | | | +|crosstalkr |? | | | | +|ctsem |3.10.1 |1 | | | +|DepthProc |2.1.5 |1 | | | +|DR.SC |3.4 |1 | | | +|easybgm |0.1.2 |1 | | | +|EcoEnsemble |1.1.0 |1 | | | +|ecolottery |1.0.0 |1 | | | +|EMAS |? | | | | +|EpiEstim |2.2-4 |1 | | | +|evolqg |0.3-4 |1 | | | +|EWSmethods |? | | | | +|fmx |? | | | | +|ForecastComb |1.3.1 |1 | | | +|GALLO |? | | | | +|gap |? | | | | +|gapfill |0.9.6-1 |1 | |1 | +|geneHapR |? | | | | +|GeneSelectR |? | | | | +|GeomComb |1.0 |1 | | | +|geomorph |? | | | | +|gJLS2 |0.2.0 |1 | | | +|hettx |0.1.3 |1 | | | +|Hmisc |? | | | | +|Hmsc |3.0-13 |1 | | | +|iClusterVB |0.1.2 |1 | | | +|[inventorize](failures.md#inventorize)|1.1.1 |__+1__ | | | +|iNZightPlots |2.15.3 |1 | | | +|iNZightRegression |1.3.4 |1 | | | +|IRexamples |0.0.4 |1 | | | +|jmBIG |0.1.2 |1 | | | +|joineRML |0.4.6 |1 | | | +|kibior |? | | | | +|kmc |0.4-2 |1 | | | +|L2E |2.0 |1 | | | +|llbayesireg |1.0.0 |1 | | | +|locuszoomr |? | | | | +|LorenzRegression |2.0.0 |1 | | | +|lsirm12pl |1.3.3 |1 | | | +|MantaID |? | | | | +|MARVEL |? | | | | +|mbsts |3.0 |1 | | | +|MitoHEAR |? | | | | +|miWQS |0.4.4 |1 | | | +|mlmts |1.1.2 |1 | | | +|mlr |? | | | | +|MOCHA |? | | | | +|MRZero |0.2.0 |1 | | | +|multilevelTools |0.1.1 |1 | | | +|multinma |0.7.1 |1 | | | +|NCA |4.0.1 |1 | | | +|netcmc |1.0.2 |1 | | | +|NetworkChange |0.8 |1 | | | +|nlmeVPC |2.6 |1 | | | +|NMADiagT |0.1.2 |1 | | | +|ohun |? | | | | +|optweight |0.2.5 |1 | | | +|OVtool |1.0.3 |1 | | | +|pagoda2 |? | | | | +|PAMpal |1.2.1 |1 | | | +|PAMscapes |0.6.0 |1 | | | +|paths |0.1.1 |1 | | | +|PathwaySpace |? | | | | +|pcvr |1.0.0 |1 | | | +|PlasmaMutationDetector |? | | | | +|PlasmaMutationDetector2 |? | | | | +|PLMIX |2.1.1 |1 | | | +|polyRAD |? | | | | +|popstudy |1.0.1 |1 | | | +|pould |1.0.1 |1 | | | +|PoweREST |0.1.0 |1 | | | +|powerly |1.8.6 |1 | | | +|pre |1.0.7 |1 | | | +|ProFAST |? | | | | +|psbcSpeedUp |2.0.7 |1 | | | +|pscore |0.4.0 |1 | | | +|qPCRtools |1.0.1 |1 | | | +|qris |1.1.1 |1 | | | +|qte |1.3.1 |1 | | | +|quantilogram |3.1.1 |1 | | | +|quid |0.0.1 |1 | | | +|RcmdrPlugin.RiskDemo |3.2 |1 | | | +|rddtools |1.6.0 |1 | | | +|RGraphSpace |? | | | | +|rms |? | | | | +|RNAseqQC |? | | | | +|robmed |1.0.2 |1 | | | +|robmedExtra |0.1.0 |1 | | | +|RPPanalyzer |1.4.9 |1 | | | +|RQdeltaCT |1.3.0 |1 | | | +|RRPP |? | | | | +|rstanarm |2.32.1 |1 | | | +|RTIGER |? | | | | +|rTwig |1.1.0 |1 | | | +|RVA |? | | | | +|scCustomize |? | | | | +|SCdeconR |1.0.0 |1 | | | +|scGate |1.6.2 |1 | | | +|SCIntRuler |0.99.6 |1 | | | +|scITD |? | | | | +|scMappR |1.0.11 |1 | | | +|scpi |2.2.5 |1 | | | +|scRNAstat |0.1.1 |1 | | | +|sectorgap |0.1.0 |1 | | | +|SeedMatchR |? | | | | +|SEERaBomb |2019.2 |1 | | | +|semicmprskcoxmsm |0.2.0 |1 | | | +|SensMap |0.7 |1 | | | +|sephora |? | | | | +|Seurat |? | | | | +|shinyTempSignal |0.0.8 |1 | | | +|sievePH |1.1 |1 | | | +|sigminer |? | | | | +|Signac |? | | | | +|SimplyAgree |0.2.0 |1 | | | +|SNPassoc |? | | | | +|snplinkage |? | | | | +|SoupX |1.6.2 |1 | | | +|sparsereg |1.2 |1 | | | +|SpatialDDLS |? | | | | +|spikeSlabGAM |1.1-19 |1 | | | +|statsr |0.3.0 |1 | | | +|streamDAG |? | | | | +|survidm |1.3.2 |1 | | | +|tempted |0.1.1 |1 | | | +|TestAnaAPP |1.1.1 |1 | | | +|[tidydr](failures.md#tidydr)|0.0.5 |__+1__ | | | +|tidyEdSurvey |0.1.3 |1 | | | +|tidyseurat |0.8.0 |1 | | | +|tidyvpc |1.5.1 |1 | | | +|TriDimRegression |1.0.2 |1 | | | +|TSrepr |1.1.0 |1 | | | +|twang |2.6.1 |1 | | | +|updog |? | | | | +|valr |? | | | | +|vdg |1.2.3 |1 | | | +|visa |0.1.0 |1 | | | +|VisualizeSimon2Stage |? | | | | +|WRTDStidal |1.1.4 |1 | | | +|xxdi |? | | | | -## New problems (242) +## New problems (469) -|package |version |error |warning |note | -|:------------------|:-------|:--------|:-------|:--------| -|[activAnalyzer](problems.md#activanalyzer)|2.1.1 |__+1__ | |1 __+1__ | -|[actxps](problems.md#actxps)|1.5.0 |__+1__ | |__+1__ | -|[AeRobiology](problems.md#aerobiology)|2.0.1 |1 | |__+1__ | -|[agricolaeplotr](problems.md#agricolaeplotr)|0.5.0 |__+1__ | | | -|[AnalysisLin](problems.md#analysislin)|0.1.2 |__+1__ | | | -|[animbook](problems.md#animbook)|1.0.0 |__+1__ | | | -|[ANN2](problems.md#ann2)|2.3.4 |__+1__ | |3 | -|[aplot](problems.md#aplot)|0.2.3 |__+1__ | | | -|[applicable](problems.md#applicable)|0.1.1 |__+1__ | | | -|[ASRgenomics](problems.md#asrgenomics)|1.1.4 |__+1__ | |1 | -|[autoplotly](problems.md#autoplotly)|0.1.4 |__+2__ | | | -|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | |__+1__ | -|[bartMan](problems.md#bartman)|0.1.0 |__+1__ | | | -|[bayesAB](problems.md#bayesab)|1.1.3 |__+1__ | | | -|[BayesGrowth](problems.md#bayesgrowth)|1.0.0 |__+1__ | |2 __+1__ | -|[BayesianReasoning](problems.md#bayesianreasoning)|0.4.2 |__+2__ | |__+1__ | -|[BayesMallows](problems.md#bayesmallows)|2.2.1 |__+1__ | |1 | -|[bayesplot](problems.md#bayesplot)|1.11.1 |1 __+1__ | |1 | -|[bayestestR](problems.md#bayestestr)|0.13.2 |1 __+1__ | | | -|[beastt](problems.md#beastt)|0.0.1 |__+2__ | |__+1__ | -|[besthr](problems.md#besthr)|0.3.2 |__+2__ | |__+1__ | -|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 | -|[biodosetools](problems.md#biodosetools)|3.6.1 |__+1__ | | | -|[boxly](problems.md#boxly)|0.1.1 |__+1__ | | | -|[braidReports](problems.md#braidreports)|0.5.4 |__+1__ | | | -|[breathtestcore](problems.md#breathtestcore)|0.8.7 |__+1__ | | | -|[brolgar](problems.md#brolgar)|1.0.1 |1 __+1__ | |1 | -|[cartograflow](problems.md#cartograflow)|1.0.5 |__+1__ | | | -|[cartographr](problems.md#cartographr)|0.2.2 |__+1__ | |1 | -|[cats](problems.md#cats)|1.0.2 |__+1__ | |1 | -|[cheem](problems.md#cheem)|0.4.0.0 |1 __+1__ | | | -|[chillR](problems.md#chillr)|0.75 |__+1__ | | | -|[chronicle](problems.md#chronicle)|0.3 |__+2__ | |1 __+1__ | -|[circhelp](problems.md#circhelp)|1.1 |__+2__ | |__+1__ | -|[clifro](problems.md#clifro)|3.2-5 |__+1__ | | | -|[clinDataReview](problems.md#clindatareview)|1.6.1 |__+2__ | |1 __+1__ | -|[clinUtils](problems.md#clinutils)|0.2.0 |__+1__ |-1 |1 __+1__ | -|[CohortPlat](problems.md#cohortplat)|1.0.5 |__+2__ | |__+1__ | -|[CoreMicrobiomeR](problems.md#coremicrobiomer)|0.1.0 |__+1__ | | | -|[correlationfunnel](problems.md#correlationfunnel)|0.2.0 |__+1__ | |1 | -|[corrViz](problems.md#corrviz)|0.1.0 |__+2__ | |1 __+1__ | -|[countfitteR](problems.md#countfitter)|1.4 |__+1__ | | | -|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | -|[crosshap](problems.md#crosshap)|1.4.0 |__+1__ | | | -|[ctrialsgov](problems.md#ctrialsgov)|0.2.5 |__+1__ | |1 | -|[cubble](problems.md#cubble)|0.3.1 |__+1__ | |1 __+1__ | -|[deeptime](problems.md#deeptime)|1.1.1 |__+1__ | | | -|[distributional](problems.md#distributional)|0.4.0 |__+1__ | | | -|[dittoViz](problems.md#dittoviz)|1.0.1 |__+2__ | | | -|[EGM](problems.md#egm)|0.1.0 |__+1__ | | | -|[entropart](problems.md#entropart)|1.6-13 |__+2__ | |__+1__ | -|[epiCleanr](problems.md#epicleanr)|0.2.0 |__+1__ | |1 | -|[esci](problems.md#esci)|1.0.3 |__+2__ | | | -|[evalITR](problems.md#evalitr)|1.0.0 |1 | |1 __+1__ | -|[eventstudyr](problems.md#eventstudyr)|1.1.3 |__+1__ | | | -|[EvoPhylo](problems.md#evophylo)|0.3.2 |1 __+1__ | |1 __+1__ | -|[expirest](problems.md#expirest)|0.1.6 |__+1__ | | | -|[explainer](problems.md#explainer)|1.0.1 |__+1__ | |1 | -|[ezEDA](problems.md#ezeda)|0.1.1 |__+1__ | | | -|[ezplot](problems.md#ezplot)|0.7.13 |__+2__ | |__+1__ | -|[fable.prophet](problems.md#fableprophet)|0.1.0 |__+1__ | |1 __+1__ | -|[fabletools](problems.md#fabletools)|0.4.2 |__+2__ | | | -|[factoextra](problems.md#factoextra)|1.0.7 |__+1__ | | | -|[fairmodels](problems.md#fairmodels)|1.2.1 |__+1__ | | | -|[fddm](problems.md#fddm)|1.0-2 |__+1__ | |1 | -|[feasts](problems.md#feasts)|0.3.2 |__+1__ | | | -|[ffp](problems.md#ffp)|0.2.2 |__+1__ | | | -|[fido](problems.md#fido)|1.1.1 |1 __+2__ | |2 | -|[flipr](problems.md#flipr)|0.3.3 |1 | |1 __+1__ | -|[foqat](problems.md#foqat)|2.0.8.2 |__+1__ | |__+1__ | -|[forestly](problems.md#forestly)|0.1.1 |__+1__ | |__+1__ | -|[frailtyEM](problems.md#frailtyem)|1.0.1 |__+1__ | |2 | -|[funcharts](problems.md#funcharts)|1.4.1 |__+1__ | | | -|[geomtextpath](problems.md#geomtextpath)|0.1.4 |__+2__ | | | -|[GGally](problems.md#ggally)|2.2.1 |__+1__ | | | -|[gganimate](problems.md#gganimate)|1.0.9 |__+2__ | |__+1__ | -|[ggbrain](problems.md#ggbrain)|0.8.1 |__+1__ | |1 __+1__ | -|[ggbreak](problems.md#ggbreak)|0.1.2 |__+2__ | |__+1__ | -|[ggdark](problems.md#ggdark)|0.2.1 |__+2__ | |1 | -|[ggdist](problems.md#ggdist)|3.3.2 |1 __+2__ | |1 __+1__ | -|[ggDoubleHeat](problems.md#ggdoubleheat)|0.1.2 |__+1__ | | | -|[ggeasy](problems.md#ggeasy)|0.1.4 |__+3__ | |__+1__ | -|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | -|[ggESDA](problems.md#ggesda)|0.2.0 |__+1__ | | | -|[ggfixest](problems.md#ggfixest)|0.1.0 |1 __+1__ | | | -|[ggforce](problems.md#ggforce)|0.4.2 |__+1__ | |1 | -|[ggformula](problems.md#ggformula)|0.12.0 | |__+1__ |1 | -|[ggfortify](problems.md#ggfortify)|0.4.17 |__+1__ | | | -|[gggenomes](problems.md#gggenomes)|1.0.0 |__+2__ | |__+1__ | -|[ggh4x](problems.md#ggh4x)|0.2.8 |1 __+2__ | |__+1__ | -|[gghighlight](problems.md#gghighlight)|0.4.1 |__+3__ | |__+1__ | -|[ggHoriPlot](problems.md#gghoriplot)|1.0.1 |__+1__ | |__+1__ | -|[ggiraph](problems.md#ggiraph)|0.8.10 |__+2__ | |1 | -|[ggiraphExtra](problems.md#ggiraphextra)|0.3.0 |__+2__ | |__+1__ | -|[ggmice](problems.md#ggmice)|0.1.0 |__+1__ | |__+1__ | -|[ggmulti](problems.md#ggmulti)|1.0.7 |__+3__ | |__+1__ | -|[ggnewscale](problems.md#ggnewscale)|0.4.10 |__+2__ | | | -|[ggparallel](problems.md#ggparallel)|0.4.0 |__+1__ | | | -|[ggpicrust2](problems.md#ggpicrust2)|1.7.3 |__+1__ | |1 | -|[ggpie](problems.md#ggpie)|0.2.5 |__+2__ | |__+1__ | -|[ggplotlyExtra](problems.md#ggplotlyextra)|0.0.1 |__+1__ | |1 | -|[ggpol](problems.md#ggpol)|0.0.7 |__+1__ | |2 | -|[ggpubr](problems.md#ggpubr)|0.6.0 |__+1__ | | | -|[ggraph](problems.md#ggraph)|2.2.1 |1 __+1__ | |1 __+1__ | -|[ggredist](problems.md#ggredist)|0.0.2 |__+1__ | | | -|[ggRtsy](problems.md#ggrtsy)|0.1.0 |__+2__ | |1 __+1__ | -|[ggseqplot](problems.md#ggseqplot)|0.8.4 |__+3__ | |__+1__ | -|[ggside](problems.md#ggside)|0.3.1 |__+1__ |__+1__ | | -|[ggspatial](problems.md#ggspatial)|1.1.9 |__+2__ | | | -|[ggtern](problems.md#ggtern)|3.5.0 |__+1__ | |2 | -|[ggupset](problems.md#ggupset)|0.4.0 |__+1__ | | | -|[ggVennDiagram](problems.md#ggvenndiagram)|1.5.2 |__+1__ | |1 __+1__ | -|[greatR](problems.md#greatr)|2.0.0 |__+1__ | |__+1__ | -|[Greymodels](problems.md#greymodels)|2.0.1 |__+1__ | | | -|[gtExtras](problems.md#gtextras)|0.5.0 |__+1__ | | | -|[HaploCatcher](problems.md#haplocatcher)|1.0.4 |__+1__ | |__+1__ | -|[healthyR](problems.md#healthyr)|0.2.2 |__+1__ | |1 __+1__ | -|[healthyR.ts](problems.md#healthyrts)|0.3.0 |__+2__ | |1 __+1__ | -|[heatmaply](problems.md#heatmaply)|1.5.0 |__+2__ | |1 __+1__ | -|[hermiter](problems.md#hermiter)|2.3.1 |__+1__ | |2 __+1__ | -|[hesim](problems.md#hesim)|0.5.4 |__+1__ | |2 | -|[hidecan](problems.md#hidecan)|1.1.0 |1 __+1__ | |__+1__ | -|[HVT](problems.md#hvt)|24.5.2 |__+1__ | | | -|[hypsoLoop](problems.md#hypsoloop)|0.2.0 | |__+1__ | | -|[ICvectorfields](problems.md#icvectorfields)|0.1.2 |__+1__ | |__+1__ | -|[idopNetwork](problems.md#idopnetwork)|0.1.2 |__+1__ | |__+1__ | -|[inferCSN](problems.md#infercsn)|1.0.5 |__+1__ | |1 | -|[insurancerating](problems.md#insurancerating)|0.7.4 |__+1__ | | | -|[inTextSummaryTable](problems.md#intextsummarytable)|3.3.3 |__+2__ | |1 __+1__ | -|[karel](problems.md#karel)|0.1.1 |__+2__ | |1 | -|[kDGLM](problems.md#kdglm)|1.2.0 |1 __+1__ | | | -|[latentcor](problems.md#latentcor)|2.0.1 |__+1__ | | | -|[lcars](problems.md#lcars)|0.3.8 |__+2__ | | | -|[lemon](problems.md#lemon)|0.4.9 |__+3__ | |__+1__ | -|[lfproQC](problems.md#lfproqc)|0.1.0 |__+2__ | |1 __+1__ | -|[LMoFit](problems.md#lmofit)|0.1.7 |__+1__ | |1 __+1__ | -|[manydata](problems.md#manydata)|0.9.3 |__+1__ | |1 | -|[MARVEL](problems.md#marvel)|1.4.0 |__+2__ | |__+1__ | -|[MBNMAdose](problems.md#mbnmadose)|0.4.3 |__+1__ | |1 __+1__ | -|[MBNMAtime](problems.md#mbnmatime)|0.2.4 |1 | |__+1__ | -|[MetaNet](problems.md#metanet)|0.1.2 |__+1__ | | | -|[metR](problems.md#metr)|0.15.0 |__+2__ | |1 __+1__ | -|[migraph](problems.md#migraph)|1.3.4 |__+1__ | | | -|[MiMIR](problems.md#mimir)|1.5 |__+1__ | | | -|[miRetrieve](problems.md#miretrieve)|1.3.4 |__+1__ | | | -|[misspi](problems.md#misspi)|0.1.0 |__+1__ | | | -|[mizer](problems.md#mizer)|2.5.1 |__+1__ | |1 | -|[mlr3spatiotempcv](problems.md#mlr3spatiotempcv)|2.3.1 |1 __+1__ | |1 | -|[mlr3viz](problems.md#mlr3viz)|0.9.0 |__+1__ | | | -|[modeltime.resample](problems.md#modeltimeresample)|0.2.3 |__+1__ | |1 | -|[move](problems.md#move)|4.2.4 |1 | |__+1__ | -|[mtb](problems.md#mtb)|0.1.8 |__+1__ | | | -|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 | -|[NetFACS](problems.md#netfacs)|0.5.0 |__+2__ | | | -|[NeuralSens](problems.md#neuralsens)|1.1.3 |__+1__ | | | -|[NHSRplotthedots](problems.md#nhsrplotthedots)|0.1.0 |__+1__ | |1 | -|[NIMAA](problems.md#nimaa)|0.2.1 |__+3__ | |2 __+1__ | -|[OBIC](problems.md#obic)|3.0.2 |__+1__ | |1 __+1__ | -|[OmicNavigator](problems.md#omicnavigator)|1.13.13 |__+1__ | |1 | -|[oncomsm](problems.md#oncomsm)|0.1.4 |__+2__ | |2 __+1__ | -|[pafr](problems.md#pafr)|0.0.2 |__+1__ | |1 | -|[patchwork](problems.md#patchwork)|1.2.0 |__+1__ | | | -|[pathviewr](problems.md#pathviewr)|1.1.7 |__+1__ | | | -|[pcutils](problems.md#pcutils)|0.2.6 |__+1__ | | | -|[pdxTrees](problems.md#pdxtrees)|0.4.0 |__+1__ | |1 __+1__ | -|[personalized](problems.md#personalized)|0.2.7 |__+1__ | | | -|[phylepic](problems.md#phylepic)|0.2.0 |__+1__ | |__+1__ | -|[Plasmidprofiler](problems.md#plasmidprofiler)|0.1.6 |__+1__ | | | -|[platetools](problems.md#platetools)|0.1.7 |__+1__ | | | -|[plotDK](problems.md#plotdk)|0.1.0 |__+1__ | |2 | -|[plotly](problems.md#plotly)|4.10.4 |__+2__ | |1 | -|[pmartR](problems.md#pmartr)|2.4.5 |__+1__ | |1 | -|[pmxTools](problems.md#pmxtools)|1.3 |__+1__ | |1 | -|[posterior](problems.md#posterior)|1.6.0 |1 | |__+1__ | -|[PPQplan](problems.md#ppqplan)|1.1.0 |1 | |2 __+1__ | -|[ppseq](problems.md#ppseq)|0.2.4 |__+1__ | |1 __+1__ | -|[precrec](problems.md#precrec)|0.14.4 |__+1__ | |1 __+1__ | 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+|[tern](problems.md#tern)|0.9.5 |__+1__ | |1 | +|[thematic](problems.md#thematic)|0.1.6 |__+2__ | | | +|[Thermistor](problems.md#thermistor)|1.1.0 |__+1__ | | | +|[tidybayes](problems.md#tidybayes)|3.0.6 |2 __+1__ | | | +|[tidycat](problems.md#tidycat)|0.1.2 |__+2__ | |1 __+1__ | +|[tidyCDISC](problems.md#tidycdisc)|0.2.1 |__+1__ | |1 | +|[tidysdm](problems.md#tidysdm)|0.9.5 |__+1__ | |1 __+1__ | +|[tidySEM](problems.md#tidysem)|0.2.7 |__+3__ | |__+1__ | +|[tidytreatment](problems.md#tidytreatment)|0.2.2 |__+1__ | |1 __+1__ | +|[timeplyr](problems.md#timeplyr)|0.8.2 |__+1__ | | | +|[timetk](problems.md#timetk)|2.9.0 |__+1__ | |1 | +|[tinyarray](problems.md#tinyarray)|2.4.2 |__+1__ | |1 | +|[tipmap](problems.md#tipmap)|0.5.2 |__+1__ | |__+1__ | +|[tornado](problems.md#tornado)|0.1.3 |__+3__ | |__+1__ | +|[TOSTER](problems.md#toster)|0.8.3 |__+3__ | |__+1__ | +|[TreatmentPatterns](problems.md#treatmentpatterns)|2.6.9 |__+1__ | | | +|[TreatmentSelection](problems.md#treatmentselection)|2.1.1 |__+1__ | | | +|[TreeDep](problems.md#treedep)|0.1.3 |__+1__ | | | +|[TreeDist](problems.md#treedist)|2.9.1 |__+1__ | |1 __+1__ | +|[treeheatr](problems.md#treeheatr)|0.2.1 |__+2__ | |__+1__ | +|[trelliscopejs](problems.md#trelliscopejs)|0.2.6 |__+1__ | | | +|[tricolore](problems.md#tricolore)|1.2.4 |__+2__ | |1 __+1__ | +|[triptych](problems.md#triptych)|0.1.3 |__+1__ | | | +|[tsnet](problems.md#tsnet)|0.1.0 |__+1__ | |2 | +|[UBayFS](problems.md#ubayfs)|1.0 |__+1__ | |__+1__ | +|[Umatrix](problems.md#umatrix)|4.0.1 |__+1__ | | | +|[umiAnalyzer](problems.md#umianalyzer)|1.0.0 |__+1__ | | | +|[UnalR](problems.md#unalr)|1.0.0 |__+2__ | |2 | +|[unmconf](problems.md#unmconf)|1.0.0 |__+1__ | |__+1__ | +|[usmap](problems.md#usmap)|0.7.1 |__+3__ | |1 __+1__ | +|[vannstats](problems.md#vannstats)|1.3.4.14 |__+1__ | | | +|[vDiveR](problems.md#vdiver)|1.2.1 |__+1__ | |1 | +|[venn](problems.md#venn)|1.12 |__+1__ | | | +|[vimpclust](problems.md#vimpclust)|0.1.0 |__+1__ | |1 __+1__ | +|[vip](problems.md#vip)|0.4.1 |__+2__ | |2 | +|[VirtualPop](problems.md#virtualpop)|2.0.2 |__+1__ | |__+1__ | +|[viscomp](problems.md#viscomp)|1.0.0 |__+1__ | | | +|[vivaldi](problems.md#vivaldi)|1.0.1 |__+3__ | |1 __+1__ | +|[voiceR](problems.md#voicer)|0.1.0 |__+2__ | |1 | +|[volcano3D](problems.md#volcano3d)|2.0.9 |__+2__ | |__+1__ | +|[voluModel](problems.md#volumodel)|0.2.2 |1 __+1__ | |__+1__ | +|[vsd](problems.md#vsd)|0.1.0 |__+1__ | |1 | +|[vvshiny](problems.md#vvshiny)|0.1.1 |__+1__ | | | +|[walker](problems.md#walker)|1.0.10 |__+1__ | |2 __+1__ | +|[WVPlots](problems.md#wvplots)|1.3.8 |__+3__ | |__+1__ | +|[xaringanthemer](problems.md#xaringanthemer)|0.4.2 |1 __+1__ | | | +|[yamlet](problems.md#yamlet)|1.0.3 |__+2__ | |1 | diff --git a/revdep/cran.md b/revdep/cran.md index 4a9f813633..4a1365f7a5 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,9 +1,9 @@ ## revdepcheck results -We checked 5166 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 5209 reverse dependencies (5199 from CRAN + 10 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 242 new problems - * We failed to check 132 packages + * We saw 469 new problems + * We failed to check 155 packages Issues with CRAN packages are summarised below. @@ -18,12 +18,25 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* adaptr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * AeRobiology checking re-building of vignette outputs ... NOTE * agricolaeplotr checking tests ... ERROR +* alien + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* AlphaPart + checking examples ... ERROR + * AnalysisLin checking examples ... ERROR @@ -33,6 +46,28 @@ Issues with CRAN packages are summarised below. * ANN2 checking tests ... ERROR +* AnnoProbe + checking examples ... ERROR + +* ANOFA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ANOPA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* AntMAN + checking examples ... ERROR + checking tests ... ERROR + +* APCI + checking tests ... ERROR + * aplot checking examples ... ERROR @@ -41,6 +76,10 @@ Issues with CRAN packages are summarised below. * ASRgenomics checking examples ... ERROR + checking tests ... ERROR + +* autocogs + checking tests ... ERROR * autoplotly checking examples ... ERROR @@ -51,9 +90,25 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* baggr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* banter + checking examples ... ERROR + * bartMan checking examples ... ERROR +* BasketballAnalyzeR + checking examples ... ERROR + +* bayefdr + checking examples ... ERROR + checking tests ... ERROR + * bayesAB checking tests ... ERROR @@ -69,49 +124,105 @@ Issues with CRAN packages are summarised below. * BayesMallows checking tests ... ERROR +* bayesplay + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * bayesplot + checking examples ... ERROR checking tests ... ERROR * bayestestR checking examples ... ERROR +* BCEA + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BDgraph + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BEAMR + checking examples ... ERROR + * beastt checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* BeeGUTS + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * besthr checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* betaclust + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * biclustermd checking tests ... ERROR * biodosetools checking tests ... ERROR +* BioPred + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* BlandAltmanLeh + checking running R code from vignettes ... ERROR + +* bmggum + checking examples ... ERROR + * boxly checking tests ... ERROR * braidReports checking examples ... ERROR +* BRcal + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * breathtestcore checking tests ... ERROR * brolgar checking examples ... ERROR +* calibrationband + checking examples ... ERROR + * cartograflow checking examples ... ERROR -* cartographr - checking tests ... ERROR +* cases + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * cats checking examples ... ERROR +* ceterisParibus + checking tests ... ERROR + +* cfda + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * cheem checking tests ... ERROR @@ -123,6 +234,11 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* CINNA + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * circhelp checking examples ... ERROR checking running R code from vignettes ... ERROR @@ -140,11 +256,43 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* cloneRate + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* clustEff + checking examples ... ERROR + +* ClustImpute + checking running R code from vignettes ... ERROR + +* cmstatr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* codaredistlm + checking examples ... ERROR + +* coefplot + checking examples ... ERROR + * CohortPlat checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* complmrob + checking examples ... ERROR + +* conjoint + checking examples ... ERROR + +* conquestr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * CoreMicrobiomeR checking examples ... ERROR @@ -156,14 +304,47 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* corx + checking tests ... ERROR + +* cosinor2 + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* CoSMoS + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * countfitteR checking tests ... ERROR +* coursekata + checking examples ... ERROR + checking tests ... ERROR + * covidcast checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* Coxmos + checking examples ... ERROR + +* cpr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* cpsvote + checking running R code from vignettes ... ERROR + +* crimeutils + checking examples ... ERROR + +* crmPack + checking examples ... ERROR + checking running R code from vignettes ... ERROR + * crosshap checking examples ... ERROR @@ -174,8 +355,37 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* curtailment + checking examples ... ERROR + +* dabestr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* DAISIEprep + checking tests ... ERROR + +* dbmss + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * deeptime + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* descriptio + checking examples ... ERROR + +* directlabels + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* disto checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * distributional checking examples ... ERROR @@ -184,17 +394,60 @@ Issues with CRAN packages are summarised below. checking examples ... ERROR checking tests ... ERROR +* dotwhisker + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* DRomics + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* dtwclust + checking tests ... ERROR + +* duke + checking tests ... ERROR + +* easysurv + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* EGAnet + checking examples ... ERROR + * EGM checking tests ... ERROR +* emmeans + checking examples ... ERROR + +* EMMIXmfa + checking examples ... ERROR + * entropart checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* EnvStats + checking examples ... ERROR + * epiCleanr checking examples ... ERROR +* epiphy + checking examples ... ERROR + +* EQUALSTATS + checking examples ... ERROR + +* ergm.multi + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * esci checking examples ... ERROR checking tests ... ERROR @@ -215,13 +468,15 @@ Issues with CRAN packages are summarised below. * explainer checking examples ... ERROR +* exuber + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ezEDA checking tests ... ERROR * ezplot checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE * fable.prophet checking running R code from vignettes ... ERROR @@ -237,41 +492,95 @@ Issues with CRAN packages are summarised below. * fairmodels checking tests ... ERROR +* fastR2 + checking examples ... ERROR + +* faux + checking re-building of vignette outputs ... NOTE + * fddm checking running R code from vignettes ... ERROR * feasts checking tests ... ERROR +* fergm + checking examples ... ERROR + * ffp checking examples ... ERROR +* fic + checking running R code from vignettes ... ERROR + * fido checking examples ... ERROR checking tests ... ERROR +* fitdistrplus + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fitlandr + checking examples ... ERROR + +* flexsurv + checking running R code from vignettes ... ERROR + * flipr checking re-building of vignette outputs ... NOTE -* foqat +* FLOPART + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* fmesher + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* fmf + checking examples ... ERROR + * forestly checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* FossilSim + checking examples ... ERROR + +* FPDclustering + checking examples ... ERROR + * frailtyEM checking examples ... ERROR * funcharts checking examples ... ERROR +* FunnelPlotR + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* genekitr + checking examples ... ERROR + +* geoheatmap + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * geomtextpath checking examples ... ERROR checking tests ... ERROR +* geostan + checking examples ... ERROR + * GGally + checking examples ... ERROR checking tests ... ERROR * gganimate @@ -288,6 +597,12 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* ggcharts + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggdark checking examples ... ERROR checking tests ... ERROR @@ -297,9 +612,6 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking re-building of vignette outputs ... NOTE -* ggDoubleHeat - checking examples ... ERROR - * ggeasy checking examples ... ERROR checking tests ... ERROR @@ -311,18 +623,38 @@ Issues with CRAN packages are summarised below. * ggESDA checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ggExtra + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ggfacto + checking examples ... ERROR * ggfixest checking tests ... ERROR +* ggfocus + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggforce checking examples ... ERROR * ggformula + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR checking for code/documentation mismatches ... WARNING + checking re-building of vignette outputs ... NOTE * ggfortify + checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * gggenomes checking examples ... ERROR @@ -330,7 +662,6 @@ Issues with CRAN packages are summarised below. checking re-building of vignette outputs ... NOTE * ggh4x - checking examples ... ERROR checking tests ... ERROR checking re-building of vignette outputs ... NOTE @@ -353,6 +684,12 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* ggmatplot + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggmice checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -363,30 +700,49 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ggnewscale +* ggpackets checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * ggparallel checking tests ... ERROR +* ggparty + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggpicrust2 checking examples ... ERROR -* ggpie +* ggplotlyExtra + checking examples ... ERROR + +* ggPMX checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ggplotlyExtra +* ggpol checking examples ... ERROR -* ggpol +* ggprism checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * ggpubr + checking examples ... ERROR checking tests ... ERROR +* ggrain + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * ggraph checking examples ... ERROR checking re-building of vignette outputs ... NOTE @@ -409,10 +765,16 @@ Issues with CRAN packages are summarised below. checking tests ... ERROR checking for code/documentation mismatches ... WARNING +* ggsmc + checking running R code from vignettes ... ERROR + * ggspatial checking examples ... ERROR checking tests ... ERROR +* ggstatsplot + checking examples ... ERROR + * ggtern checking examples ... ERROR @@ -423,6 +785,27 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* GimmeMyPlot + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* giniVarCI + checking examples ... ERROR + +* gMCPLite + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* gMOIP + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* GofCens + checking examples ... ERROR + * greatR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -430,6 +813,12 @@ Issues with CRAN packages are summarised below. * Greymodels checking examples ... ERROR +* gsDesign + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * gtExtras checking tests ... ERROR @@ -455,11 +844,18 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* hesim - checking tests ... ERROR +* heumilkr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* hidecan - checking tests ... ERROR +* hilldiv + checking examples ... ERROR + +* hmclearn + checking examples ... ERROR + +* HTLR + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * HVT @@ -468,7 +864,17 @@ Issues with CRAN packages are summarised below. * hypsoLoop checking whether package ‘hypsoLoop’ can be installed ... WARNING -* ICvectorfields +* ibdsim2 + checking examples ... ERROR + +* ICtest + checking examples ... ERROR + +* idiogramFISH + checking installed package size ... NOTE + +* IDMIR + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -476,7 +882,27 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* inferCSN +* ihclust + checking examples ... ERROR + +* immunarch + checking examples ... ERROR + +* incidental + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* infer + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* injurytools + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* inlabru checking examples ... ERROR * insurancerating @@ -487,6 +913,32 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* IPV + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* IRon + checking examples ... ERROR + +* irt + checking examples ... ERROR + +* isoorbi + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ivDiag + checking examples ... ERROR + +* ivreg + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* jarbes + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * karel checking examples ... ERROR checking tests ... ERROR @@ -494,6 +946,10 @@ Issues with CRAN packages are summarised below. * kDGLM checking examples ... ERROR +* KMEANS.KNN + checking examples ... ERROR + checking tests ... ERROR + * latentcor checking examples ... ERROR @@ -512,18 +968,55 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* lgpr + checking tests ... ERROR + +* LightLogR + checking examples ... ERROR + * LMoFit checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* manydata +* lnmixsurv checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* LocalControl + checking running R code from vignettes ... ERROR + +* LocalCop + checking re-building of vignette outputs ... NOTE + +* LongDat + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE -* MARVEL +* longreadvqs checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* lpdensity + checking examples ... ERROR + +* lspartition + checking examples ... ERROR + +* LSTbook + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + +* manydata + checking tests ... ERROR + +* manymome + checking examples ... ERROR + +* mapbayr + checking examples ... ERROR + * MBNMAdose checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -531,26 +1024,58 @@ Issues with CRAN packages are summarised below. * MBNMAtime checking re-building of vignette outputs ... NOTE +* mecoturn + checking examples ... ERROR + * MetaNet checking examples ... ERROR * metR checking examples ... ERROR + checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* metrica + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* miceRanger + checking running R code from vignettes ... ERROR + +* microbial + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MicrobiomeSurv + checking examples ... ERROR + * migraph checking tests ... ERROR +* mikropml + checking tests ... ERROR + * MiMIR checking examples ... ERROR * miRetrieve checking tests ... ERROR +* MiscMetabar + checking examples ... ERROR + checking tests ... ERROR + * misspi checking examples ... ERROR +* mixpoissonreg + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * mizer checking tests ... ERROR @@ -559,47 +1084,146 @@ Issues with CRAN packages are summarised below. * mlr3viz checking examples ... ERROR + checking tests ... ERROR * modeltime.resample checking tests ... ERROR -* move - checking installed package size ... NOTE +* moreparty + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mosaicCalc + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mosaicData + checking examples ... ERROR + +* mosaicModel + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mppR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* MSCMT + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* mstate + checking examples ... ERROR + checking running R code from vignettes ... ERROR * mtb checking tests ... ERROR +* mulgar + checking examples ... ERROR + +* MultivariateAnalysis + checking examples ... ERROR + +* mxfda + checking installed package size ... NOTE + * neatmaps checking examples ... ERROR +* neatStats + checking examples ... ERROR + +* netcom + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * NetFACS checking examples ... ERROR checking running R code from vignettes ... ERROR -* NeuralSens +* neuroUp checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * NHSRplotthedots checking tests ... ERROR +* nichetools + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * NIMAA checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* nonmem2R + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* nphRCT + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* nprobust + checking examples ... ERROR + +* nzelect + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * OBIC checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* oceanic + checking examples ... ERROR + +* oddsratio + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* ofpetrial + checking examples ... ERROR + * OmicNavigator checking tests ... ERROR +* omu + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* OncoBayes2 + checking examples ... ERROR + * oncomsm checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* OneSampleLogRankTest + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* onpoint + checking examples ... ERROR + +* ordbetareg + checking examples ... ERROR + +* packcircles + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * pafr checking tests ... ERROR @@ -609,6 +1233,13 @@ Issues with CRAN packages are summarised below. * pathviewr checking tests ... ERROR +* patientProfilesVis + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* PCADSC + checking examples ... ERROR + * pcutils checking examples ... ERROR @@ -619,16 +1250,29 @@ Issues with CRAN packages are summarised below. * personalized checking tests ... ERROR -* phylepic +* phyloseqGraphTest + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* PieGlyph + checking examples ... ERROR + checking tests ... ERROR + checking re-building of vignette outputs ... NOTE + * Plasmidprofiler checking examples ... ERROR * platetools checking tests ... ERROR +* PLNmodels + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* plotBart + checking tests ... ERROR + * plotDK checking tests ... ERROR @@ -652,16 +1296,20 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* precrec +* PPtreeregViz + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* priorsense +* precintcon checking examples ... ERROR + +* precrec checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* ProAE +* priorsense + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -671,58 +1319,143 @@ Issues with CRAN packages are summarised below. * processmapR checking tests ... ERROR +* projpred + checking examples ... ERROR + checking running R code from vignettes ... ERROR + * psborrow checking tests ... ERROR +* pubh + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* PUPMSI + checking examples ... ERROR + +* qacBase + checking examples ... ERROR + +* qPCRhelper + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * r2dii.plot checking tests ... ERROR +* r2spss + checking examples ... ERROR + checking running R code from vignettes ... ERROR + +* radiant.basics + checking examples ... ERROR + +* radiant.data + checking examples ... ERROR + +* radiant.model + checking examples ... ERROR + * Radviz checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* randomForestExplainer + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * rassta checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR -* REddyProc - checking installed package size ... NOTE +* rater + checking tests ... ERROR + +* RBesT + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* rddensity + checking examples ... ERROR + +* RecordTest + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* reda + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * redist checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* reReg +* registr + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* reliabilitydiag + checking examples ... ERROR + +* relliptical checking examples ... ERROR +* reportRmd + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * reservr checking examples ... ERROR checking re-building of vignette outputs ... NOTE -* rKOMICS +* RestoreNet + checking examples ... ERROR + +* rfPermute checking examples ... ERROR * RKorAPClient checking tests ... ERROR -* RNAseqQC - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - * roahd checking examples ... ERROR +* robCompositions + checking examples ... ERROR + * romic + checking examples ... ERROR checking tests ... ERROR * roptions checking examples ... ERROR +* rSAFE + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * santaR checking tests ... ERROR +* saros + checking examples ... ERROR + checking tests ... ERROR + +* scatterpie + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * scdtb checking tests ... ERROR @@ -736,10 +1469,30 @@ Issues with CRAN packages are summarised below. * SCVA checking examples ... ERROR +* sdmTMB + checking examples ... ERROR + * SDMtune checking tests ... ERROR -* SeaVal +* sedproxy + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* see + checking examples ... ERROR + +* seedreg + checking examples ... ERROR + +* semfindr + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* sensiPhy checking examples ... ERROR * sglg @@ -751,21 +1504,34 @@ Issues with CRAN packages are summarised below. * SHAPforxgboost checking examples ... ERROR -* SHELF +* ShapleyOutlier + checking examples ... ERROR + checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE * shinipsum checking tests ... ERROR -* SimNPH - checking tests ... ERROR +* signatureSurvival + checking examples ... ERROR -* smallsets +* SimCorrMix checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* spbal +* SimMultiCorrData + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* SimNPH + checking tests ... ERROR + +* slendr + checking examples ... ERROR + +* smallsets + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE @@ -775,34 +1541,90 @@ Issues with CRAN packages are summarised below. * sport checking tests ... ERROR +* spotoroo + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * SqueakR checking re-building of vignette outputs ... NOTE +* stability + checking examples ... ERROR + * statgenGWAS checking tests ... ERROR +* statgenHTP + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* sugrrants + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* superb + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * surveyexplorer checking examples ... ERROR +* survivalAnalysis + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* survminer + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* survParamSim + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* survstan + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* SVMMaj + checking examples ... ERROR + checking running R code from vignettes ... ERROR + * Sysrecon checking examples ... ERROR * tabledown checking examples ... ERROR -* TCIU - checking examples ... ERROR +* tcgaViz checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* tensorEVD +* TCIU + checking examples ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* tcpl + checking tests ... ERROR + +* tern + checking examples ... ERROR + * thematic checking examples ... ERROR checking tests ... ERROR +* Thermistor + checking examples ... ERROR + * tidybayes checking examples ... ERROR @@ -818,16 +1640,29 @@ Issues with CRAN packages are summarised below. checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* tidySEM + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * tidytreatment checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE +* timeplyr + checking examples ... ERROR + * timetk checking tests ... ERROR * tinyarray checking examples ... ERROR +* tipmap + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * tornado checking examples ... ERROR checking tests ... ERROR @@ -843,6 +1678,21 @@ Issues with CRAN packages are summarised below. * TreatmentPatterns checking tests ... ERROR +* TreatmentSelection + checking examples ... ERROR + +* TreeDep + checking examples ... ERROR + +* TreeDist + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* treeheatr + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + * trelliscopejs checking tests ... ERROR @@ -857,26 +1707,88 @@ Issues with CRAN packages are summarised below. * tsnet checking tests ... ERROR +* UBayFS + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* Umatrix + checking examples ... ERROR + * umiAnalyzer checking examples ... ERROR -* valr +* UnalR + checking examples ... ERROR checking tests ... ERROR +* unmconf + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* usmap + checking examples ... ERROR + checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* vannstats + checking examples ... ERROR + +* vDiveR + checking examples ... ERROR + +* venn + checking examples ... ERROR + +* vimpclust + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* vip + checking examples ... ERROR + checking tests ... ERROR + +* VirtualPop + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* viscomp + checking examples ... ERROR + * vivaldi checking examples ... ERROR checking tests ... ERROR checking running R code from vignettes ... ERROR checking re-building of vignette outputs ... NOTE -* vivid +* voiceR + checking examples ... ERROR + checking tests ... ERROR + +* volcano3D + checking examples ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* voluModel + checking examples ... ERROR + checking re-building of vignette outputs ... NOTE + +* vsd checking examples ... ERROR * vvshiny checking tests ... ERROR -* wilson +* walker + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE + +* WVPlots + checking examples ... ERROR checking tests ... ERROR + checking running R code from vignettes ... ERROR + checking re-building of vignette outputs ... NOTE * xaringanthemer checking tests ... ERROR @@ -887,135 +1799,158 @@ Issues with CRAN packages are summarised below. ### Failed to check -* abctools (NA) -* animalEKF (NA) -* ANOM (NA) -* atRisk (NA) -* AutoScore (NA) -* bayesdfa (NA) -* bayesDP (NA) -* BayesianFactorZoo (NA) -* BayesSurvive (NA) -* BCClong (NA) -* BGGM (NA) -* binsreg (NA) -* bmstdr (NA) -* bspcov (NA) -* BuyseTest (NA) -* CalibrationCurves (NA) -* CARBayesST (NA) -* CaseBasedReasoning (NA) -* CGPfunctions (NA) -* cmprskcoxmsm (NA) -* contrast (NA) -* coxed (NA) -* CRMetrics (NA) -* csmpv (NA) -* ctsem (NA) -* DepthProc (NA) -* DR.SC (NA) -* DynNom (NA) -* easybgm (NA) -* ecolottery (NA) -* EpiEstim (NA) -* evolqg (NA) -* ForecastComb (NA) -* gapfill (NA) -* GeomComb (NA) -* ggrcs (NA) -* ggrisk (NA) -* gJLS2 (NA) -* Greg (NA) -* greport (NA) -* hettx (NA) -* hIRT (NA) -* Hmsc (NA) -* inventorize (NA) -* iNZightPlots (NA) -* iNZightRegression (NA) -* IRexamples (NA) -* jmBIG (NA) -* joineRML (NA) -* JWileymisc (NA) -* kmc (NA) -* L2E (NA) -* llbayesireg (NA) -* LorenzRegression (NA) -* lsirm12pl (NA) -* mbsts (NA) -* MendelianRandomization (NA) -* MetabolicSurv (NA) -* miWQS (NA) -* MRZero (NA) -* Multiaovbay (NA) -* multilevelTools (NA) -* multinma (NA) -* NCA (NA) -* netcmc (NA) -* NetworkChange (NA) -* nlmeVPC (NA) -* NMADiagT (NA) -* optweight (NA) -* OVtool (NA) -* paths (NA) -* PLMIX (NA) -* popstudy (NA) -* pould (NA) -* powerly (NA) -* pre (NA) -* ProFAST (NA) -* psbcSpeedUp (NA) -* pscore (NA) -* psfmi (NA) -* qPCRtools (NA) -* qreport (NA) -* qris (NA) -* qte (NA) -* quid (NA) -* RATest (NA) -* RcmdrPlugin.RiskDemo (NA) -* rddtools (NA) -* riskRegression (NA) -* rms (NA) -* rmsb (NA) -* robmed (NA) -* robmedExtra (NA) -* RPPanalyzer (NA) -* RQdeltaCT (NA) -* scCustomize (NA) -* SCdeconR (NA) -* scGate (NA) -* SCIntRuler (NA) -* scMappR (NA) -* scpi (NA) -* scRNAstat (NA) -* sectorgap (NA) -* SEERaBomb (NA) -* semicmprskcoxmsm (NA) -* SensMap (NA) -* Seurat (NA) -* shinyTempSignal (NA) -* sievePH (NA) -* Signac (NA) -* SimplyAgree (NA) -* sMSROC (NA) -* SNPassoc (NA) -* snplinkage (NA) -* SoupX (NA) -* sparsereg (NA) -* spikeSlabGAM (NA) -* statsr (NA) -* streamDAG (NA) -* survHE (NA) -* survidm (NA) -* tempted (NA) -* tidydr (NA) -* tidyEdSurvey (NA) -* tidyseurat (NA) -* tidyvpc (NA) -* TriDimRegression (NA) -* TSrepr (NA) -* twang (NA) -* vdg (NA) -* visa (NA) -* WRTDStidal (NA) +* abctools (NA) +* adjclust (NA) +* animalEKF (NA) +* ANOM (NA) +* atRisk (NA) +* AutoScore (NA) +* baRulho (NA) +* bayesDP (NA) +* BayesianFactorZoo (NA) +* BayesSurvive (NA) +* BCClong (NA) +* BGGM (NA) +* binsreg (NA) +* bspcov (NA) +* bsub (NA) +* BuyseTest (NA) +* CARBayesST (NA) +* CGPfunctions (NA) +* chemodiv (NA) +* cinaR (NA) +* cmprskcoxmsm (NA) +* CNVScope (NA) +* COMMA (NA) +* conos (NA) +* counterfactuals (NA) +* CRMetrics (NA) +* crosstalkr (NA) +* ctsem (NA) +* DepthProc (NA) +* DR.SC (NA) +* easybgm (NA) +* EcoEnsemble (NA) +* ecolottery (NA) +* EMAS (NA) +* EpiEstim (NA) +* evolqg (NA) +* ForecastComb (NA) +* GALLO (NA) +* gap (NA) +* gapfill (NA) +* geneHapR (NA) +* GeneSelectR (NA) +* GeomComb (NA) +* gJLS2 (NA) +* hettx (NA) +* Hmisc (NA) +* Hmsc (NA) +* iClusterVB (NA) +* inventorize (NA) +* iNZightPlots (NA) +* iNZightRegression (NA) +* IRexamples (NA) +* jmBIG (NA) +* joineRML (NA) +* kibior (NA) +* kmc (NA) +* L2E (NA) +* llbayesireg (NA) +* locuszoomr (NA) +* LorenzRegression (NA) +* lsirm12pl (NA) +* MARVEL (NA) +* mbsts (NA) +* MitoHEAR (NA) +* miWQS (NA) +* mlmts (NA) +* mlr (NA) +* MOCHA (NA) +* MRZero (NA) +* multilevelTools (NA) +* multinma (NA) +* NCA (NA) +* netcmc (NA) +* NetworkChange (NA) +* nlmeVPC (NA) +* NMADiagT (NA) +* ohun (NA) +* optweight (NA) +* OVtool (NA) +* pagoda2 (NA) +* PAMpal (NA) +* PAMscapes (NA) +* paths (NA) +* pcvr (NA) +* PlasmaMutationDetector (NA) +* PlasmaMutationDetector2 (NA) +* PLMIX (NA) +* polyRAD (NA) +* popstudy (NA) +* pould (NA) +* PoweREST (NA) +* powerly (NA) +* pre (NA) +* ProFAST (NA) +* psbcSpeedUp (NA) +* pscore (NA) +* qPCRtools (NA) +* qris (NA) +* qte (NA) +* quantilogram (NA) +* quid (NA) +* RcmdrPlugin.RiskDemo (NA) +* rddtools (NA) +* RNAseqQC (NA) +* robmed (NA) +* robmedExtra (NA) +* RPPanalyzer (NA) +* RQdeltaCT (NA) +* rstanarm (NA) +* RTIGER (NA) +* rTwig (NA) +* RVA (NA) +* scCustomize (NA) +* SCdeconR (NA) +* scGate (NA) +* SCIntRuler (NA) +* scITD (NA) +* scMappR (NA) +* scpi (NA) +* scRNAstat (NA) +* sectorgap (NA) +* SeedMatchR (NA) +* SEERaBomb (NA) +* semicmprskcoxmsm (NA) +* SensMap (NA) +* sephora (NA) +* Seurat (NA) +* shinyTempSignal (NA) +* sievePH (NA) +* sigminer (NA) +* Signac (NA) +* SimplyAgree (NA) +* SNPassoc (NA) +* snplinkage (NA) +* SoupX (NA) +* sparsereg (NA) +* SpatialDDLS (NA) +* spikeSlabGAM (NA) +* statsr (NA) +* streamDAG (NA) +* survidm (NA) +* tempted (NA) +* TestAnaAPP (NA) +* tidydr (NA) +* tidyEdSurvey (NA) +* tidyseurat (NA) +* tidyvpc (NA) +* TriDimRegression (NA) +* TSrepr (NA) +* twang (NA) +* updog (NA) +* valr (NA) +* vdg (NA) +* visa (NA) +* WRTDStidal (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 84ae909aa5..444f4e174b 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -69,6 +69,82 @@ ERROR: lazy loading failed for package ‘abctools’ * removing ‘/tmp/workdir/abctools/old/abctools.Rcheck/abctools’ +``` +# adjclust + +
+ +* Version: 0.6.9 +* GitHub: https://github.com/pneuvial/adjclust +* Source code: https://github.com/cran/adjclust +* Date/Publication: 2024-02-08 08:50:05 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "adjclust")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/adjclust/new/adjclust.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘adjclust/DESCRIPTION’ ... OK +... + When sourcing ‘hicClust.R’: +Error: there is no package called ‘HiTC’ +Execution halted + + ‘hicClust.Rmd’ using ‘UTF-8’... failed + ‘notesCHAC.Rmd’ using ‘UTF-8’... OK + ‘snpClust.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/adjclust/old/adjclust.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘adjclust/DESCRIPTION’ ... OK +... + When sourcing ‘hicClust.R’: +Error: there is no package called ‘HiTC’ +Execution halted + + ‘hicClust.Rmd’ using ‘UTF-8’... failed + ‘notesCHAC.Rmd’ using ‘UTF-8’... OK + ‘snpClust.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 2 NOTEs + + + + + ``` # animalEKF @@ -272,131 +348,141 @@ Run `revdepcheck::cloud_details(, "AutoScore")` for more info -## In both - -* checking whether package ‘AutoScore’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘AutoScore’ ... -** package ‘AutoScore’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘AutoScore’ -* removing ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck/AutoScore’ +* using log directory ‘/tmp/workdir/AutoScore/new/AutoScore.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘AutoScore/DESCRIPTION’ ... OK +... +* this is package ‘AutoScore’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘survAUC’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘AutoScore’ ... -** package ‘AutoScore’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘AutoScore’ -* removing ‘/tmp/workdir/AutoScore/old/AutoScore.Rcheck/AutoScore’ +* using log directory ‘/tmp/workdir/AutoScore/old/AutoScore.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘AutoScore/DESCRIPTION’ ... OK +... +* this is package ‘AutoScore’ version ‘1.0.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘survAUC’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# bayesdfa +# baRulho
-* Version: 1.3.3 -* GitHub: https://github.com/fate-ewi/bayesdfa -* Source code: https://github.com/cran/bayesdfa -* Date/Publication: 2024-02-26 20:50:06 UTC -* Number of recursive dependencies: 89 +* Version: 2.1.2 +* GitHub: https://github.com/ropensci/baRulho +* Source code: https://github.com/cran/baRulho +* Date/Publication: 2024-08-31 13:10:07 UTC +* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "bayesdfa")` for more info +Run `revdepcheck::cloud_details(, "baRulho")` for more info
-## In both - -* checking whether package ‘bayesdfa’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘bayesdfa’ ... -** package ‘bayesdfa’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/baRulho/new/baRulho.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘baRulho/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'warbleR', 'ohun' + +Package suggested but not available for checking: ‘Rraven’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 -ERROR: compilation failed for package ‘bayesdfa’ -* removing ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa’ ``` ### CRAN ``` -* installing *source* package ‘bayesdfa’ ... -** package ‘bayesdfa’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/baRulho/old/baRulho.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘baRulho/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'warbleR', 'ohun' + +Package suggested but not available for checking: ‘Rraven’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1 -ERROR: compilation failed for package ‘bayesdfa’ -* removing ‘/tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa’ ``` @@ -546,7 +632,7 @@ ERROR: lazy loading failed for package ‘BayesianFactorZoo’ * GitHub: https://github.com/ocbe-uio/BayesSurvive * Source code: https://github.com/cran/BayesSurvive * Date/Publication: 2024-06-04 13:20:12 UTC -* Number of recursive dependencies: 128 +* Number of recursive dependencies: 129 Run `revdepcheck::cloud_details(, "BayesSurvive")` for more info @@ -581,8 +667,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘BayesSurvive’ * removing ‘/tmp/workdir/BayesSurvive/new/BayesSurvive.Rcheck/BayesSurvive’ @@ -608,8 +694,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘BayesSurvive’ * removing ‘/tmp/workdir/BayesSurvive/old/BayesSurvive.Rcheck/BayesSurvive’ @@ -702,7 +788,7 @@ ERROR: lazy loading failed for package ‘BCClong’ * GitHub: https://github.com/donaldRwilliams/BGGM * Source code: https://github.com/cran/BGGM * Date/Publication: 2024-07-05 20:30:02 UTC -* Number of recursive dependencies: 208 +* Number of recursive dependencies: 209 Run `revdepcheck::cloud_details(, "BGGM")` for more info @@ -776,10 +862,10 @@ ERROR: lazy loading failed for package ‘BGGM’
-* Version: 1.0 +* Version: 1.1 * GitHub: NA * Source code: https://github.com/cran/binsreg -* Date/Publication: 2023-07-11 12:00:24 UTC +* Date/Publication: 2024-07-23 14:30:01 UTC * Number of recursive dependencies: 35 Run `revdepcheck::cloud_details(, "binsreg")` for more info @@ -830,26 +916,26 @@ ERROR: lazy loading failed for package ‘binsreg’ ``` -# bmstdr +# bspcov
-* Version: 0.7.9 -* GitHub: https://github.com/sujit-sahu/bmstdr -* Source code: https://github.com/cran/bmstdr -* Date/Publication: 2023-12-18 15:00:02 UTC -* Number of recursive dependencies: 215 +* Version: 1.0.0 +* GitHub: https://github.com/statjs/bspcov +* Source code: https://github.com/cran/bspcov +* Date/Publication: 2024-02-06 16:50:08 UTC +* Number of recursive dependencies: 122 -Run `revdepcheck::cloud_details(, "bmstdr")` for more info +Run `revdepcheck::cloud_details(, "bspcov")` for more info
## In both -* checking whether package ‘bmstdr’ can be installed ... ERROR +* checking whether package ‘bspcov’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bmstdr/new/bmstdr.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/00install.out’ for details. ``` ## Installation @@ -857,77 +943,61 @@ Run `revdepcheck::cloud_details(, "bmstdr")` for more info ### Devel ``` -* installing *source* package ‘bmstdr’ ... -** package ‘bmstdr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bspcov’ ... +** package ‘bspcov’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... +** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘bmstdr’ -* removing ‘/tmp/workdir/bmstdr/new/bmstdr.Rcheck/bmstdr’ +ERROR: lazy loading failed for package ‘bspcov’ +* removing ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/bspcov’ ``` ### CRAN ``` -* installing *source* package ‘bmstdr’ ... -** package ‘bmstdr’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bspcov’ ... +** package ‘bspcov’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 - - -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... +** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘bmstdr’ -* removing ‘/tmp/workdir/bmstdr/old/bmstdr.Rcheck/bmstdr’ +ERROR: lazy loading failed for package ‘bspcov’ +* removing ‘/tmp/workdir/bspcov/old/bspcov.Rcheck/bspcov’ ``` -# bspcov +# bsub
-* Version: 1.0.0 -* GitHub: https://github.com/statjs/bspcov -* Source code: https://github.com/cran/bspcov -* Date/Publication: 2024-02-06 16:50:08 UTC -* Number of recursive dependencies: 121 +* Version: 1.1.0 +* GitHub: https://github.com/jokergoo/bsub +* Source code: https://github.com/cran/bsub +* Date/Publication: 2021-07-01 15:50:10 UTC +* Number of recursive dependencies: 79 -Run `revdepcheck::cloud_details(, "bspcov")` for more info +Run `revdepcheck::cloud_details(, "bsub")` for more info
## In both -* checking whether package ‘bspcov’ can be installed ... ERROR +* checking whether package ‘bsub’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/bsub/new/bsub.Rcheck/00install.out’ for details. ``` ## Installation @@ -935,38 +1005,36 @@ Run `revdepcheck::cloud_details(, "bspcov")` for more info ### Devel ``` -* installing *source* package ‘bspcov’ ... -** package ‘bspcov’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bsub’ ... +** package ‘bsub’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘bspcov’ -* removing ‘/tmp/workdir/bspcov/new/bspcov.Rcheck/bspcov’ +ERROR: lazy loading failed for package ‘bsub’ +* removing ‘/tmp/workdir/bsub/new/bsub.Rcheck/bsub’ ``` ### CRAN ``` -* installing *source* package ‘bspcov’ ... -** package ‘bspcov’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bsub’ ... +** package ‘bsub’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘bspcov’ -* removing ‘/tmp/workdir/bspcov/old/bspcov.Rcheck/bspcov’ +ERROR: lazy loading failed for package ‘bsub’ +* removing ‘/tmp/workdir/bsub/old/bsub.Rcheck/bsub’ ``` @@ -1013,7 +1081,7 @@ installing to /tmp/workdir/BuyseTest/new/BuyseTest.Rcheck/00LOCK-BuyseTest/00new ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + there is no package called ‘rms’ Error: unable to load R code in package ‘BuyseTest’ Execution halted ERROR: lazy loading failed for package ‘BuyseTest’ @@ -1040,75 +1108,13 @@ installing to /tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/00LOCK-BuyseTest/00new ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + there is no package called ‘rms’ Error: unable to load R code in package ‘BuyseTest’ Execution halted ERROR: lazy loading failed for package ‘BuyseTest’ * removing ‘/tmp/workdir/BuyseTest/old/BuyseTest.Rcheck/BuyseTest’ -``` -# CalibrationCurves - -
- -* Version: 2.0.3 -* GitHub: NA -* Source code: https://github.com/cran/CalibrationCurves -* Date/Publication: 2024-07-02 08:50:02 UTC -* Number of recursive dependencies: 78 - -Run `revdepcheck::cloud_details(, "CalibrationCurves")` for more info - -
- -## In both - -* checking whether package ‘CalibrationCurves’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/new/CalibrationCurves.Rcheck/CalibrationCurves’ - - -``` -### CRAN - -``` -* installing *source* package ‘CalibrationCurves’ ... -** package ‘CalibrationCurves’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CalibrationCurves’ -* removing ‘/tmp/workdir/CalibrationCurves/old/CalibrationCurves.Rcheck/CalibrationCurves’ - - ``` # CARBayesST @@ -1118,7 +1124,7 @@ ERROR: lazy loading failed for package ‘CalibrationCurves’ * GitHub: https://github.com/duncanplee/CARBayesST * Source code: https://github.com/cran/CARBayesST * Date/Publication: 2023-10-30 16:40:02 UTC -* Number of recursive dependencies: 117 +* Number of recursive dependencies: 118 Run `revdepcheck::cloud_details(, "CARBayesST")` for more info @@ -1181,84 +1187,6 @@ ERROR: lazy loading failed for package ‘CARBayesST’ * removing ‘/tmp/workdir/CARBayesST/old/CARBayesST.Rcheck/CARBayesST’ -``` -# CaseBasedReasoning - -
- -* Version: 0.3 -* GitHub: https://github.com/sipemu/case-based-reasoning -* Source code: https://github.com/cran/CaseBasedReasoning -* Date/Publication: 2023-05-02 08:40:02 UTC -* Number of recursive dependencies: 106 - -Run `revdepcheck::cloud_details(, "CaseBasedReasoning")` for more info - -
- -## In both - -* checking whether package ‘CaseBasedReasoning’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘CaseBasedReasoning’ ... -** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distanceAPI.cpp -o distanceAPI.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distances.cpp -o distances.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c order.cpp -o order.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c weightedKNN.cpp -o weightedKNN.o -... -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o order.o weightedKNN.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/00LOCK-CaseBasedReasoning/00new/CaseBasedReasoning/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CaseBasedReasoning’ -* removing ‘/tmp/workdir/CaseBasedReasoning/new/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ - - -``` -### CRAN - -``` -* installing *source* package ‘CaseBasedReasoning’ ... -** package ‘CaseBasedReasoning’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distanceAPI.cpp -o distanceAPI.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c distances.cpp -o distances.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c order.cpp -o order.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -c weightedKNN.cpp -o weightedKNN.o -... -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CaseBasedReasoning.so RcppExports.o distanceAPI.o distances.o order.o weightedKNN.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/00LOCK-CaseBasedReasoning/00new/CaseBasedReasoning/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘CaseBasedReasoning’ -* removing ‘/tmp/workdir/CaseBasedReasoning/old/CaseBasedReasoning.Rcheck/CaseBasedReasoning’ - - ``` # CGPfunctions @@ -1268,7 +1196,7 @@ ERROR: lazy loading failed for package ‘CaseBasedReasoning’ * GitHub: https://github.com/ibecav/CGPfunctions * Source code: https://github.com/cran/CGPfunctions * Date/Publication: 2020-11-12 14:50:09 UTC -* Number of recursive dependencies: 158 +* Number of recursive dependencies: 148 Run `revdepcheck::cloud_details(, "CGPfunctions")` for more info @@ -1323,6 +1251,158 @@ ERROR: lazy loading failed for package ‘CGPfunctions’ * removing ‘/tmp/workdir/CGPfunctions/old/CGPfunctions.Rcheck/CGPfunctions’ +``` +# chemodiv + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/hpetren/chemodiv +* Source code: https://github.com/cran/chemodiv +* Date/Publication: 2023-08-17 17:52:33 UTC +* Number of recursive dependencies: 170 + +Run `revdepcheck::cloud_details(, "chemodiv")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/chemodiv/new/chemodiv.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘chemodiv/DESCRIPTION’ ... OK +... +* this is package ‘chemodiv’ version ‘0.3.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'fmcsR', 'ChemmineR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/chemodiv/old/chemodiv.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘chemodiv/DESCRIPTION’ ... OK +... +* this is package ‘chemodiv’ version ‘0.3.0’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'fmcsR', 'ChemmineR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# cinaR + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/eonurk/cinaR +* Source code: https://github.com/cran/cinaR +* Date/Publication: 2022-05-18 14:00:09 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "cinaR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/cinaR/new/cinaR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘cinaR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Packages required but not available: + 'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', + 'TxDb.Mmusculus.UCSC.mm10.knownGene' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/cinaR/old/cinaR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘cinaR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Packages required but not available: + 'ChIPseeker', 'TxDb.Hsapiens.UCSC.hg38.knownGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', + 'TxDb.Mmusculus.UCSC.mm10.knownGene' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # cmprskcoxmsm @@ -1386,152 +1466,102 @@ ERROR: lazy loading failed for package ‘cmprskcoxmsm’ ``` -# contrast +# CNVScope
-* Version: 0.24.2 -* GitHub: https://github.com/Alanocallaghan/contrast -* Source code: https://github.com/cran/contrast -* Date/Publication: 2022-10-05 17:20:09 UTC -* Number of recursive dependencies: 111 +* Version: 3.7.2 +* GitHub: https://github.com/jamesdalg/CNVScope +* Source code: https://github.com/cran/CNVScope +* Date/Publication: 2022-03-30 23:40:08 UTC +* Number of recursive dependencies: 206 -Run `revdepcheck::cloud_details(, "contrast")` for more info +Run `revdepcheck::cloud_details(, "CNVScope")` for more info
-## In both - -* checking whether package ‘contrast’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/contrast/new/contrast.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/new/contrast.Rcheck/contrast’ - +* using log directory ‘/tmp/workdir/CNVScope/new/CNVScope.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CNVScope/DESCRIPTION’ ... OK +... +Packages required but not available: 'GenomicInteractions', 'rtracklayer' -``` -### CRAN +Packages suggested but not available for checking: + 'ComplexHeatmap', 'HiCseg', 'GenomicFeatures', + 'BSgenome.Hsapiens.UCSC.hg19' -``` -* installing *source* package ‘contrast’ ... -** package ‘contrast’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘contrast’ -* removing ‘/tmp/workdir/contrast/old/contrast.Rcheck/contrast’ - - -``` -# coxed - -
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR -* Version: 0.3.3 -* GitHub: https://github.com/jkropko/coxed -* Source code: https://github.com/cran/coxed -* Date/Publication: 2020-08-02 01:20:07 UTC -* Number of recursive dependencies: 95 -Run `revdepcheck::cloud_details(, "coxed")` for more info -
-## In both -* checking whether package ‘coxed’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/coxed/new/coxed.Rcheck/00install.out’ for details. - ``` +``` +### CRAN -## Installation +``` +* using log directory ‘/tmp/workdir/CNVScope/old/CNVScope.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CNVScope/DESCRIPTION’ ... OK +... +Packages required but not available: 'GenomicInteractions', 'rtracklayer' -### Devel +Packages suggested but not available for checking: + 'ComplexHeatmap', 'HiCseg', 'GenomicFeatures', + 'BSgenome.Hsapiens.UCSC.hg19' -``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/new/coxed.Rcheck/coxed’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR -``` -### CRAN -``` -* installing *source* package ‘coxed’ ... -** package ‘coxed’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘rms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘coxed’ -* removing ‘/tmp/workdir/coxed/old/coxed.Rcheck/coxed’ ``` -# CRMetrics +# COMMA
-* Version: 0.3.0 -* GitHub: https://github.com/khodosevichlab/CRMetrics -* Source code: https://github.com/cran/CRMetrics -* Date/Publication: 2023-09-01 09:00:06 UTC -* Number of recursive dependencies: 239 +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/COMMA +* Date/Publication: 2024-07-21 10:10:05 UTC +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "CRMetrics")` for more info +Run `revdepcheck::cloud_details(, "COMMA")` for more info
## In both -* checking whether package ‘CRMetrics’ can be installed ... ERROR +* checking whether package ‘COMMA’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/COMMA/new/COMMA.Rcheck/00install.out’ for details. ``` ## Installation @@ -1539,8 +1569,8 @@ Run `revdepcheck::cloud_details(, "CRMetrics")` for more info ### Devel ``` -* installing *source* package ‘CRMetrics’ ... -** package ‘CRMetrics’ successfully unpacked and MD5 sums checked +* installing *source* package ‘COMMA’ ... +** package ‘COMMA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -1549,16 +1579,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘CRMetrics’ -* removing ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/CRMetrics’ +ERROR: lazy loading failed for package ‘COMMA’ +* removing ‘/tmp/workdir/COMMA/new/COMMA.Rcheck/COMMA’ ``` ### CRAN ``` -* installing *source* package ‘CRMetrics’ ... -** package ‘CRMetrics’ successfully unpacked and MD5 sums checked +* installing *source* package ‘COMMA’ ... +** package ‘COMMA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst @@ -1567,192 +1597,432 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘CRMetrics’ -* removing ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/CRMetrics’ +ERROR: lazy loading failed for package ‘COMMA’ +* removing ‘/tmp/workdir/COMMA/old/COMMA.Rcheck/COMMA’ ``` -# csmpv +# conos
-* Version: 1.0.3 -* GitHub: NA -* Source code: https://github.com/cran/csmpv -* Date/Publication: 2024-03-01 18:12:44 UTC -* Number of recursive dependencies: 178 +* Version: 1.5.2 +* GitHub: https://github.com/kharchenkolab/conos +* Source code: https://github.com/cran/conos +* Date/Publication: 2024-02-26 19:30:05 UTC +* Number of recursive dependencies: 240 -Run `revdepcheck::cloud_details(, "csmpv")` for more info +Run `revdepcheck::cloud_details(, "conos")` for more info
-## In both - -* checking whether package ‘csmpv’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/new/csmpv.Rcheck/csmpv’ +* using log directory ‘/tmp/workdir/conos/new/conos.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘conos/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Package suggested but not available for checking: ‘pagoda2’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘csmpv’ ... -** package ‘csmpv’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘csmpv’ -* removing ‘/tmp/workdir/csmpv/old/csmpv.Rcheck/csmpv’ +* using log directory ‘/tmp/workdir/conos/old/conos.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘conos/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Package suggested but not available for checking: ‘pagoda2’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# ctsem +# counterfactuals
-* Version: 3.10.0 -* GitHub: https://github.com/cdriveraus/ctsem -* Source code: https://github.com/cran/ctsem -* Date/Publication: 2024-05-09 14:40:03 UTC -* Number of recursive dependencies: 158 +* Version: 0.1.4 +* GitHub: https://github.com/dandls/counterfactuals +* Source code: https://github.com/cran/counterfactuals +* Date/Publication: 2024-05-14 19:00:02 UTC +* Number of recursive dependencies: 227 -Run `revdepcheck::cloud_details(, "ctsem")` for more info +Run `revdepcheck::cloud_details(, "counterfactuals")` for more info
-## In both - -* checking whether package ‘ctsem’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/counterfactuals/new/counterfactuals.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘counterfactuals/DESCRIPTION’ ... OK +... +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘how-to-add-new-cf-methods.html.asis’ using ‘UTF-8’... OK + ‘introduction.html.asis’ using ‘UTF-8’... OK + ‘other_models.html.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ ``` ### CRAN ``` -* installing *source* package ‘ctsem’ ... -** package ‘ctsem’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 +* using log directory ‘/tmp/workdir/counterfactuals/old/counterfactuals.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘counterfactuals/DESCRIPTION’ ... OK +... +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... NONE + ‘how-to-add-new-cf-methods.html.asis’ using ‘UTF-8’... OK + ‘introduction.html.asis’ using ‘UTF-8’... OK + ‘other_models.html.asis’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, -... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here -/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] - 654 | return internal::first_aligned::alignment),Derived>(m); - | ^~~~~~~~~ -g++: fatal error: Killed signal terminated program cc1plus -compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 -ERROR: compilation failed for package ‘ctsem’ -* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ ``` -# DepthProc +# CRMetrics
-* Version: 2.1.5 -* GitHub: https://github.com/zzawadz/DepthProc -* Source code: https://github.com/cran/DepthProc -* Date/Publication: 2022-02-03 20:30:02 UTC -* Number of recursive dependencies: 134 +* Version: 0.3.0 +* GitHub: https://github.com/khodosevichlab/CRMetrics +* Source code: https://github.com/cran/CRMetrics +* Date/Publication: 2023-09-01 09:00:06 UTC +* Number of recursive dependencies: 239 -Run `revdepcheck::cloud_details(, "DepthProc")` for more info +Run `revdepcheck::cloud_details(, "CRMetrics")` for more info
-## In both - -* checking whether package ‘DepthProc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘DepthProc’ ... -** package ‘DepthProc’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o -... -installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs +* using log directory ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘CRMetrics’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/CRMetrics/new/CRMetrics.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘CRMetrics/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘CRMetrics’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/CRMetrics/old/CRMetrics.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + + + +``` +# crosstalkr + +
+ +* Version: 1.0.5 +* GitHub: NA +* Source code: https://github.com/cran/crosstalkr +* Date/Publication: 2024-05-17 11:40:09 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "crosstalkr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/crosstalkr/new/crosstalkr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘crosstalkr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ensembldb’ + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/crosstalkr/old/crosstalkr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘crosstalkr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘ensembldb’ + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v86’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# ctsem + +
+ +* Version: 3.10.1 +* GitHub: https://github.com/cdriveraus/ctsem +* Source code: https://github.com/cran/ctsem +* Date/Publication: 2024-08-19 14:40:06 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "ctsem")` for more info + +
+ +## In both + +* checking whether package ‘ctsem’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’ + + +``` +### CRAN + +``` +* installing *source* package ‘ctsem’ ... +** package ‘ctsem’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1 +ERROR: compilation failed for package ‘ctsem’ +* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ + + +``` +# DepthProc + +
+ +* Version: 2.1.5 +* GitHub: https://github.com/zzawadz/DepthProc +* Source code: https://github.com/cran/DepthProc +* Date/Publication: 2022-02-03 20:30:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "DepthProc")` for more info + +
+ +## In both + +* checking whether package ‘DepthProc’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/DepthProc/new/DepthProc.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘DepthProc’ ... +** package ‘DepthProc’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Depth.cpp -o Depth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationEstimators.cpp -o LocationEstimators.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepth.cpp -o LocationScaleDepth.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c LocationScaleDepthCPP.cpp -o LocationScaleDepthCPP.o +... +installing to /tmp/workdir/DepthProc/new/DepthProc.Rcheck/00LOCK-DepthProc/00new/DepthProc/libs ** R ** data ** inst @@ -1870,26 +2140,26 @@ ERROR: lazy loading failed for package ‘DR.SC’ ``` -# DynNom +# easybgm
-* Version: 5.1 -* GitHub: NA -* Source code: https://github.com/cran/DynNom -* Date/Publication: 2024-06-07 12:20:21 UTC -* Number of recursive dependencies: 104 +* Version: 0.1.2 +* GitHub: https://github.com/KarolineHuth/easybgm +* Source code: https://github.com/cran/easybgm +* Date/Publication: 2024-03-13 13:40:02 UTC +* Number of recursive dependencies: 175 -Run `revdepcheck::cloud_details(, "DynNom")` for more info +Run `revdepcheck::cloud_details(, "easybgm")` for more info
## In both -* checking whether package ‘DynNom’ can be installed ... ERROR +* checking whether package ‘easybgm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. ``` ## Installation @@ -1897,8 +2167,8 @@ Run `revdepcheck::cloud_details(, "DynNom")` for more info ### Devel ``` -* installing *source* package ‘DynNom’ ... -** package ‘DynNom’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading @@ -1906,16 +2176,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DynNom’ -* removing ‘/tmp/workdir/DynNom/new/DynNom.Rcheck/DynNom’ +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ ``` ### CRAN ``` -* installing *source* package ‘DynNom’ ... -** package ‘DynNom’ successfully unpacked and MD5 sums checked +* installing *source* package ‘easybgm’ ... +** package ‘easybgm’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading @@ -1923,31 +2193,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘DynNom’ -* removing ‘/tmp/workdir/DynNom/old/DynNom.Rcheck/DynNom’ +ERROR: lazy loading failed for package ‘easybgm’ +* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ ``` -# easybgm +# EcoEnsemble
-* Version: 0.1.2 -* GitHub: https://github.com/KarolineHuth/easybgm -* Source code: https://github.com/cran/easybgm -* Date/Publication: 2024-03-13 13:40:02 UTC -* Number of recursive dependencies: 174 +* Version: 1.1.0 +* GitHub: https://github.com/CefasRepRes/EcoEnsemble +* Source code: https://github.com/cran/EcoEnsemble +* Date/Publication: 2024-08-19 17:20:06 UTC +* Number of recursive dependencies: 91 -Run `revdepcheck::cloud_details(, "easybgm")` for more info +Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info
## In both -* checking whether package ‘easybgm’ can be installed ... ERROR +* checking whether package ‘EcoEnsemble’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/00install.out’ for details. ``` ## Installation @@ -1955,34 +2225,54 @@ Run `revdepcheck::cloud_details(, "easybgm")` for more info ### Devel ``` -* installing *source* package ‘easybgm’ ... -** package ‘easybgm’ successfully unpacked and MD5 sums checked +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘easybgm’ -* removing ‘/tmp/workdir/easybgm/new/easybgm.Rcheck/easybgm’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 -``` -### CRAN +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/new/EcoEnsemble.Rcheck/EcoEnsemble’ + ``` -* installing *source* package ‘easybgm’ ... -** package ‘easybgm’ successfully unpacked and MD5 sums checked +### CRAN + +``` +* installing *source* package ‘EcoEnsemble’ ... +** package ‘EcoEnsemble’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘easybgm’ -* removing ‘/tmp/workdir/easybgm/old/easybgm.Rcheck/easybgm’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 + + +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c KF_back.cpp -o KF_back.o +In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ensemble_model_hierarchical_namespace::model_ensemble_model_hierarchical; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ensemble_model_hierarchical.o] Error 1 +ERROR: compilation failed for package ‘EcoEnsemble’ +* removing ‘/tmp/workdir/EcoEnsemble/old/EcoEnsemble.Rcheck/EcoEnsemble’ ``` @@ -2045,6 +2335,82 @@ ERROR: lazy loading failed for package ‘ecolottery’ * removing ‘/tmp/workdir/ecolottery/old/ecolottery.Rcheck/ecolottery’ +``` +# EMAS + +
+ +* Version: 0.2.2 +* GitHub: NA +* Source code: https://github.com/cran/EMAS +* Date/Publication: 2022-08-11 13:50:07 UTC +* Number of recursive dependencies: 186 + +Run `revdepcheck::cloud_details(, "EMAS")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/EMAS/new/EMAS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘EMAS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: + 'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19', + 'IlluminaHumanMethylation450kanno.ilmn12.hg19' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/EMAS/old/EMAS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘EMAS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: + 'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19', + 'IlluminaHumanMethylation450kanno.ilmn12.hg19' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # EpiEstim @@ -2181,6 +2547,76 @@ ERROR: lazy loading failed for package ‘evolqg’ * removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’ +``` +# EWSmethods + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/EWSmethods +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "EWSmethods")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# fmx + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/fmx +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "fmx")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # ForecastComb @@ -2243,6 +2679,158 @@ ERROR: lazy loading failed for package ‘ForecastComb’ * removing ‘/tmp/workdir/ForecastComb/old/ForecastComb.Rcheck/ForecastComb’ +``` +# GALLO + +
+ +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/GALLO +* Date/Publication: 2024-06-04 15:30:20 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "GALLO")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/GALLO/new/GALLO.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GALLO/DESCRIPTION’ ... OK +... +* this is package ‘GALLO’ version ‘1.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/GALLO/old/GALLO.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GALLO/DESCRIPTION’ ... OK +... +* this is package ‘GALLO’ version ‘1.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# gap + +
+ +* Version: 1.6 +* GitHub: https://github.com/jinghuazhao/R +* Source code: https://github.com/cran/gap +* Date/Publication: 2024-08-27 04:40:06 UTC +* Number of recursive dependencies: 199 + +Run `revdepcheck::cloud_details(, "gap")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/gap/new/gap.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘gap/DESCRIPTION’ ... OK +... +--- failed re-building ‘jss.Rnw’ + +SUMMARY: processing the following file failed: + ‘jss.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 4 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/gap/old/gap.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘gap/DESCRIPTION’ ... OK +... +--- failed re-building ‘jss.Rnw’ + +SUMMARY: processing the following file failed: + ‘jss.Rnw’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 4 NOTEs + + + + + ``` # gapfill @@ -2300,31 +2888,183 @@ ERROR: lazy loading failed for package ‘gapfill’ * removing ‘/tmp/workdir/gapfill/new/gapfill.Rcheck/gapfill’ -``` -### CRAN +``` +### CRAN + +``` +* installing *source* package ‘gapfill’ ... +** package ‘gapfill’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs +** R +... +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘gapfill’ +* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ + + +``` +# geneHapR + +
+ +* Version: 1.2.4 +* GitHub: NA +* Source code: https://github.com/cran/geneHapR +* Date/Publication: 2024-03-01 14:32:40 UTC +* Number of recursive dependencies: 180 + +Run `revdepcheck::cloud_details(, "geneHapR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/geneHapR/new/geneHapR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘geneHapR/DESCRIPTION’ ... OK +... +* this is package ‘geneHapR’ version ‘1.2.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/geneHapR/old/geneHapR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘geneHapR/DESCRIPTION’ ... OK +... +* this is package ‘geneHapR’ version ‘1.2.4’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# GeneSelectR + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/dzhakparov/GeneSelectR +* Source code: https://github.com/cran/GeneSelectR +* Date/Publication: 2024-02-03 14:00:05 UTC +* Number of recursive dependencies: 191 + +Run `revdepcheck::cloud_details(, "GeneSelectR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/GeneSelectR/new/GeneSelectR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK +... ++ build_vignettes = FALSE) + + When sourcing ‘example.R’: +Error: there is no package called ‘devtools’ +Execution halted + + ‘example.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/GeneSelectR/old/GeneSelectR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘GeneSelectR/DESCRIPTION’ ... OK +... ++ build_vignettes = FALSE) + + When sourcing ‘example.R’: +Error: there is no package called ‘devtools’ +Execution halted + + ‘example.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 WARNING, 1 NOTE + + -``` -* installing *source* package ‘gapfill’ ... -** package ‘gapfill’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gapfill.cpp -o gapfill.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o gapfill.so RcppExports.o gapfill.o -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/gapfill/old/gapfill.Rcheck/00LOCK-gapfill/00new/gapfill/libs -** R -... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘gapfill’ -* removing ‘/tmp/workdir/gapfill/old/gapfill.Rcheck/gapfill’ ``` @@ -2386,129 +3126,38 @@ ERROR: lazy loading failed for package ‘GeomComb’ ``` -# ggrcs +# geomorph
-* Version: 0.4.0 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/ggrcs -* Date/Publication: 2024-06-29 02:40:02 UTC -* Number of recursive dependencies: 78 +* Source code: https://github.com/cran/geomorph +* Number of recursive dependencies: 72 -Run `revdepcheck::cloud_details(, "ggrcs")` for more info +Run `revdepcheck::cloud_details(, "geomorph")` for more info
-## In both - -* checking whether package ‘ggrcs’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/new/ggrcs.Rcheck/ggrcs’ - - -``` -### CRAN - -``` -* installing *source* package ‘ggrcs’ ... -** package ‘ggrcs’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrcs’ -* removing ‘/tmp/workdir/ggrcs/old/ggrcs.Rcheck/ggrcs’ - - -``` -# ggrisk - -
- -* Version: 1.3 -* GitHub: https://github.com/yikeshu0611/ggrisk -* Source code: https://github.com/cran/ggrisk -* Date/Publication: 2021-08-09 07:40:06 UTC -* Number of recursive dependencies: 115 -Run `revdepcheck::cloud_details(, "ggrisk")` for more info -
-## In both -* checking whether package ‘ggrisk’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/00install.out’ for details. - ``` -## Installation -### Devel +``` +### CRAN ``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/new/ggrisk.Rcheck/ggrisk’ -``` -### CRAN -``` -* installing *source* package ‘ggrisk’ ... -** package ‘ggrisk’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘ggrisk’ -* removing ‘/tmp/workdir/ggrisk/old/ggrisk.Rcheck/ggrisk’ + ``` @@ -2576,26 +3225,26 @@ ERROR: lazy loading failed for package ‘gJLS2’ ``` -# Greg +# hettx
-* Version: 2.0.2 -* GitHub: https://github.com/gforge/Greg -* Source code: https://github.com/cran/Greg -* Date/Publication: 2024-01-29 13:30:21 UTC -* Number of recursive dependencies: 151 +* Version: 0.1.3 +* GitHub: https://github.com/bfifield/hettx +* Source code: https://github.com/cran/hettx +* Date/Publication: 2023-08-19 22:22:34 UTC +* Number of recursive dependencies: 85 -Run `revdepcheck::cloud_details(, "Greg")` for more info +Run `revdepcheck::cloud_details(, "hettx")` for more info
## In both -* checking whether package ‘Greg’ can be installed ... ERROR +* checking whether package ‘hettx’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Greg/new/Greg.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. ``` ## Installation @@ -2603,183 +3252,139 @@ Run `revdepcheck::cloud_details(, "Greg")` for more info ### Devel ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/new/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ ``` ### CRAN ``` -* installing *source* package ‘Greg’ ... -** package ‘Greg’ successfully unpacked and MD5 sums checked +* installing *source* package ‘hettx’ ... +** package ‘hettx’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Greg’ -* removing ‘/tmp/workdir/Greg/old/Greg.Rcheck/Greg’ +ERROR: lazy loading failed for package ‘hettx’ +* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ ``` -# greport +# Hmisc
-* Version: 0.7-4 -* GitHub: https://github.com/harrelfe/greport -* Source code: https://github.com/cran/greport -* Date/Publication: 2023-09-02 22:20:02 UTC -* Number of recursive dependencies: 84 +* Version: 5.1-3 +* GitHub: NA +* Source code: https://github.com/cran/Hmisc +* Date/Publication: 2024-05-28 07:10:02 UTC +* Number of recursive dependencies: 170 -Run `revdepcheck::cloud_details(, "greport")` for more info +Run `revdepcheck::cloud_details(, "Hmisc")` for more info
-## In both - -* checking whether package ‘greport’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/greport/new/greport.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/new/greport.Rcheck/greport’ +* using log directory ‘/tmp/workdir/Hmisc/new/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: 4 NOTEs -``` -### CRAN -``` -* installing *source* package ‘greport’ ... -** package ‘greport’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘greport’ -* removing ‘/tmp/workdir/greport/old/greport.Rcheck/greport’ ``` -# hettx - -
- -* Version: 0.1.3 -* GitHub: https://github.com/bfifield/hettx -* Source code: https://github.com/cran/hettx -* Date/Publication: 2023-08-19 22:22:34 UTC -* Number of recursive dependencies: 85 - -Run `revdepcheck::cloud_details(, "hettx")` for more info - -
- -## In both - -* checking whether package ‘hettx’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/hettx/new/hettx.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel +### CRAN ``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/new/hettx.Rcheck/hettx’ +* using log directory ‘/tmp/workdir/Hmisc/old/Hmisc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Hmisc/DESCRIPTION’ ... OK +... +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking line endings in C/C++/Fortran sources/headers ... OK +* checking compiled code ... OK +* checking examples ... OK +* DONE +Status: 4 NOTEs -``` -### CRAN -``` -* installing *source* package ‘hettx’ ... -** package ‘hettx’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘hettx’ -* removing ‘/tmp/workdir/hettx/old/hettx.Rcheck/hettx’ ``` -# hIRT +# Hmsc
-* Version: 0.3.0 -* GitHub: https://github.com/xiangzhou09/hIRT -* Source code: https://github.com/cran/hIRT -* Date/Publication: 2020-03-26 17:10:02 UTC -* Number of recursive dependencies: 88 +* Version: 3.0-13 +* GitHub: https://github.com/hmsc-r/HMSC +* Source code: https://github.com/cran/Hmsc +* Date/Publication: 2022-08-11 14:10:14 UTC +* Number of recursive dependencies: 76 -Run `revdepcheck::cloud_details(, "hIRT")` for more info +Run `revdepcheck::cloud_details(, "Hmsc")` for more info
## In both -* checking whether package ‘hIRT’ can be installed ... ERROR +* checking whether package ‘Hmsc’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. ``` ## Installation @@ -2787,61 +3392,63 @@ Run `revdepcheck::cloud_details(, "hIRT")` for more info ### Devel ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/new/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ ``` ### CRAN ``` -* installing *source* package ‘hIRT’ ... -** package ‘hIRT’ successfully unpacked and MD5 sums checked +* installing *source* package ‘Hmsc’ ... +** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘hIRT’ -* removing ‘/tmp/workdir/hIRT/old/hIRT.Rcheck/hIRT’ +ERROR: lazy loading failed for package ‘Hmsc’ +* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ ``` -# Hmsc - -
- -* Version: 3.0-13 -* GitHub: https://github.com/hmsc-r/HMSC -* Source code: https://github.com/cran/Hmsc -* Date/Publication: 2022-08-11 14:10:14 UTC -* Number of recursive dependencies: 76 +# iClusterVB -Run `revdepcheck::cloud_details(, "Hmsc")` for more info +
+ +* Version: 0.1.2 +* GitHub: https://github.com/AbdalkarimA/iClusterVB +* Source code: https://github.com/cran/iClusterVB +* Date/Publication: 2024-08-20 19:10:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "iClusterVB")` for more info
## In both -* checking whether package ‘Hmsc’ can be installed ... ERROR +* checking whether package ‘iClusterVB’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00install.out’ for details. ``` ## Installation @@ -2849,10 +3456,17 @@ Run `revdepcheck::cloud_details(, "Hmsc")` for more info ### Devel ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iClusterVB’ ... +** package ‘iClusterVB’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs ** R +... ** data *** moving datasets to lazyload DB ** inst @@ -2861,18 +3475,25 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/new/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘iClusterVB’ +* removing ‘/tmp/workdir/iClusterVB/new/iClusterVB.Rcheck/iClusterVB’ ``` ### CRAN ``` -* installing *source* package ‘Hmsc’ ... -** package ‘Hmsc’ successfully unpacked and MD5 sums checked +* installing *source* package ‘iClusterVB’ ... +** package ‘iClusterVB’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c CAVI_algorithms.cpp -o CAVI_algorithms.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o iClusterVB.so CAVI_algorithms.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/00LOCK-iClusterVB/00new/iClusterVB/libs ** R +... ** data *** moving datasets to lazyload DB ** inst @@ -2881,8 +3502,8 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Hmsc’ -* removing ‘/tmp/workdir/Hmsc/old/Hmsc.Rcheck/Hmsc’ +ERROR: lazy loading failed for package ‘iClusterVB’ +* removing ‘/tmp/workdir/iClusterVB/old/iClusterVB.Rcheck/iClusterVB’ ``` @@ -2935,7 +3556,6 @@ ERROR: lazy loading failed for package ‘inventorize’ ** R ** byte-compile and prepare package for lazy loading Warning in qgamma(service_level, alpha, beta) : NaNs produced -Warning in qgamma(service_level, alpha, beta) : NaNs produced ** help *** installing help indices ** building package indices @@ -3014,7 +3634,7 @@ ERROR: lazy loading failed for package ‘iNZightPlots’ * GitHub: https://github.com/iNZightVIT/iNZightRegression * Source code: https://github.com/cran/iNZightRegression * Date/Publication: 2024-04-05 02:32:59 UTC -* Number of recursive dependencies: 158 +* Number of recursive dependencies: 159 Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info @@ -3280,77 +3900,79 @@ ERROR: lazy loading failed for package ‘joineRML’ ``` -# JWileymisc +# kibior
-* Version: 1.4.1 -* GitHub: https://github.com/JWiley/JWileymisc -* Source code: https://github.com/cran/JWileymisc -* Date/Publication: 2023-10-05 04:50:02 UTC -* Number of recursive dependencies: 167 +* Version: 0.1.1 +* GitHub: https://github.com/regisoc/kibior +* Source code: https://github.com/cran/kibior +* Date/Publication: 2021-01-28 15:20:02 UTC +* Number of recursive dependencies: 140 -Run `revdepcheck::cloud_details(, "JWileymisc")` for more info +Run `revdepcheck::cloud_details(, "kibior")` for more info
-## In both - -* checking whether package ‘JWileymisc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/new/JWileymisc.Rcheck/JWileymisc’ +* using log directory ‘/tmp/workdir/kibior/new/kibior.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘kibior/DESCRIPTION’ ... OK +... +* this is package ‘kibior’ version ‘0.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘JWileymisc’ ... -** package ‘JWileymisc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘JWileymisc’ -* removing ‘/tmp/workdir/JWileymisc/old/JWileymisc.Rcheck/JWileymisc’ +* using log directory ‘/tmp/workdir/kibior/old/kibior.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘kibior/DESCRIPTION’ ... OK +... +* this is package ‘kibior’ version ‘0.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -3551,16 +4173,92 @@ ERROR: lazy loading failed for package ‘llbayesireg’ * removing ‘/tmp/workdir/llbayesireg/old/llbayesireg.Rcheck/llbayesireg’ +``` +# locuszoomr + +
+ +* Version: 0.3.4 +* GitHub: https://github.com/myles-lewis/locuszoomr +* Source code: https://github.com/cran/locuszoomr +* Date/Publication: 2024-09-06 10:10:02 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "locuszoomr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/locuszoomr/new/locuszoomr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'rtracklayer' + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/locuszoomr/old/locuszoomr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘locuszoomr/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'rtracklayer' + +Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # LorenzRegression
-* Version: 1.0.0 -* GitHub: NA +* Version: 2.0.0 +* GitHub: https://github.com/AlJacq/LorenzRegression * Source code: https://github.com/cran/LorenzRegression -* Date/Publication: 2023-02-28 17:32:34 UTC -* Number of recursive dependencies: 63 +* Date/Publication: 2024-09-09 11:20:33 UTC +* Number of recursive dependencies: 83 Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info @@ -3634,10 +4332,10 @@ ERROR: lazy loading failed for package ‘LorenzRegression’
-* Version: 1.3.1 +* Version: 1.3.3 * GitHub: NA * Source code: https://github.com/cran/lsirm12pl -* Date/Publication: 2023-06-22 14:12:35 UTC +* Date/Publication: 2024-08-28 23:00:02 UTC * Number of recursive dependencies: 124 Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info @@ -3663,10 +4361,10 @@ Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o ... ** R ** data @@ -3690,21 +4388,132 @@ ERROR: lazy loading failed for package ‘lsirm12pl’ ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c log_likelihood.cpp -o log_likelihood.o g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl.cpp -o lsirm1pl.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma.cpp -o lsirm1pl_fixed_gamma.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm1pl_fixed_gamma_mar.cpp -o lsirm1pl_fixed_gamma_mar.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsirm2pl.cpp -o lsirm2pl.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c lsm.cpp -o lsm.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c utility_cpp.cpp -o utility_cpp.o +... +** R +** data +*** moving datasets to lazyload DB +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘lsirm12pl’ +* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ + + +``` +# MantaID + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/MantaID +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "MantaID")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# MARVEL + +
+ +* Version: 1.4.0 +* GitHub: NA +* Source code: https://github.com/cran/MARVEL +* Date/Publication: 2022-10-31 10:22:50 UTC +* Number of recursive dependencies: 231 + +Run `revdepcheck::cloud_details(, "MARVEL")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/MARVEL/new/MARVEL.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MARVEL/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘MARVEL.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/MARVEL/old/MARVEL.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MARVEL/DESCRIPTION’ ... OK ... -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘lsirm12pl’ -* removing ‘/tmp/workdir/lsirm12pl/old/lsirm12pl.Rcheck/lsirm12pl’ +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘MARVEL.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + ``` @@ -3768,98 +4577,102 @@ ERROR: lazy loading failed for package ‘mbsts’ ``` -# MendelianRandomization +# MitoHEAR
-* Version: 0.10.0 +* Version: 0.1.0 * GitHub: NA -* Source code: https://github.com/cran/MendelianRandomization -* Date/Publication: 2024-04-12 10:10:02 UTC -* Number of recursive dependencies: 88 +* Source code: https://github.com/cran/MitoHEAR +* Date/Publication: 2022-03-01 21:20:02 UTC +* Number of recursive dependencies: 183 -Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info +Run `revdepcheck::cloud_details(, "MitoHEAR")` for more info
-## In both - -* checking whether package ‘MendelianRandomization’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ +* using log directory ‘/tmp/workdir/MitoHEAR/new/MitoHEAR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MitoHEAR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'karyoploteR', 'regioneR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘MendelianRandomization’ ... -** package ‘MendelianRandomization’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c mvmrcML.cpp -o mvmrcML.o -g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o MendelianRandomization.so RcppExports.o mvmrcML.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR -installing to /tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/00LOCK-MendelianRandomization/00new/MendelianRandomization/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MendelianRandomization’ -* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ +* using log directory ‘/tmp/workdir/MitoHEAR/old/MitoHEAR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MitoHEAR/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'karyoploteR', 'regioneR' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# MetabolicSurv +# miWQS
-* Version: 1.1.2 -* GitHub: https://github.com/OlajumokeEvangelina/MetabolicSurv -* Source code: https://github.com/cran/MetabolicSurv -* Date/Publication: 2021-06-11 08:30:02 UTC -* Number of recursive dependencies: 131 +* Version: 0.4.4 +* GitHub: https://github.com/phargarten2/miWQS +* Source code: https://github.com/cran/miWQS +* Date/Publication: 2021-04-02 21:50:02 UTC +* Number of recursive dependencies: 152 -Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info +Run `revdepcheck::cloud_details(, "miWQS")` for more info
## In both -* checking whether package ‘MetabolicSurv’ can be installed ... ERROR +* checking whether package ‘miWQS’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. ``` ## Installation @@ -3867,8 +4680,8 @@ Run `revdepcheck::cloud_details(, "MetabolicSurv")` for more info ### Devel ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -3879,16 +4692,16 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/new/MetabolicSurv.Rcheck/MetabolicSurv’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ ``` ### CRAN ``` -* installing *source* package ‘MetabolicSurv’ ... -** package ‘MetabolicSurv’ successfully unpacked and MD5 sums checked +* installing *source* package ‘miWQS’ ... +** package ‘miWQS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data @@ -3899,31 +4712,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘MetabolicSurv’ -* removing ‘/tmp/workdir/MetabolicSurv/old/MetabolicSurv.Rcheck/MetabolicSurv’ +ERROR: lazy loading failed for package ‘miWQS’ +* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ ``` -# miWQS +# mlmts
-* Version: 0.4.4 -* GitHub: https://github.com/phargarten2/miWQS -* Source code: https://github.com/cran/miWQS -* Date/Publication: 2021-04-02 21:50:02 UTC -* Number of recursive dependencies: 151 +* Version: 1.1.2 +* GitHub: NA +* Source code: https://github.com/cran/mlmts +* Date/Publication: 2024-08-18 08:40:06 UTC +* Number of recursive dependencies: 242 -Run `revdepcheck::cloud_details(, "miWQS")` for more info +Run `revdepcheck::cloud_details(, "mlmts")` for more info
## In both -* checking whether package ‘miWQS’ can be installed ... ERROR +* checking whether package ‘mlmts’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/00install.out’ for details. ``` ## Installation @@ -3931,121 +4744,215 @@ Run `revdepcheck::cloud_details(, "miWQS")` for more info ### Devel ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mlmts’ ... +** package ‘mlmts’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘mlmts’ +* removing ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/mlmts’ ``` ### CRAN ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ successfully unpacked and MD5 sums checked +* installing *source* package ‘mlmts’ ... +** package ‘mlmts’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error: unable to load R code in package ‘mlmts’ Execution halted -ERROR: lazy loading failed for package ‘miWQS’ -* removing ‘/tmp/workdir/miWQS/old/miWQS.Rcheck/miWQS’ +ERROR: lazy loading failed for package ‘mlmts’ +* removing ‘/tmp/workdir/mlmts/old/mlmts.Rcheck/mlmts’ ``` -# MRZero +# mlr
-* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/MRZero -* Date/Publication: 2024-04-14 09:30:03 UTC -* Number of recursive dependencies: 82 +* Version: 2.19.2 +* GitHub: https://github.com/mlr-org/mlr +* Source code: https://github.com/cran/mlr +* Date/Publication: 2024-06-12 10:50:02 UTC +* Number of recursive dependencies: 362 -Run `revdepcheck::cloud_details(, "MRZero")` for more info +Run `revdepcheck::cloud_details(, "mlr")` for more info
-## In both +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/mlr/new/mlr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘mlr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘mlr.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + -* checking whether package ‘MRZero’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. - ``` -## Installation + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/mlr/old/mlr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘mlr/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in ‘tests’ ... OK +* checking tests ... OK + Running ‘testthat.R’ +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘mlr.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +# MOCHA + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/MOCHA +* Date/Publication: 2024-01-25 12:20:12 UTC +* Number of recursive dependencies: 249 + +Run `revdepcheck::cloud_details(, "MOCHA")` for more info + +
+ +## Error before installation ### Devel ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ +* using log directory ‘/tmp/workdir/MOCHA/new/MOCHA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MOCHA/DESCRIPTION’ ... OK +... + +Packages suggested but not available for checking: + 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19', + 'chromVAR', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘MRZero’ ... -** package ‘MRZero’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘MRZero’ -* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ +* using log directory ‘/tmp/workdir/MOCHA/old/MOCHA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘MOCHA/DESCRIPTION’ ... OK +... + +Packages suggested but not available for checking: + 'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', + 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19', + 'chromVAR', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` -# Multiaovbay +# MRZero
-* Version: 0.1.0 +* Version: 0.2.0 * GitHub: NA -* Source code: https://github.com/cran/Multiaovbay -* Date/Publication: 2023-03-17 17:20:02 UTC -* Number of recursive dependencies: 153 +* Source code: https://github.com/cran/MRZero +* Date/Publication: 2024-04-14 09:30:03 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info +Run `revdepcheck::cloud_details(, "MRZero")` for more info
## In both -* checking whether package ‘Multiaovbay’ can be installed ... ERROR +* checking whether package ‘MRZero’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/00install.out’ for details. ``` ## Installation @@ -4053,34 +4960,34 @@ Run `revdepcheck::cloud_details(, "Multiaovbay")` for more info ### Devel ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/new/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/new/MRZero.Rcheck/MRZero’ ``` ### CRAN ``` -* installing *source* package ‘Multiaovbay’ ... -** package ‘Multiaovbay’ successfully unpacked and MD5 sums checked +* installing *source* package ‘MRZero’ ... +** package ‘MRZero’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.0 is required + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘Multiaovbay’ -* removing ‘/tmp/workdir/Multiaovbay/old/Multiaovbay.Rcheck/Multiaovbay’ +ERROR: lazy loading failed for package ‘MRZero’ +* removing ‘/tmp/workdir/MRZero/old/MRZero.Rcheck/MRZero’ ``` @@ -4192,14 +5099,14 @@ using C++17 g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ /opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/new/multinma.Rcheck/multinma’ @@ -4219,14 +5126,14 @@ using C++17 g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, ... -/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_mspline_namespace::model_survival_mspline; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_survival_param_namespace::model_survival_param; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’ /opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ g++: fatal error: Killed signal terminated program cc1plus compilation terminated. -make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_mspline.o] Error 1 +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_survival_param.o] Error 1 ERROR: compilation failed for package ‘multinma’ * removing ‘/tmp/workdir/multinma/old/multinma.Rcheck/multinma’ @@ -4378,7 +5285,7 @@ ERROR: lazy loading failed for package ‘netcmc’ * GitHub: https://github.com/jongheepark/NetworkChange * Source code: https://github.com/cran/NetworkChange * Date/Publication: 2022-03-04 07:30:02 UTC -* Number of recursive dependencies: 132 +* Number of recursive dependencies: 133 Run `revdepcheck::cloud_details(, "NetworkChange")` for more info @@ -4561,6 +5468,82 @@ ERROR: lazy loading failed for package ‘NMADiagT’ * removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ +``` +# ohun + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/ropensci/ohun +* Source code: https://github.com/cran/ohun +* Date/Publication: 2024-08-19 18:40:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "ohun")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/ohun/new/ohun.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ohun/DESCRIPTION’ ... OK +... +* this is package ‘ohun’ version ‘1.0.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘warbleR’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/ohun/old/ohun.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘ohun/DESCRIPTION’ ... OK +... +* this is package ‘ohun’ version ‘1.0.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘warbleR’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # optweight @@ -4572,16 +5555,212 @@ ERROR: lazy loading failed for package ‘NMADiagT’ * Date/Publication: 2019-09-16 15:40:02 UTC * Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "optweight")` for more info +Run `revdepcheck::cloud_details(, "optweight")` for more info + +
+ +## In both + +* checking whether package ‘optweight’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ + + +``` +### CRAN + +``` +* installing *source* package ‘optweight’ ... +** package ‘optweight’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘optweight’ +* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ + + +``` +# OVtool + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/OVtool +* Date/Publication: 2021-11-02 08:10:07 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "OVtool")` for more info + +
+ +## In both + +* checking whether package ‘OVtool’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ + + +``` +### CRAN + +``` +* installing *source* package ‘OVtool’ ... +** package ‘OVtool’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘OVtool’ +* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ + + +``` +# pagoda2 + +
+ +* Version: 1.0.12 +* GitHub: https://github.com/kharchenkolab/pagoda2 +* Source code: https://github.com/cran/pagoda2 +* Date/Publication: 2024-02-27 00:50:02 UTC +* Number of recursive dependencies: 162 + +Run `revdepcheck::cloud_details(, "pagoda2")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/pagoda2/new/pagoda2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pagoda2/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rjson’ + +Package suggested but not available for checking: ‘scde’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/pagoda2/old/pagoda2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘pagoda2/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rjson’ + +Package suggested but not available for checking: ‘scde’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# PAMpal + +
+ +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/PAMpal +* Date/Publication: 2024-07-11 22:50:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "PAMpal")` for more info
## In both -* checking whether package ‘optweight’ can be installed ... ERROR +* checking whether package ‘PAMpal’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/optweight/new/optweight.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/PAMpal/new/PAMpal.Rcheck/00install.out’ for details. ``` ## Installation @@ -4589,57 +5768,63 @@ Run `revdepcheck::cloud_details(, "optweight")` for more info ### Devel ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMpal’ ... +** package ‘PAMpal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/new/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘PAMpal’ +* removing ‘/tmp/workdir/PAMpal/new/PAMpal.Rcheck/PAMpal’ ``` ### CRAN ``` -* installing *source* package ‘optweight’ ... -** package ‘optweight’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMpal’ ... +** package ‘PAMpal’ successfully unpacked and MD5 sums checked ** using staged installation ** R +** data +*** moving datasets to lazyload DB +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘optweight’ -* removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ +ERROR: lazy loading failed for package ‘PAMpal’ +* removing ‘/tmp/workdir/PAMpal/old/PAMpal.Rcheck/PAMpal’ ``` -# OVtool +# PAMscapes
-* Version: 1.0.3 +* Version: 0.6.0 * GitHub: NA -* Source code: https://github.com/cran/OVtool -* Date/Publication: 2021-11-02 08:10:07 UTC -* Number of recursive dependencies: 157 +* Source code: https://github.com/cran/PAMscapes +* Date/Publication: 2024-07-09 22:50:02 UTC +* Number of recursive dependencies: 110 -Run `revdepcheck::cloud_details(, "OVtool")` for more info +Run `revdepcheck::cloud_details(, "PAMscapes")` for more info
## In both -* checking whether package ‘OVtool’ can be installed ... ERROR +* checking whether package ‘PAMscapes’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/PAMscapes/new/PAMscapes.Rcheck/00install.out’ for details. ``` ## Installation @@ -4647,38 +5832,36 @@ Run `revdepcheck::cloud_details(, "OVtool")` for more info ### Devel ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMscapes’ ... +** package ‘PAMscapes’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/new/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘PAMscapes’ +* removing ‘/tmp/workdir/PAMscapes/new/PAMscapes.Rcheck/PAMscapes’ ``` ### CRAN ``` -* installing *source* package ‘OVtool’ ... -** package ‘OVtool’ successfully unpacked and MD5 sums checked +* installing *source* package ‘PAMscapes’ ... +** package ‘PAMscapes’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘twang’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rjson’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘OVtool’ -* removing ‘/tmp/workdir/OVtool/old/OVtool.Rcheck/OVtool’ +ERROR: lazy loading failed for package ‘PAMscapes’ +* removing ‘/tmp/workdir/PAMscapes/old/PAMscapes.Rcheck/PAMscapes’ ``` @@ -4745,6 +5928,263 @@ ERROR: lazy loading failed for package ‘paths’ * removing ‘/tmp/workdir/paths/old/paths.Rcheck/paths’ +``` +# PathwaySpace + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/PathwaySpace +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# pcvr + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/danforthcenter/pcvr +* Source code: https://github.com/cran/pcvr +* Date/Publication: 2024-09-05 17:30:02 UTC +* Number of recursive dependencies: 189 + +Run `revdepcheck::cloud_details(, "pcvr")` for more info + +
+ +## In both + +* checking whether package ‘pcvr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/new/pcvr.Rcheck/pcvr’ + + +``` +### CRAN + +``` +* installing *source* package ‘pcvr’ ... +** package ‘pcvr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘pcvr’ +* removing ‘/tmp/workdir/pcvr/old/pcvr.Rcheck/pcvr’ + + +``` +# PlasmaMutationDetector + +
+ +* Version: 1.7.2 +* GitHub: NA +* Source code: https://github.com/cran/PlasmaMutationDetector +* Date/Publication: 2018-06-11 07:43:09 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "PlasmaMutationDetector")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector/new/PlasmaMutationDetector.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector’ version ‘1.7.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector/old/PlasmaMutationDetector.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector’ version ‘1.7.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# PlasmaMutationDetector2 + +
+ +* Version: 1.1.11 +* GitHub: NA +* Source code: https://github.com/cran/PlasmaMutationDetector2 +* Date/Publication: 2022-05-03 10:00:08 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "PlasmaMutationDetector2")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector2/new/PlasmaMutationDetector2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector2/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector2’ version ‘1.1.11’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/PlasmaMutationDetector2/old/PlasmaMutationDetector2.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘PlasmaMutationDetector2/DESCRIPTION’ ... OK +... +* this is package ‘PlasmaMutationDetector2’ version ‘1.1.11’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'VariantAnnotation', 'rtracklayer' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # PLMIX @@ -4754,7 +6194,7 @@ ERROR: lazy loading failed for package ‘paths’ * GitHub: NA * Source code: https://github.com/cran/PLMIX * Date/Publication: 2019-09-04 11:50:02 UTC -* Number of recursive dependencies: 138 +* Number of recursive dependencies: 139 Run `revdepcheck::cloud_details(, "PLMIX")` for more info @@ -4823,6 +6263,82 @@ ERROR: lazy loading failed for package ‘PLMIX’ * removing ‘/tmp/workdir/PLMIX/old/PLMIX.Rcheck/PLMIX’ +``` +# polyRAD + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/lvclark/polyRAD +* Source code: https://github.com/cran/polyRAD +* Date/Publication: 2022-11-06 21:50:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "polyRAD")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/polyRAD/new/polyRAD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘polyRAD/DESCRIPTION’ ... OK +... + + When sourcing ‘polyRADtutorial.R’: +Error: Probabilities must be finite and non-negative! +Execution halted + + ‘isolocus_sorting.Rmd’ using ‘UTF-8’... OK + ‘polyRADtutorial.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 3 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/polyRAD/old/polyRAD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘polyRAD/DESCRIPTION’ ... OK +... + + When sourcing ‘polyRADtutorial.R’: +Error: Probabilities must be finite and non-negative! +Execution halted + + ‘isolocus_sorting.Rmd’ using ‘UTF-8’... OK + ‘polyRADtutorial.Rmd’ using ‘UTF-8’... failed +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 3 NOTEs + + + + + ``` # popstudy @@ -4923,9 +6439,9 @@ Run `revdepcheck::cloud_details(, "pould")` for more info *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘pould’ * removing ‘/tmp/workdir/pould/new/pould.Rcheck/pould’ @@ -4943,14 +6459,78 @@ ERROR: lazy loading failed for package ‘pould’ *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘pould’ * removing ‘/tmp/workdir/pould/old/pould.Rcheck/pould’ +``` +# PoweREST + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/PoweREST +* Date/Publication: 2024-09-09 09:30:02 UTC +* Number of recursive dependencies: 171 + +Run `revdepcheck::cloud_details(, "PoweREST")` for more info + +
+ +## In both + +* checking whether package ‘PoweREST’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/PoweREST/new/PoweREST.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘PoweREST’ ... +** package ‘PoweREST’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘PoweREST’ +* removing ‘/tmp/workdir/PoweREST/new/PoweREST.Rcheck/PoweREST’ + + +``` +### CRAN + +``` +* installing *source* package ‘PoweREST’ ... +** package ‘PoweREST’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘PoweREST’ +* removing ‘/tmp/workdir/PoweREST/old/PoweREST.Rcheck/PoweREST’ + + ``` # powerly @@ -5170,7 +6750,7 @@ Status: 1 ERROR * GitHub: https://github.com/ocbe-uio/psbcSpeedUp * Source code: https://github.com/cran/psbcSpeedUp * Date/Publication: 2024-07-01 09:00:02 UTC -* Number of recursive dependencies: 129 +* Number of recursive dependencies: 130 Run `revdepcheck::cloud_details(, "psbcSpeedUp")` for more info @@ -5205,8 +6785,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘psbcSpeedUp’ * removing ‘/tmp/workdir/psbcSpeedUp/new/psbcSpeedUp.Rcheck/psbcSpeedUp’ @@ -5232,8 +6812,8 @@ checking whether g++ -std=gnu++17 accepts -g... yes ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted ERROR: lazy loading failed for package ‘psbcSpeedUp’ * removing ‘/tmp/workdir/psbcSpeedUp/old/psbcSpeedUp.Rcheck/psbcSpeedUp’ @@ -5311,70 +6891,6 @@ ERROR: lazy loading failed for package ‘pscore’ * removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ -``` -# psfmi - -
- -* Version: 1.4.0 -* GitHub: https://github.com/mwheymans/psfmi -* Source code: https://github.com/cran/psfmi -* Date/Publication: 2023-06-17 22:40:02 UTC -* Number of recursive dependencies: 164 - -Run `revdepcheck::cloud_details(, "psfmi")` for more info - -
- -## In both - -* checking whether package ‘psfmi’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/new/psfmi.Rcheck/psfmi’ - - -``` -### CRAN - -``` -* installing *source* package ‘psfmi’ ... -** package ‘psfmi’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘psfmi’ -* removing ‘/tmp/workdir/psfmi/old/psfmi.Rcheck/psfmi’ - - ``` # qPCRtools @@ -5436,26 +6952,26 @@ ERROR: lazy loading failed for package ‘qPCRtools’ ``` -# qreport +# qris
-* Version: 1.0-1 -* GitHub: NA -* Source code: https://github.com/cran/qreport -* Date/Publication: 2024-05-26 21:50:03 UTC -* Number of recursive dependencies: 77 +* Version: 1.1.1 +* GitHub: https://github.com/Kyuhyun07/qris +* Source code: https://github.com/cran/qris +* Date/Publication: 2024-03-05 14:40:03 UTC +* Number of recursive dependencies: 55 -Run `revdepcheck::cloud_details(, "qreport")` for more info +Run `revdepcheck::cloud_details(, "qris")` for more info
## In both -* checking whether package ‘qreport’ can be installed ... ERROR +* checking whether package ‘qris’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qreport/new/qreport.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. ``` ## Installation @@ -5463,57 +6979,77 @@ Run `revdepcheck::cloud_details(, "qreport")` for more info ### Devel ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +... +installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/new/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ ``` ### CRAN ``` -* installing *source* package ‘qreport’ ... -** package ‘qreport’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qris’ ... +** package ‘qris’ successfully unpacked and MD5 sums checked ** using staged installation +** libs +using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++11 +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o +... +installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qreport’ -* removing ‘/tmp/workdir/qreport/old/qreport.Rcheck/qreport’ +ERROR: lazy loading failed for package ‘qris’ +* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ ``` -# qris +# qte
-* Version: 1.1.1 -* GitHub: https://github.com/Kyuhyun07/qris -* Source code: https://github.com/cran/qris -* Date/Publication: 2024-03-05 14:40:03 UTC -* Number of recursive dependencies: 55 +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/qte +* Date/Publication: 2022-09-01 14:30:02 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "qris")` for more info +Run `revdepcheck::cloud_details(, "qte")` for more info
## In both -* checking whether package ‘qris’ can be installed ... ERROR +* checking whether package ‘qte’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qris/new/qris.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. ``` ## Installation @@ -5521,77 +7057,63 @@ Run `revdepcheck::cloud_details(, "qris")` for more info ### Devel ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/new/qris.Rcheck/00LOCK-qris/00new/qris/libs ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/new/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ ``` ### CRAN ``` -* installing *source* package ‘qris’ ... -** package ‘qris’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++11 -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Amat.cpp -o Amat.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ghat.cpp -o ghat.o -... -installing to /tmp/workdir/qris/old/qris.Rcheck/00LOCK-qris/00new/qris/libs +* installing *source* package ‘qte’ ... +** package ‘qte’ successfully unpacked and MD5 sums checked +** using staged installation ** R +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qris’ -* removing ‘/tmp/workdir/qris/old/qris.Rcheck/qris’ +ERROR: lazy loading failed for package ‘qte’ +* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ ``` -# qte +# quantilogram
-* Version: 1.3.1 +* Version: 3.1.1 * GitHub: NA -* Source code: https://github.com/cran/qte -* Date/Publication: 2022-09-01 14:30:02 UTC -* Number of recursive dependencies: 87 +* Source code: https://github.com/cran/quantilogram +* Date/Publication: 2024-08-27 12:40:02 UTC +* Number of recursive dependencies: 58 -Run `revdepcheck::cloud_details(, "qte")` for more info +Run `revdepcheck::cloud_details(, "quantilogram")` for more info
## In both -* checking whether package ‘qte’ can be installed ... ERROR +* checking whether package ‘quantilogram’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/qte/new/qte.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/quantilogram/new/quantilogram.Rcheck/00install.out’ for details. ``` ## Installation @@ -5599,40 +7121,38 @@ Run `revdepcheck::cloud_details(, "qte")` for more info ### Devel ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quantilogram’ ... +** package ‘quantilogram’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/new/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘quantilogram’ +* removing ‘/tmp/workdir/quantilogram/new/quantilogram.Rcheck/quantilogram’ ``` ### CRAN ``` -* installing *source* package ‘qte’ ... -** package ‘qte’ successfully unpacked and MD5 sums checked +* installing *source* package ‘quantilogram’ ... +** package ‘quantilogram’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB -** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘qte’ -* removing ‘/tmp/workdir/qte/old/qte.Rcheck/qte’ +ERROR: lazy loading failed for package ‘quantilogram’ +* removing ‘/tmp/workdir/quantilogram/old/quantilogram.Rcheck/quantilogram’ ``` @@ -5700,26 +7220,26 @@ ERROR: lazy loading failed for package ‘quid’ ``` -# RATest +# RcmdrPlugin.RiskDemo
-* Version: 0.1.10 -* GitHub: https://github.com/ignaciomsarmiento/RATest -* Source code: https://github.com/cran/RATest -* Date/Publication: 2022-09-29 04:30:02 UTC -* Number of recursive dependencies: 54 +* Version: 3.2 +* GitHub: NA +* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo +* Date/Publication: 2024-02-06 09:20:02 UTC +* Number of recursive dependencies: 200 -Run `revdepcheck::cloud_details(, "RATest")` for more info +Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info
## In both -* checking whether package ‘RATest’ can be installed ... ERROR +* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RATest/new/RATest.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. ``` ## Installation @@ -5727,63 +7247,277 @@ Run `revdepcheck::cloud_details(, "RATest")` for more info ### Devel ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/new/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` ### CRAN ``` -* installing *source* package ‘RATest’ ... -** package ‘RATest’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... +** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data -*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RATest’ -* removing ‘/tmp/workdir/RATest/old/RATest.Rcheck/RATest’ +ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ +* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ ``` -# RcmdrPlugin.RiskDemo +# rddtools
-* Version: 3.2 +* Version: 1.6.0 +* GitHub: https://github.com/bquast/rddtools +* Source code: https://github.com/cran/rddtools +* Date/Publication: 2022-01-10 12:42:49 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "rddtools")` for more info + +
+ +## In both + +* checking whether package ‘rddtools’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ + + +``` +### CRAN + +``` +* installing *source* package ‘rddtools’ ... +** package ‘rddtools’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Execution halted +ERROR: lazy loading failed for package ‘rddtools’ +* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ + + +``` +# RGraphSpace + +
+ +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/RcmdrPlugin.RiskDemo -* Date/Publication: 2024-02-06 09:20:02 UTC -* Number of recursive dependencies: 200 +* Source code: https://github.com/cran/RGraphSpace +* Number of recursive dependencies: 65 -Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info +Run `revdepcheck::cloud_details(, "RGraphSpace")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# rms + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/rms +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "rms")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + +``` +# RNAseqQC + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/frederikziebell/RNAseqQC +* Source code: https://github.com/cran/RNAseqQC +* Date/Publication: 2024-07-15 14:40:02 UTC +* Number of recursive dependencies: 162 + +Run `revdepcheck::cloud_details(, "RNAseqQC")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/RNAseqQC/new/RNAseqQC.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RNAseqQC/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'ComplexHeatmap' + +Package suggested but not available for checking: ‘recount3’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/RNAseqQC/old/RNAseqQC.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RNAseqQC/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ensembldb', 'ComplexHeatmap' + +Package suggested but not available for checking: ‘recount3’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +# robmed + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/aalfons/robmed +* Source code: https://github.com/cran/robmed +* Date/Publication: 2023-06-16 23:00:02 UTC +* Number of recursive dependencies: 60 + +Run `revdepcheck::cloud_details(, "robmed")` for more info
## In both -* checking whether package ‘RcmdrPlugin.RiskDemo’ can be installed ... ERROR +* checking whether package ‘robmed’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. ``` ## Installation @@ -5791,71 +7525,63 @@ Run `revdepcheck::cloud_details(, "RcmdrPlugin.RiskDemo")` for more info ### Devel ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/new/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ ``` ### CRAN ``` -* installing *source* package ‘RcmdrPlugin.RiskDemo’ ... -** package ‘RcmdrPlugin.RiskDemo’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmed’ ... +** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading -Warning in check_dep_version() : - ABI version mismatch: -lme4 was built with Matrix ABI version 1 -Current Matrix ABI version is 0 -Please re-install lme4 from source or restore original ‘Matrix’ package Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RcmdrPlugin.RiskDemo’ -* removing ‘/tmp/workdir/RcmdrPlugin.RiskDemo/old/RcmdrPlugin.RiskDemo.Rcheck/RcmdrPlugin.RiskDemo’ +ERROR: lazy loading failed for package ‘robmed’ +* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ ``` -# rddtools +# robmedExtra
-* Version: 1.6.0 -* GitHub: https://github.com/bquast/rddtools -* Source code: https://github.com/cran/rddtools -* Date/Publication: 2022-01-10 12:42:49 UTC -* Number of recursive dependencies: 106 +* Version: 0.1.0 +* GitHub: https://github.com/aalfons/robmedExtra +* Source code: https://github.com/cran/robmedExtra +* Date/Publication: 2023-06-02 14:40:02 UTC +* Number of recursive dependencies: 90 -Run `revdepcheck::cloud_details(, "rddtools")` for more info +Run `revdepcheck::cloud_details(, "robmedExtra")` for more info
## In both -* checking whether package ‘rddtools’ can be installed ... ERROR +* checking whether package ‘robmedExtra’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. ``` ## Installation @@ -5863,59 +7589,57 @@ Run `revdepcheck::cloud_details(, "rddtools")` for more info ### Devel ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/new/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ ``` ### CRAN ``` -* installing *source* package ‘rddtools’ ... -** package ‘rddtools’ successfully unpacked and MD5 sums checked +* installing *source* package ‘robmedExtra’ ... +** package ‘robmedExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data ** inst ** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘np’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): +Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Execution halted -ERROR: lazy loading failed for package ‘rddtools’ -* removing ‘/tmp/workdir/rddtools/old/rddtools.Rcheck/rddtools’ +ERROR: lazy loading failed for package ‘robmedExtra’ +* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ ``` -# riskRegression +# RPPanalyzer
-* Version: 2023.12.21 -* GitHub: https://github.com/tagteam/riskRegression -* Source code: https://github.com/cran/riskRegression -* Date/Publication: 2023-12-19 17:00:02 UTC -* Number of recursive dependencies: 186 +* Version: 1.4.9 +* GitHub: NA +* Source code: https://github.com/cran/RPPanalyzer +* Date/Publication: 2024-01-25 11:00:02 UTC +* Number of recursive dependencies: 82 -Run `revdepcheck::cloud_details(, "riskRegression")` for more info +Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info
## In both -* checking whether package ‘riskRegression’ can be installed ... ERROR +* checking whether package ‘RPPanalyzer’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. ``` ## Installation @@ -5923,17 +7647,9 @@ Run `revdepcheck::cloud_details(, "riskRegression")` for more info ### Devel ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R ** data ** inst @@ -5942,25 +7658,17 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/new/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ ``` ### CRAN ``` -* installing *source* package ‘riskRegression’ ... -** package ‘riskRegression’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RPPanalyzer’ ... +** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c aucCVFun.cpp -o aucCVFun.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c baseHaz.cpp -o baseHaz.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c calcSeCSC.cpp -o calcSeCSC.o -... ** R ** data ** inst @@ -5969,36 +7677,31 @@ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘riskRegression’ -* removing ‘/tmp/workdir/riskRegression/old/riskRegression.Rcheck/riskRegression’ +ERROR: lazy loading failed for package ‘RPPanalyzer’ +* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ ``` -# rms +# RQdeltaCT
-* Version: 6.8-1 -* GitHub: https://github.com/harrelfe/rms -* Source code: https://github.com/cran/rms -* Date/Publication: 2024-05-27 12:00:02 UTC -* Number of recursive dependencies: 145 +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/RQdeltaCT +* Date/Publication: 2024-04-17 15:50:02 UTC +* Number of recursive dependencies: 166 -Run `revdepcheck::cloud_details(, "rms")` for more info +Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info
## In both -* checking whether package ‘rms’ can be installed ... ERROR +* checking whether package ‘RQdeltaCT’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/rms/new/rms.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘rmsb’ + See ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/00install.out’ for details. ``` ## Installation @@ -6006,129 +7709,98 @@ Run `revdepcheck::cloud_details(, "rms")` for more info ### Devel ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/new/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/RQdeltaCT’ ``` ### CRAN ``` -* installing *source* package ‘rms’ ... -** package ‘rms’ successfully unpacked and MD5 sums checked +* installing *source* package ‘RQdeltaCT’ ... +** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked ** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using Fortran compiler: ‘GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o -gfortran -fpic -g -O2 -c lrmfit.f -o lrmfit.o -gfortran -fpic -g -O2 -c mlmats.f -o mlmats.o -gfortran -fpic -g -O2 -c ormuv.f -o ormuv.o -... ** R -** demo +** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘rms’ -* removing ‘/tmp/workdir/rms/old/rms.Rcheck/rms’ +ERROR: lazy loading failed for package ‘RQdeltaCT’ +* removing ‘/tmp/workdir/RQdeltaCT/old/RQdeltaCT.Rcheck/RQdeltaCT’ ``` -# rmsb +# RRPP
-* Version: 1.1-1 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/rmsb -* Date/Publication: 2024-07-08 11:10:03 UTC -* Number of recursive dependencies: 135 +* Source code: https://github.com/cran/RRPP +* Number of recursive dependencies: 68 -Run `revdepcheck::cloud_details(, "rmsb")` for more info +Run `revdepcheck::cloud_details(, "RRPP")` for more info
-## In both - -* checking whether package ‘rmsb’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked -** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’ + + + + ``` ### CRAN ``` -* installing *source* package ‘rmsb’ ... -** package ‘rmsb’ successfully unpacked and MD5 sums checked -** using staged installation -Error in loadNamespace(x) : there is no package called ‘rstantools’ -Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart -Execution halted -ERROR: configuration failed for package ‘rmsb’ -* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’ + + + + ``` -# robmed +# rstanarm
-* Version: 1.0.2 -* GitHub: https://github.com/aalfons/robmed -* Source code: https://github.com/cran/robmed -* Date/Publication: 2023-06-16 23:00:02 UTC -* Number of recursive dependencies: 60 +* Version: 2.32.1 +* GitHub: https://github.com/stan-dev/rstanarm +* Source code: https://github.com/cran/rstanarm +* Date/Publication: 2024-01-18 23:00:03 UTC +* Number of recursive dependencies: 138 -Run `revdepcheck::cloud_details(, "robmed")` for more info +Run `revdepcheck::cloud_details(, "rstanarm")` for more info
## In both -* checking whether package ‘robmed’ can be installed ... ERROR +* checking whether package ‘rstanarm’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/robmed/new/robmed.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details. ``` ## Installation @@ -6136,121 +7808,153 @@ Run `revdepcheck::cloud_details(, "robmed")` for more info ### Devel ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" + + +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:16: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 +rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’ ``` ### CRAN ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rstanarm’ ... +** package ‘rstanarm’ successfully unpacked and MD5 sums checked ** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘robmed’ -* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +using C++17 +"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan +Wrote C++ file "stan_files/bernoulli.cc" + + +... +/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/quad_form.hpp:88:16: required from here +/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__m128d’} [-Wignored-attributes] + 654 | return internal::first_aligned::alignment),Derived>(m); + | ^~~~~~~~~ +g++: fatal error: Killed signal terminated program cc1plus +compilation terminated. +make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/continuous.o] Error 1 +rm stan_files/bernoulli.cc stan_files/binomial.cc stan_files/continuous.cc +ERROR: compilation failed for package ‘rstanarm’ +* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’ ``` -# robmedExtra +# RTIGER
-* Version: 0.1.0 -* GitHub: https://github.com/aalfons/robmedExtra -* Source code: https://github.com/cran/robmedExtra -* Date/Publication: 2023-06-02 14:40:02 UTC -* Number of recursive dependencies: 96 +* Version: 2.1.0 +* GitHub: NA +* Source code: https://github.com/cran/RTIGER +* Date/Publication: 2023-03-29 09:20:02 UTC +* Number of recursive dependencies: 160 -Run `revdepcheck::cloud_details(, "robmedExtra")` for more info +Run `revdepcheck::cloud_details(, "RTIGER")` for more info
-## In both - -* checking whether package ‘robmedExtra’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/robmedExtra’ +* using log directory ‘/tmp/workdir/RTIGER/new/RTIGER.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RTIGER/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘tutorial_RTIGER.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘robmedExtra’ ... -** package ‘robmedExtra’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘robmed’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Execution halted -ERROR: lazy loading failed for package ‘robmedExtra’ -* removing ‘/tmp/workdir/robmedExtra/old/robmedExtra.Rcheck/robmedExtra’ +* using log directory ‘/tmp/workdir/RTIGER/old/RTIGER.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RTIGER/DESCRIPTION’ ... OK +... +* checking installed files from ‘inst/doc’ ... OK +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘tutorial_RTIGER.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + ``` -# RPPanalyzer +# rTwig
-* Version: 1.4.9 -* GitHub: NA -* Source code: https://github.com/cran/RPPanalyzer -* Date/Publication: 2024-01-25 11:00:02 UTC -* Number of recursive dependencies: 82 +* Version: 1.1.0 +* GitHub: https://github.com/aidanmorales/rTwig +* Source code: https://github.com/cran/rTwig +* Date/Publication: 2024-08-21 00:50:02 UTC +* Number of recursive dependencies: 147 -Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info +Run `revdepcheck::cloud_details(, "rTwig")` for more info
## In both -* checking whether package ‘RPPanalyzer’ can be installed ... ERROR +* checking whether package ‘rTwig’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/rTwig/new/rTwig.Rcheck/00install.out’ for details. ``` ## Installation @@ -6258,102 +7962,130 @@ Run `revdepcheck::cloud_details(, "RPPanalyzer")` for more info ### Devel ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rTwig’ ... +** package ‘rTwig’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/new/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘rTwig’ +* removing ‘/tmp/workdir/rTwig/new/rTwig.Rcheck/rTwig’ ``` ### CRAN ``` -* installing *source* package ‘RPPanalyzer’ ... -** package ‘RPPanalyzer’ successfully unpacked and MD5 sums checked +* installing *source* package ‘rTwig’ ... +** package ‘rTwig’ successfully unpacked and MD5 sums checked ** using staged installation -** R +** libs +using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c box_counting.cpp -o box_counting.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c colors.cpp -o colors.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c convex_hull.cpp -o convex_hull.o +g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c cylinder_mesh.cpp -o cylinder_mesh.o +... ** data +*** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘RPPanalyzer’ -* removing ‘/tmp/workdir/RPPanalyzer/old/RPPanalyzer.Rcheck/RPPanalyzer’ +ERROR: lazy loading failed for package ‘rTwig’ +* removing ‘/tmp/workdir/rTwig/old/rTwig.Rcheck/rTwig’ ``` -# RQdeltaCT +# RVA
-* Version: 1.3.0 -* GitHub: NA -* Source code: https://github.com/cran/RQdeltaCT -* Date/Publication: 2024-04-17 15:50:02 UTC -* Number of recursive dependencies: 165 +* Version: 0.0.5 +* GitHub: https://github.com/THERMOSTATS/RVA +* Source code: https://github.com/cran/RVA +* Date/Publication: 2021-11-01 21:40:02 UTC +* Number of recursive dependencies: 207 -Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info +Run `revdepcheck::cloud_details(, "RVA")` for more info
-## In both - -* checking whether package ‘RQdeltaCT’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘RQdeltaCT’ ... -** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘RQdeltaCT’ -* removing ‘/tmp/workdir/RQdeltaCT/new/RQdeltaCT.Rcheck/RQdeltaCT’ +* using log directory ‘/tmp/workdir/RVA/new/RVA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RVA/DESCRIPTION’ ... OK +... +* this is package ‘RVA’ version ‘0.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ComplexHeatmap', 'rWikiPathways' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` ### CRAN ``` -* installing *source* package ‘RQdeltaCT’ ... -** package ‘RQdeltaCT’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘RQdeltaCT’ -* removing ‘/tmp/workdir/RQdeltaCT/old/RQdeltaCT.Rcheck/RQdeltaCT’ +* using log directory ‘/tmp/workdir/RVA/old/RVA.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘RVA/DESCRIPTION’ ... OK +... +* this is package ‘RVA’ version ‘0.0.5’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'ComplexHeatmap', 'rWikiPathways' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -6371,54 +8103,65 @@ Run `revdepcheck::cloud_details(, "scCustomize")` for more info
-## In both +## Error before installation -* checking whether package ‘scCustomize’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. - ``` +### Devel -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘Nebulosa’ - ``` +``` +* using log directory ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scCustomize/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘scCustomize’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE -## Installation -### Devel -``` -* installing *source* package ‘scCustomize’ ... -** package ‘scCustomize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘scCustomize’ -* removing ‘/tmp/workdir/scCustomize/new/scCustomize.Rcheck/scCustomize’ ``` ### CRAN ``` -* installing *source* package ‘scCustomize’ ... -** package ‘scCustomize’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘scCustomize’ -* removing ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/scCustomize’ +* using log directory ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scCustomize/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘scCustomize’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/scCustomize/old/scCustomize.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -6617,16 +8360,92 @@ g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o SCIntRuler installing to /tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/00LOCK-SCIntRuler/00new/SCIntRuler/libs ** R ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘SCIntRuler’ -* removing ‘/tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/SCIntRuler’ +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SCIntRuler’ +* removing ‘/tmp/workdir/SCIntRuler/old/SCIntRuler.Rcheck/SCIntRuler’ + + +``` +# scITD + +
+ +* Version: 1.0.4 +* GitHub: NA +* Source code: https://github.com/cran/scITD +* Date/Publication: 2023-09-08 16:00:02 UTC +* Number of recursive dependencies: 233 + +Run `revdepcheck::cloud_details(, "scITD")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/scITD/new/scITD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scITD/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'simplifyEnrichment', 'conos', 'pagoda2' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/scITD/old/scITD.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘scITD/DESCRIPTION’ ... OK +... +* checking package dependencies ... ERROR +Package required but not available: ‘ComplexHeatmap’ + +Packages suggested but not available for checking: + 'simplifyEnrichment', 'conos', 'pagoda2' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + ``` @@ -6638,7 +8457,7 @@ ERROR: lazy loading failed for package ‘SCIntRuler’ * GitHub: NA * Source code: https://github.com/cran/scMappR * Date/Publication: 2023-06-30 08:40:08 UTC -* Number of recursive dependencies: 234 +* Number of recursive dependencies: 241 Run `revdepcheck::cloud_details(, "scMappR")` for more info @@ -6913,6 +8732,82 @@ ERROR: lazy loading failed for package ‘sectorgap’ * removing ‘/tmp/workdir/sectorgap/old/sectorgap.Rcheck/sectorgap’ +``` +# SeedMatchR + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/SeedMatchR +* Date/Publication: 2023-10-24 20:30:02 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "SeedMatchR")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SeedMatchR/new/SeedMatchR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SeedMatchR/DESCRIPTION’ ... OK +... +* this is package ‘SeedMatchR’ version ‘1.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'msa', 'GenomicFeatures' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SeedMatchR/old/SeedMatchR.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SeedMatchR/DESCRIPTION’ ... OK +... +* this is package ‘SeedMatchR’ version ‘1.1.1’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Packages required but not available: 'msa', 'GenomicFeatures' + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # SEERaBomb @@ -7113,6 +9008,82 @@ ERROR: lazy loading failed for package ‘SensMap’ * removing ‘/tmp/workdir/SensMap/old/SensMap.Rcheck/SensMap’ +``` +# sephora + +
+ +* Version: 0.1.31 +* GitHub: NA +* Source code: https://github.com/cran/sephora +* Date/Publication: 2024-01-17 18:40:02 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "sephora")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/sephora/new/sephora.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sephora/DESCRIPTION’ ... OK +... +* this is package ‘sephora’ version ‘0.1.31’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘spiralize’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/sephora/old/sephora.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sephora/DESCRIPTION’ ... OK +... +* this is package ‘sephora’ version ‘0.1.31’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘spiralize’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # Seurat @@ -7122,73 +9093,71 @@ ERROR: lazy loading failed for package ‘SensMap’ * GitHub: https://github.com/satijalab/seurat * Source code: https://github.com/cran/Seurat * Date/Publication: 2024-05-10 17:23:17 UTC -* Number of recursive dependencies: 266 +* Number of recursive dependencies: 267 Run `revdepcheck::cloud_details(, "Seurat")` for more info
-## In both - -* checking whether package ‘Seurat’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘Seurat’ ... -** package ‘Seurat’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Seurat/DESCRIPTION’ ... OK ... -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘Seurat’ -* removing ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/Seurat’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Seurat’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Seurat/new/Seurat.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘Seurat’ ... -** package ‘Seurat’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -using C++17 -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c ModularityOptimizer.cpp -o ModularityOptimizer.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RModularityOptimizer.cpp -o RModularityOptimizer.o -In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:205, +* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Seurat/DESCRIPTION’ ... OK ... -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error: package or namespace load failed for ‘SeuratObject’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): - namespace ‘Matrix’ 1.5-4.1 is being loaded, but >= 1.6.4 is required -Execution halted -ERROR: lazy loading failed for package ‘Seurat’ -* removing ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/Seurat’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Seurat’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -7321,82 +9290,156 @@ ERROR: lazy loading failed for package ‘sievePH’ * removing ‘/tmp/workdir/sievePH/old/sievePH.Rcheck/sievePH’ +``` +# sigminer + +
+ +* Version: 2.3.1 +* GitHub: https://github.com/ShixiangWang/sigminer +* Source code: https://github.com/cran/sigminer +* Date/Publication: 2024-05-11 08:50:02 UTC +* Number of recursive dependencies: 209 + +Run `revdepcheck::cloud_details(, "sigminer")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/sigminer/new/sigminer.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sigminer/DESCRIPTION’ ... OK +... + 18. └─rlang::abort(...) +Execution halted +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘cnsignature.Rmd’ using ‘UTF-8’... OK + ‘sigminer.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR, 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/sigminer/old/sigminer.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘sigminer/DESCRIPTION’ ... OK +... +* checking files in ‘vignettes’ ... OK +* checking examples ... OK +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘cnsignature.Rmd’ using ‘UTF-8’... OK + ‘sigminer.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + ``` # Signac
-* Version: 1.13.0 +* Version: 1.14.0 * GitHub: https://github.com/stuart-lab/signac * Source code: https://github.com/cran/Signac -* Date/Publication: 2024-04-04 02:42:57 UTC -* Number of recursive dependencies: 250 +* Date/Publication: 2024-08-21 07:40:02 UTC +* Number of recursive dependencies: 247 Run `revdepcheck::cloud_details(, "Signac")` for more info
-## In both - -* checking whether package ‘Signac’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘Signac’ ... -** package ‘Signac’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o +* using log directory ‘/tmp/workdir/Signac/new/Signac.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Signac/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘Signac’ -* removing ‘/tmp/workdir/Signac/new/Signac.Rcheck/Signac’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Signac’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Signac/new/Signac.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘Signac’ ... -** package ‘Signac’ successfully unpacked and MD5 sums checked -** using staged installation -** libs -using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c filter.cpp -o filter.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c group.cpp -o group.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c split.cpp -o split.o -g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c validate.cpp -o validate.o +* using log directory ‘/tmp/workdir/Signac/old/Signac.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘Signac/DESCRIPTION’ ... OK ... -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.4 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘Signac’ -* removing ‘/tmp/workdir/Signac/old/Signac.Rcheck/Signac’ +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘Signac’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/Signac/old/Signac.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -7473,68 +9516,6 @@ ERROR: lazy loading failed for package ‘SimplyAgree’ * removing ‘/tmp/workdir/SimplyAgree/old/SimplyAgree.Rcheck/SimplyAgree’ -``` -# sMSROC - -
- -* Version: 0.1.2 -* GitHub: NA -* Source code: https://github.com/cran/sMSROC -* Date/Publication: 2023-12-07 15:50:02 UTC -* Number of recursive dependencies: 119 - -Run `revdepcheck::cloud_details(, "sMSROC")` for more info - -
- -## In both - -* checking whether package ‘sMSROC’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/sMSROC/new/sMSROC.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘sMSROC’ ... -** package ‘sMSROC’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sMSROC’ -* removing ‘/tmp/workdir/sMSROC/new/sMSROC.Rcheck/sMSROC’ - - -``` -### CRAN - -``` -* installing *source* package ‘sMSROC’ ... -** package ‘sMSROC’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘sMSROC’ -* removing ‘/tmp/workdir/sMSROC/old/sMSROC.Rcheck/sMSROC’ - - ``` # SNPassoc @@ -7544,57 +9525,71 @@ ERROR: lazy loading failed for package ‘sMSROC’ * GitHub: https://github.com/isglobal-brge/SNPassoc * Source code: https://github.com/cran/SNPassoc * Date/Publication: 2022-12-14 20:20:02 UTC -* Number of recursive dependencies: 166 +* Number of recursive dependencies: 168 Run `revdepcheck::cloud_details(, "SNPassoc")` for more info
-## In both - -* checking whether package ‘SNPassoc’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/00install.out’ for details. - ``` - -## Installation +## Error before installation ### Devel ``` -* installing *source* package ‘SNPassoc’ ... -** package ‘SNPassoc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘SNPassoc’ -* removing ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/SNPassoc’ +* using log directory ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SNPassoc/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘SNPassoc’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/SNPassoc/new/SNPassoc.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` ### CRAN ``` -* installing *source* package ‘SNPassoc’ ... -** package ‘SNPassoc’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘SNPassoc’ -* removing ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck/SNPassoc’ +* using log directory ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SNPassoc/DESCRIPTION’ ... OK +... +* checking if there is a namespace ... OK +* checking for executable files ... OK +* checking for hidden files and directories ... OK +* checking for portable file names ... OK +* checking for sufficient/correct file permissions ... OK +* checking whether package ‘SNPassoc’ can be installed ... ERROR +Installation failed. +See ‘/tmp/workdir/SNPassoc/old/SNPassoc.Rcheck/00install.out’ for details. +* DONE +Status: 1 ERROR, 1 NOTE + + + ``` @@ -7602,11 +9597,11 @@ ERROR: lazy loading failed for package ‘SNPassoc’
-* Version: 1.0.0 +* Version: 1.2.0 * GitHub: NA * Source code: https://github.com/cran/snplinkage -* Date/Publication: 2023-05-04 08:10:02 UTC -* Number of recursive dependencies: 145 +* Date/Publication: 2024-09-09 19:10:02 UTC +* Number of recursive dependencies: 153 Run `revdepcheck::cloud_details(, "snplinkage")` for more info @@ -7628,7 +9623,7 @@ Run `revdepcheck::cloud_details(, "snplinkage")` for more info * using option ‘--no-manual’ * checking for file ‘snplinkage/DESCRIPTION’ ... OK ... -* this is package ‘snplinkage’ version ‘1.0.0’ +* this is package ‘snplinkage’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -7658,7 +9653,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘snplinkage/DESCRIPTION’ ... OK ... -* this is package ‘snplinkage’ version ‘1.0.0’ +* this is package ‘snplinkage’ version ‘1.2.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -7746,7 +9741,7 @@ ERROR: lazy loading failed for package ‘SoupX’ * GitHub: NA * Source code: https://github.com/cran/sparsereg * Date/Publication: 2016-03-10 23:32:18 -* Number of recursive dependencies: 49 +* Number of recursive dependencies: 50 Run `revdepcheck::cloud_details(, "sparsereg")` for more info @@ -7811,6 +9806,82 @@ ERROR: lazy loading failed for package ‘sparsereg’ * removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ +``` +# SpatialDDLS + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/diegommcc/SpatialDDLS +* Source code: https://github.com/cran/SpatialDDLS +* Date/Publication: 2024-04-26 16:10:02 UTC +* Number of recursive dependencies: 207 + +Run `revdepcheck::cloud_details(, "SpatialDDLS")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SpatialDDLS/new/SpatialDDLS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SpatialDDLS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SpatialExperiment’ + +Package suggested but not available for checking: ‘ComplexHeatmap’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SpatialDDLS/old/SpatialDDLS.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘SpatialDDLS/DESCRIPTION’ ... OK +... +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘SpatialExperiment’ + +Package suggested but not available for checking: ‘ComplexHeatmap’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # spikeSlabGAM @@ -8008,83 +10079,13 @@ Status: 1 ERROR * checking package dependencies ... ERROR Package required but not available: ‘asbio’ -See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ -manual. -* DONE -Status: 1 ERROR - - - - - -``` -# survHE - -
- -* Version: 2.0.1 -* GitHub: https://github.com/giabaio/survHE -* Source code: https://github.com/cran/survHE -* Date/Publication: 2023-03-19 22:10:02 UTC -* Number of recursive dependencies: 130 - -Run `revdepcheck::cloud_details(, "survHE")` for more info - -
- -## In both - -* checking whether package ‘survHE’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/survHE/new/survHE.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - 'survHEinla', 'survHEhmc' - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘survHE’ ... -** package ‘survHE’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘survHE’ -* removing ‘/tmp/workdir/survHE/new/survHE.Rcheck/survHE’ +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR -``` -### CRAN -``` -* installing *source* package ‘survHE’ ... -** package ‘survHE’ successfully unpacked and MD5 sums checked -** using staged installation -** R -** data -*** moving datasets to lazyload DB -** inst -** byte-compile and prepare package for lazy loading -Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : - namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required -Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace -Execution halted -ERROR: lazy loading failed for package ‘survHE’ -* removing ‘/tmp/workdir/survHE/old/survHE.Rcheck/survHE’ ``` @@ -8223,6 +10224,76 @@ ERROR: lazy loading failed for package ‘tempted’ * removing ‘/tmp/workdir/tempted/old/tempted.Rcheck/tempted’ +``` +# TestAnaAPP + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/jiangyouxiang/TestAnaAPP +* Source code: https://github.com/cran/TestAnaAPP +* Date/Publication: 2024-09-10 07:30:02 UTC +* Number of recursive dependencies: 250 + +Run `revdepcheck::cloud_details(, "TestAnaAPP")` for more info + +
+ +## In both + +* checking whether package ‘TestAnaAPP’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TestAnaAPP’ ... +** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TestAnaAPP’ +* removing ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck/TestAnaAPP’ + + +``` +### CRAN + +``` +* installing *source* package ‘TestAnaAPP’ ... +** package ‘TestAnaAPP’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Warning in check_dep_version() : + ABI version mismatch: +lme4 was built with Matrix ABI version 1 +Current Matrix ABI version is 0 +Please re-install lme4 from source or restore original ‘Matrix’ package +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘rms’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TestAnaAPP’ +* removing ‘/tmp/workdir/TestAnaAPP/old/TestAnaAPP.Rcheck/TestAnaAPP’ + + ``` # tidydr @@ -8232,7 +10303,7 @@ ERROR: lazy loading failed for package ‘tempted’ * GitHub: https://github.com/YuLab-SMU/tidydr * Source code: https://github.com/cran/tidydr * Date/Publication: 2023-03-08 09:20:02 UTC -* Number of recursive dependencies: 74 +* Number of recursive dependencies: 79 Run `revdepcheck::cloud_details(, "tidydr")` for more info @@ -8360,7 +10431,7 @@ ERROR: lazy loading failed for package ‘tidyEdSurvey’ * GitHub: https://github.com/stemangiola/tidyseurat * Source code: https://github.com/cran/tidyseurat * Date/Publication: 2024-01-10 04:50:02 UTC -* Number of recursive dependencies: 207 +* Number of recursive dependencies: 208 Run `revdepcheck::cloud_details(, "tidyseurat")` for more info @@ -8612,10 +10683,10 @@ ERROR: lazy loading failed for package ‘TSrepr’
-* Version: 2.6 +* Version: 2.6.1 * GitHub: NA * Source code: https://github.com/cran/twang -* Date/Publication: 2023-12-06 00:30:02 UTC +* Date/Publication: 2024-07-22 16:10:01 UTC * Number of recursive dependencies: 53 Run `revdepcheck::cloud_details(, "twang")` for more info @@ -8681,6 +10752,158 @@ ERROR: lazy loading failed for package ‘twang’ * removing ‘/tmp/workdir/twang/old/twang.Rcheck/twang’ +``` +# updog + +
+ +* Version: 2.1.5 +* GitHub: https://github.com/dcgerard/updog +* Source code: https://github.com/cran/updog +* Date/Publication: 2023-11-29 15:50:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "updog")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/updog/new/updog.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘updog/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘multidog.Rmd’ using ‘UTF-8’... OK + ‘oracle_calculations.Rmd’ using ‘UTF-8’... OK + ‘simulate_ngs.Rmd’ using ‘UTF-8’... OK + ‘smells_like_updog.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/updog/old/updog.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘updog/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘multidog.Rmd’ using ‘UTF-8’... OK + ‘oracle_calculations.Rmd’ using ‘UTF-8’... OK + ‘simulate_ngs.Rmd’ using ‘UTF-8’... OK + ‘smells_like_updog.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 NOTEs + + + + + +``` +# valr + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/rnabioco/valr +* Source code: https://github.com/cran/valr +* Date/Publication: 2024-08-30 22:10:03 UTC +* Number of recursive dependencies: 176 + +Run `revdepcheck::cloud_details(, "valr")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/valr/new/valr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘valr/DESCRIPTION’ ... OK +... +* this is package ‘valr’ version ‘0.8.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/valr/old/valr.Rcheck’ +* using R version 4.3.1 (2023-06-16) +* using platform: x86_64-pc-linux-gnu (64-bit) +* R was compiled by + gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 + GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 +* running under: Ubuntu 22.04.4 LTS +* using session charset: UTF-8 +* using option ‘--no-manual’ +* checking for file ‘valr/DESCRIPTION’ ... OK +... +* this is package ‘valr’ version ‘0.8.2’ +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... ERROR +Package required but not available: ‘rtracklayer’ + +See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ +manual. +* DONE +Status: 1 ERROR + + + + + ``` # vdg @@ -8817,6 +11040,41 @@ ERROR: lazy loading failed for package ‘visa’ * removing ‘/tmp/workdir/visa/old/visa.Rcheck/visa’ +``` +# VisualizeSimon2Stage + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/VisualizeSimon2Stage +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "VisualizeSimon2Stage")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # WRTDStidal @@ -8881,4 +11139,39 @@ ERROR: lazy loading failed for package ‘WRTDStidal’ * removing ‘/tmp/workdir/WRTDStidal/old/WRTDStidal.Rcheck/WRTDStidal’ +``` +# xxdi + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/xxdi +* Number of recursive dependencies: 37 + +Run `revdepcheck::cloud_details(, "xxdi")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` diff --git a/revdep/problems.md b/revdep/problems.md index 8e2e437056..73ee83725d 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,1317 +1,28608 @@ -# activAnalyzer (patchwork) +# activAnalyzer + +
+ +* Version: 2.1.1 +* GitHub: https://github.com/pydemull/activAnalyzer +* Source code: https://github.com/cran/activAnalyzer +* Date/Publication: 2024-05-05 22:40:03 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "activAnalyzer")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘activAnalyzer.Rmd’ + ... + > p3 <- accum_metrics_sed$p_UBD + + > p4 <- accum_metrics_sed$p_gini + + > (p1 | p2)/(p3 | p4) + plot_layout(guides = "collect") & + + theme(legend.position = "bottom") + + When sourcing ‘activAnalyzer.R’: + Error: object is not a unit + Execution halted + + ‘activAnalyzer.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘activAnalyzer.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.0Mb + extdata 2.0Mb + ``` + +# actxps + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/mattheaphy/actxps +* Source code: https://github.com/cran/actxps +* Date/Publication: 2024-06-25 12:40:02 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "actxps")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘actxps.Rmd’ + ... + # ℹ 2 more variables: ae_expected_1 , ae_expected_2 + + > autoplot(exp_res) + Warning: thematic was unable to resolve `bg='auto'`. Try providing an actual color (or `NA`) to the `bg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `fg='auto'`. Try providing an actual color (or `NA`) to the `fg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `accent='auto'`. Try providing an actual color (or `NA`) to the `accent` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + + ... + + When sourcing ‘transactions.R’: + Error: Internal error: adjust_color() expects an input of length 1 + Execution halted + + ‘actxps.Rmd’ using ‘UTF-8’... failed + ‘exp_summary.Rmd’ using ‘UTF-8’... OK + ‘exposures.Rmd’ using ‘UTF-8’... OK + ‘misc.Rmd’ using ‘UTF-8’... failed + ‘transactions.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘actxps.Rmd’ using rmarkdown + Warning: thematic was unable to resolve `bg='auto'`. Try providing an actual color (or `NA`) to the `bg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `fg='auto'`. Try providing an actual color (or `NA`) to the `fg` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + Warning: thematic was unable to resolve `accent='auto'`. Try providing an actual color (or `NA`) to the `accent` argument of `thematic_on()`. By the way, 'auto' is only officially supported in `shiny::renderPlot()`, some rmarkdown scenarios (specifically, `html_document()` with `theme!=NULL`), in RStudio, or if `auto_config_set()` is used. + + Quitting from lines 129-130 [plot] (actxps.Rmd) + Error: processing vignette 'actxps.Rmd' failed with diagnostics: + Internal error: adjust_color() expects an input of length 1 + --- failed re-building ‘actxps.Rmd’ + ... + Quitting from lines 205-211 [trx-plot] (transactions.Rmd) + Error: processing vignette 'transactions.Rmd' failed with diagnostics: + Internal error: adjust_color() expects an input of length 1 + --- failed re-building ‘transactions.Rmd’ + + SUMMARY: processing the following files failed: + ‘actxps.Rmd’ ‘misc.Rmd’ ‘transactions.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# adaptr + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/INCEPTdk/adaptr +* Source code: https://github.com/cran/adaptr +* Date/Publication: 2024-05-03 12:10:02 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "adaptr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘adaptr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_history + > ### Title: Plot trial metric history + > ### Aliases: plot_history plot_history.trial_result + > ### plot_history.trial_results + > + > ### ** Examples + > + ... + + # Run a single simulation with a fixed random seed + + res <- run_trial(binom_trial, seed = 12345) + + + + # Plot total allocations to each arm according to overall total allocations + + plot_history(res, x_value = "total n", y_value = "n") + + + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_history ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(adaptr) + Loading 'adaptr' package v1.4.0. + For instructions, type 'help("adaptr")' + or see https://inceptdk.github.io/adaptr/. + > + > test_check("adaptr") + ... + • plot_history/history-plot-binomial-single-ratio-ys-look.svg + • plot_metrics_ecdf/errors.svg + • plot_metrics_ecdf/selected.svg + • plot_metrics_ecdf/size-only.svg + • plot_metrics_ecdf/superior.svg + • plot_status/status-plot-across-arms-binomial.svg + • plot_status/status-plot-for-all-arms-binomial.svg + • plot_status/status-plot-for-arm-c-binom.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Overview.Rmd’ + ... + + > plot_convergence(calibrated_binom_trial$best_sims, + + metrics = c("size mean", "prob_superior", "prob_equivalence"), + + n_split = 4) + + > plot_status(calibrated_binom_trial$best_sims, x_value = "total n") + + When sourcing ‘Overview.R’: + Error: argument is of length zero + Execution halted + + ‘Advanced-example.Rmd’ using ‘UTF-8’... OK + ‘Basic-examples.Rmd’ using ‘UTF-8’... OK + ‘Overview.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Advanced-example.Rmd’ using rmarkdown + ``` + +# AeRobiology + +
+ +* Version: 2.0.1 +* GitHub: NA +* Source code: https://github.com/cran/AeRobiology +* Date/Publication: 2019-06-03 06:20:03 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "AeRobiology")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘my-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘my-vignette.Rmd’ + ... + Warning: Ignoring unknown labels: + • `size = "14"` + + > iplot_abundance(munich_pollen, interpolation = FALSE, + + export.plot = FALSE, export.result = FALSE, n.types = 3, + + y.start = 2011, y.end = .... [TRUNCATED] + + When sourcing ‘my-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘my-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +# agricolaeplotr + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/jensharbers/agricolaeplotr +* Source code: https://github.com/cran/agricolaeplotr +* Date/Publication: 2024-01-17 16:42:04 UTC +* Number of recursive dependencies: 144 + +Run `revdepcheck::cloud_details(, "agricolaeplotr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(agricolaeplotr) + + Type 'citation("agricolaeplotr")' for citing this R package in publications. + + Attaching package: 'agricolaeplotr' + + ... + `expected` is a character vector ('ROW') + ── Failure ('testall.R:847:3'): plot a plot design from FielDHub package shows COLUMN as x axis ── + p$labels$x (`actual`) not identical to "COLUMN" (`expected`). + + `actual` is NULL + `expected` is a character vector ('COLUMN') + + [ FAIL 30 | WARN 92 | SKIP 0 | PASS 107 ] + Error: Test failures + Execution halted + ``` + +# alien + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/alien +* Date/Publication: 2024-06-19 16:20:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "alien")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic_usage.Rmd’ + ... + 2 0.3330822 6.848124e-06 1.620061e+04 + 3 0.3377835 1.902532e-07 5.997150e+05 + 4 0.3425512 5.285577e-09 2.220028e+07 + + > plot_snc(model, cumulative = T) + coord_cartesian(ylim = c(0, + + 150)) + scale_y_continuous(breaks = seq(0, 150, 50)) + ylab("Cumulative discove ..." ... [TRUNCATED] + + When sourcing ‘basic_usage.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘basic_usage.Rmd’ using ‘UTF-8’... failed + ‘native_discoveries.Rmd’ using ‘UTF-8’... OK + ‘simulations.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘basic_usage.Rmd’ using rmarkdown + ``` + +# AlphaPart + +
+ +* Version: 0.9.8 +* GitHub: NA +* Source code: https://github.com/cran/AlphaPart +* Date/Publication: 2022-11-15 21:40:05 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "AlphaPart")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AlphaPart-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.plotSummaryAlphaPart + > ### Title: Print a plot generate by the function 'plotSummaryAlphaPart' + > ### Aliases: print.plotSummaryAlphaPart + > + > ### ** Examples + > + > ## Partition additive genetic values + ... + 4 4 1 105.00000 66 39.00000 + + > + > ## Plot the partitions + > p <- plot(ret, ylab=c("BV for trait 1", "BV for trait 2"), xlab="Generation") + > print(p[[1]]) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: print ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘alphapart-variance.Rmd’ + ... + + > data <- readRDS("./../inst/extdata/AlphaPartCattleSim.rds") %>% + + dplyr::mutate(across(generation:mother, as.numeric)) %>% + + dplyr::rename .... [TRUNCATED] + Warning in gzfile(file, "rb") : + cannot open compressed file './../inst/extdata/AlphaPartCattleSim.rds', probable reason 'No such file or directory' + + When sourcing ‘alphapart-variance.R’: + Error: cannot open the connection + Execution halted + + ‘alphapart-variance.Rmd’ using ‘UTF-8’... failed + ‘alphapart-vignette.Rmd’ using ‘UTF-8’... OK + ``` + +# AnalysisLin + +
+ +* Version: 0.1.2 +* GitHub: NA +* Source code: https://github.com/cran/AnalysisLin +* Date/Publication: 2024-01-30 00:10:10 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "AnalysisLin")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AnalysisLin-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bar_plot + > ### Title: Bar Plots for Categorical Variables + > ### Aliases: bar_plot + > + > ### ** Examples + > + > data(iris) + > bar_plot(iris) + Error in pm[[2]] : subscript out of bounds + Calls: bar_plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# animbook + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/KrisanatA/animbook +* Source code: https://github.com/cran/animbook +* Date/Publication: 2023-12-05 17:50:07 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "animbook")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘animbook-Ex.R’ failed + The error most likely occurred in: + + > ### Name: anim_animate + > ### Title: Modified the ggplot object + > ### Aliases: anim_animate + > + > ### ** Examples + > + > animbook <- anim_prep(data = osiris, id = ID, values = sales, time = year, group = japan) + ... + transform it into an animated object + > + > animate <- anim_animate(plot) + You can now pass it to gganimate::animate(). + The recommended setting is nframes = 89 + > + > plotly::ggplotly(animate) + Error in pm[[2]] : subscript out of bounds + Calls: -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# ANN2 + +
+ +* Version: 2.3.4 +* GitHub: https://github.com/bflammers/ANN2 +* Source code: https://github.com/cran/ANN2 +* Date/Publication: 2020-12-01 10:00:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "ANN2")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ANN2) + > + > # Only test if not on mac + > if (tolower(Sys.info()[["sysname"]]) != "darwin") { + + test_check("ANN2") + + } + ... + ── Failure ('test-plotting.R:59:3'): the reconstruction_plot.ANN() function works correctly ── + p_AE$labels$colour not equal to "col". + target is NULL, current is character + ── Failure ('test-plotting.R:77:3'): the compression_plot.ANN() function works correctly ── + p_AE$labels$colour not equal to "col". + target is NULL, current is character + + [ FAIL 5 | WARN 1 | SKIP 4 | PASS 143 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 58.9Mb + sub-directories of 1Mb or more: + cereal 1.4Mb + libs 57.3Mb + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# AnnoProbe + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/jmzeng1314/AnnoProbe +* Source code: https://github.com/cran/AnnoProbe +* Date/Publication: 2022-11-14 08:30:11 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "AnnoProbe")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AnnoProbe-Ex.R’ failed + The error most likely occurred in: + + > ### Name: check_diff_genes + > ### Title: Check a list of genes how they show difference. + > ### Aliases: check_diff_genes + > + > ### ** Examples + > + > attach(GSE95166) + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +# ANOFA + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/dcousin3/ANOFA +* Source code: https://github.com/cran/ANOFA +* Date/Publication: 2023-11-18 14:20:08 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "ANOFA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ANOFA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Gillet1993 + > ### Title: Gillet1993 + > ### Aliases: Gillet1993 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + > # run the base analysis + > w <- anofa( Freq ~ species * location * florished, Gillet1993) + > + > # display a plot of the results + > anofaPlot(w) + superb::FYI: The variables will be plotted in that order: species, location, florished (use factorOrder to change). + Error in superb::superbPlot(cdata, BSFactors = bsfact, variables = as.character(w$freqColumn), : + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Calls: anofaPlot -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > test_check("ANOFA") + Loading required package: ANOFA + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 149 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-ANOFA-2.R:36:5'): TESTS of emFrequencies function (2/3) ──────── + ... + statistic = "count", errorbar = "CI", gamma = confidenceLevel, + plotStyle = plotStyle, errorbarParams = errorbarParams, ...)`: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Backtrace: + ▆ + 1. └─ANOFA::anofaPlot(w, Freq ~ B) at test-ANOFA-3.R:46:5 + 2. └─superb::superbPlot(...) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 149 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ConfidenceIntervals.Rmd’ + ... + > library(ANOFA) + + > w <- anofa(obsfreq ~ vocation * gender, LightMargolin1971) + + > anofaPlot(w) + superb::FYI: The variables will be plotted in that order: vocation, gender (use factorOrder to change). + + ... + + > anofaPlot(w) + + When sourcing ‘WhatIsANOFA.R’: + Error: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Execution halted + + ‘ConfidenceIntervals.Rmd’ using ‘UTF-8’... failed + ‘DataFormatsForFrequencies.Rmd’ using ‘UTF-8’... OK + ‘WhatIsANOFA.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ConfidenceIntervals.Rmd’ using rmarkdown + + Quitting from lines 70-73 [unnamed-chunk-2] (ConfidenceIntervals.Rmd) + Error: processing vignette 'ConfidenceIntervals.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘ConfidenceIntervals.Rmd’ + + --- re-building ‘DataFormatsForFrequencies.Rmd’ using rmarkdown + ... + Quitting from lines 108-109 [unnamed-chunk-4] (WhatIsANOFA.Rmd) + Error: processing vignette 'WhatIsANOFA.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘WhatIsANOFA.Rmd’ + + SUMMARY: processing the following files failed: + ‘ConfidenceIntervals.Rmd’ ‘WhatIsANOFA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ANOPA + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/dcousin3/ANOPA +* Source code: https://github.com/cran/ANOPA +* Date/Publication: 2024-03-22 19:40:05 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "ANOPA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ANOPA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ArringtonEtAl2002 + > ### Title: Arrington et al. (2002) dataset + > ### Aliases: ArringtonEtAl2002 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + Africa Nocturnal Omnivore 0 0 + North America Nocturnal Detritivore 0 0 + Warning: ANOPA::warning(1): Some cells have zero over zero data. Imputing... + > + > # make a plot with all the factors + > anopaPlot(w) + Error in superb::superbPlot(wdata, BSFactors = bsfact, WSFactors = wsfact, : + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Calls: anopaPlot -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > test_check("ANOPA") + Loading required package: ANOPA + ------------------------------------------------------------ + Design is: 2 x ( 3 ) with 2 independent groups. + ------------------------------------------------------------ + 1.Between-Subject Factors ( 2 groups ) : + ... + 1) "UA" else "none"), plotStyle = plotStyle, errorbarParams = errorbarParams, + ...)`: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Backtrace: + ▆ + 1. └─ANOPA::anopaPlot(w) at test-ANOPA-4.R:106:9 + 2. └─superb::superbPlot(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 131 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘A-WhatIsANOPA.Rmd’ + ... + > w <- anopa({ + + nSuccess + + nParticipants + + } ~ DistractingTask, ArticleExample1) + + > anopaPlot(w) + + ... + When sourcing ‘E-ArcsineIsAsinine.R’: + Error: superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + Execution halted + + ‘A-WhatIsANOPA.Rmd’ using ‘UTF-8’... failed + ‘B-DataFormatsForProportions.Rmd’ using ‘UTF-8’... OK + ‘C-ConfidenceIntervals.Rmd’ using ‘UTF-8’... failed + ‘D-ArringtonExample.Rmd’ using ‘UTF-8’... failed + ‘E-ArcsineIsAsinine.Rmd’ using ‘UTF-8’... failed + ‘F-TestingTypeIError.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘A-WhatIsANOPA.Rmd’ using rmarkdown + + Quitting from lines 182-183 [unnamed-chunk-5] (A-WhatIsANOPA.Rmd) + Error: processing vignette 'A-WhatIsANOPA.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘A-WhatIsANOPA.Rmd’ + + --- re-building ‘B-DataFormatsForProportions.Rmd’ using rmarkdown + --- finished re-building ‘B-DataFormatsForProportions.Rmd’ + ... + + --- re-building ‘F-TestingTypeIError.Rmd’ using rmarkdown + --- finished re-building ‘F-TestingTypeIError.Rmd’ + + SUMMARY: processing the following files failed: + ‘A-WhatIsANOPA.Rmd’ ‘C-ConfidenceIntervals.Rmd’ + ‘D-ArringtonExample.Rmd’ ‘E-ArcsineIsAsinine.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# AntMAN + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/bbodin/AntMAN +* Source code: https://github.com/cran/AntMAN +* Date/Publication: 2021-07-23 10:00:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "AntMAN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘AntMAN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: AM_mix_hyperparams_uninorm + > ### Title: univariate Normal mixture hyperparameters + > ### Aliases: AM_mix_hyperparams_uninorm + > + > ### ** Examples + > + > + ... + Press [enter] to continue + Plotting pmf for M,K + NULL + Press [enter] to continue + Plotting traces from M,K + Press [enter] to continue + Plotting values from M,K + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘UnitTest_AM_binder.R’ + Running ‘UnitTest_AM_coclustering.R’ + Running ‘UnitTest_AM_demo.R’ + Running ‘UnitTest_AM_extract.R’ + Running ‘UnitTest_AM_mcmc.R’ + Running the tests in ‘tests/UnitTest_AM_mcmc.R’ failed. + Complete output: + > ####################################################################################### + > ############### + > ############### AntMAN Package : Tests and Examples + ... + Press [enter] to continue + Plotting pmf for M,K + NULL + Press [enter] to continue + Plotting traces from M,K + Press [enter] to continue + Plotting values from M,K + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + libs 6.4Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Rdpack’ ‘mcclust’ + All declared Imports should be used. + ``` + +# APCI + +
+ +* Version: 1.0.8 +* GitHub: NA +* Source code: https://github.com/cran/APCI +* Date/Publication: 2024-09-02 20:20:06 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "APCI")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘1_tests.R’ + Running the tests in ‘tests/1_tests.R’ failed. + Complete output: + > # install the package and use this script to test the package + > library("APCI") + > # or: remotes::install_github("jiahui1902/APCI") + > test_data <- APCI::women9017 + > test_data$acc <- as.factor(test_data$acc) + > test_data$pcc <- as.factor(test_data$pcc) + > test_data$educc <- as.factor(test_data$educc) + ... + -0.335818939 0.165402344 0.138957101 -0.357703237 0.229441985 + acc8:pcc3 acc9:pcc3 acc1:pcc4 acc2:pcc4 acc3:pcc4 + -0.147848556 0.146360984 -0.436635793 0.062363971 0.289676120 + acc4:pcc4 acc5:pcc4 acc6:pcc4 acc7:pcc4 acc8:pcc4 + 0.266502847 0.199035811 -0.082410026 -0.140171983 -0.274808726 + acc9:pcc4 acc1:pcc5 acc2:pcc5 acc3:pcc5 acc4:pcc5 + 0.070541348 0.052280642 0.320968547 -0.136111903 -0.102002632 + acc5:pcc5 acc6:pcc5 acc7:pcc5 acc8:pcc5 acc9:pcc5 + -0.553458810 -0.333938836 0.340338956 0.670285259 -0.300340437 + Killed + ``` + +# aplot + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/YuLab-SMU/aplot +* Source code: https://github.com/cran/aplot +* Date/Publication: 2024-06-17 09:50:01 UTC +* Number of recursive dependencies: 50 + +Run `revdepcheck::cloud_details(, "aplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘aplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: insert_left + > ### Title: plot-insertion + > ### Aliases: insert_left insert_right insert_top insert_bottom + > + > ### ** Examples + > + > library(ggplot2) + ... + > ap + > ap[2, 1] <- ap[2, 1] + theme_bw() + > ap[2, 1] <- ap[2, 1] + + + aes(color = as.factor(am)) + + + scale_color_manual(values = c('steelblue', 'darkgreen')) + > ap[1, 1] <- ap[1, 1] + theme(axis.line.x.bottom=element_line()) + > ap + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# applicable + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/tidymodels/applicable +* Source code: https://github.com/cran/applicable +* Date/Publication: 2024-04-25 00:00:04 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "applicable")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(applicable) + Loading required package: ggplot2 + > + > test_check("applicable") + Loading required package: dplyr + ... + `expected` is a character vector ('percentile') + ── Failure ('test-plot.R:36:3'): output of autoplot.apd_pca is correct when options=distance are provided ── + ad_plot$labels$y (`actual`) not equal to "percentile" (`expected`). + + `actual` is NULL + `expected` is a character vector ('percentile') + + [ FAIL 3 | WARN 0 | SKIP 22 | PASS 90 ] + Error: Test failures + Execution halted + ``` + +# ASRgenomics + +
+ +* Version: 1.1.4 +* GitHub: NA +* Source code: https://github.com/cran/ASRgenomics +* Date/Publication: 2024-01-29 21:20:02 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "ASRgenomics")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ASRgenomics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: kinship.pca + > ### Title: Performs a Principal Component Analysis (PCA) based on a kinship + > ### matrix K + > ### Aliases: kinship.pca + > + > ### ** Examples + > + ... + 13. │ └─ggplot2:::`+.gg`(...) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + ... + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 249 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.9Mb + sub-directories of 1Mb or more: + data 8.5Mb + ``` + +# autocogs + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/schloerke/autocogs +* Source code: https://github.com/cran/autocogs +* Date/Publication: 2021-05-29 17:00:05 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "autocogs")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(autocogs) + > + > test_check("autocogs") + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 228 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 8. └─autocogs (local) FUN(X[[i]], ...) + 9. └─base::lapply(...) + 10. └─autocogs (local) FUN(X[[i]], ...) + 11. ├─base::do.call(fn, args) + 12. └─autocogs (local) ``(...) + 13. └─base::do.call(loess, c(core_params, params$method.args)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 228 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’ + All declared Imports should be used. + ``` + +# autoplotly + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/terrytangyuan/autoplotly +* Source code: https://github.com/cran/autoplotly +* Date/Publication: 2021-04-18 06:50:11 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "autoplotly")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘autoplotly-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplotly + > ### Title: Automatic Visualization of Popular Statistical Results Using + > ### 'plotly.js' and 'ggplot2' + > ### Aliases: autoplotly + > + > ### ** Examples + > + > # Automatically generate interactive plot for results produced by `stats::prcomp` + > p <- autoplotly(prcomp(iris[c(1, 2, 3, 4)]), data = iris, + + colour = 'Species', label = TRUE, label.size = 3, frame = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplotly ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(autoplotly) + > + > test_check("autoplotly") + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 5. └─ggfortify::ggbiplot(...) + 6. └─ggplot2:::`+.gg`(...) + 7. └─ggplot2:::add_ggplot(e1, e2, e2name) + 8. ├─ggplot2::ggplot_add(object, p, objectname) + 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 3 | WARN 0 | SKIP 0 | PASS 1 ] + Error: Test failures + Execution halted + ``` + +# autoReg + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/cardiomoon/autoReg +* Source code: https://github.com/cran/autoReg +* Date/Publication: 2023-11-14 05:53:27 UTC +* Number of recursive dependencies: 214 + +Run `revdepcheck::cloud_details(, "autoReg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘autoReg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: adjustedPlot.survreg + > ### Title: Draw predicted survival curve with an object survreg + > ### Aliases: adjustedPlot.survreg + > + > ### ** Examples + > + > library(survival) + > x=survreg(Surv(time, status) ~ rx, data=anderson,dist="exponential") + > adjustedPlot(x) + > adjustedPlot(x,addCox=TRUE) + Warning: Removed 42 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Automatic_Regression_Modeling.Rmd’ + ... + Species setosa (N=50) Mean ± SD 5.0 ± 0.4 + versicolor (N=50) Mean ± SD 5.9 ± 0.5 1.46 (1.24 to 1.68, p<.001) 1.44 (1.16 to 1.71, p<.001) 1.47 (1.23 to 1.70, p<.001) + virginica (N=50) Mean ± SD 6.6 ± 0.6 1.95 (1.75 to 2.14, p<.001) 1.87 (1.62 to 2.11, p<.001) 1.97 (1.76 to 2.17, p<.001) + ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— + + > modelPlot(fit1, imputed = TRUE) + + ... + + When sourcing ‘Survival.R’: + Error: argument is of length zero + Execution halted + + ‘Automatic_Regression_Modeling.Rmd’ using ‘UTF-8’... failed + ‘Bootstrap_Prediction.Rmd’ using ‘UTF-8’... OK + ‘Getting_started.Rmd’ using ‘UTF-8’... failed + ‘Statiastical_test_in_gaze.Rmd’ using ‘UTF-8’... OK + ‘Survival.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Automatic_Regression_Modeling.Rmd’ using rmarkdown + + Quitting from lines 142-143 [unnamed-chunk-15] (Automatic_Regression_Modeling.Rmd) + Error: processing vignette 'Automatic_Regression_Modeling.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘Automatic_Regression_Modeling.Rmd’ + + --- re-building ‘Bootstrap_Prediction.Rmd’ using rmarkdown + ``` + +# baggr + +
+ +* Version: 0.7.8 +* GitHub: https://github.com/wwiecek/baggr +* Source code: https://github.com/cran/baggr +* Date/Publication: 2024-02-12 18:20:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "baggr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘baggr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: baggr_plot + > ### Title: Plotting method in baggr package + > ### Aliases: baggr_plot + > + > ### ** Examples + > + > fit <- baggr(schools, pooling = "none") + Automatically chose Rubin model with aggregate data based on input data. + Setting prior for mean in each group using 10 times the max effect : + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(baggr) + Loading required package: Rcpp + This is baggr; see vignette('baggr') for tutorial, ?baggr for basic help. + For execution on a local, multicore CPU with excess RAM call: + options(mc.cores = parallel::detectCores()) + > + ... + 10. └─bayesplot::mcmc_areas(...) + 11. └─ggplot2:::`+.gg`(...) + 12. └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. ├─ggplot2::ggplot_add(object, p, objectname) + 14. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 6 | WARN 0 | SKIP 6 | PASS 488 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘baggr.Rmd’ + ... + 2.5% 0.4303903 + mean 0.8619752 + 97.5% 0.9998572 + + + > plot(baggr_schools, order = FALSE) + + When sourcing ‘baggr.R’: + Error: argument is of length zero + Execution halted + + ‘baggr.Rmd’ using ‘UTF-8’... failed + ‘baggr_binary.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘baggr.Rmd’ using rmarkdown + + Quitting from lines 272-273 [unnamed-chunk-9] (baggr.Rmd) + Error: processing vignette 'baggr.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘baggr.Rmd’ + + --- re-building ‘baggr_binary.Rmd’ using rmarkdown + --- finished re-building ‘baggr_binary.Rmd’ + + SUMMARY: processing the following file failed: + ‘baggr.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 196.3Mb + sub-directories of 1Mb or more: + libs 194.5Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# banter + +
+ +* Version: 0.9.6 +* GitHub: NA +* Source code: https://github.com/cran/banter +* Date/Publication: 2023-02-12 21:32:29 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "banter")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘banter-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotDetectorTrace + > ### Title: Plot BANTER Detector Traces + > ### Aliases: plotDetectorTrace + > + > ### ** Examples + > + > data(train.data) + ... + > bant.mdl <- addBanterDetector( + + bant.mdl, train.data$detectors, + + ntree = 50, sampsize = 1, num.cores = 1 + + ) + > + > plotDetectorTrace(bant.mdl) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plotDetectorTrace ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# bartMan + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/bartMan +* Date/Publication: 2024-07-24 12:10:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "bartMan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bartMan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mdsBart + > ### Title: mdsBart + > ### Aliases: mdsBart + > + > ### ** Examples + > + > if (requireNamespace("dbarts", quietly = TRUE)) { + ... + | + |======================================================================| 100% + Extracting Observation Data... + + Getting proximites... + Getting MDS... + Performing procrustes... + Error in if (new_name %in% existing) { : argument is of length zero + Calls: mdsBart -> suppressMessages -> withCallingHandlers + Execution halted + ``` + +# BasketballAnalyzeR + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/sndmrc/BasketballAnalyzeR +* Source code: https://github.com/cran/BasketballAnalyzeR +* Date/Publication: 2020-06-26 09:00:11 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "BasketballAnalyzeR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BasketballAnalyzeR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatterplot + > ### Title: Draws a scatter plot or a matrix of scatter plots + > ### Aliases: scatterplot + > + > ### ** Examples + > + > # Single scatter plot + ... + > X <- data.frame(AST=Pbox.sel$AST/Pbox.sel$MIN,TOV=Pbox.sel$TOV/Pbox.sel$MIN) + > X$PTSpm <- Pbox.sel$PTS/Pbox.sel$MIN + > mypal <- colorRampPalette(c("blue","yellow","red")) + > scatterplot(X, data.var=c("AST","TOV"), z.var="PTSpm", labels=1:nrow(X), palette=mypal) + > # Matrix of scatter plots + > data <- Pbox[1:50, c("PTS","P3M","P2M","OREB","Team")] + > scatterplot(data, data.var=1:4, z.var="Team") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.9Mb + sub-directories of 1Mb or more: + data 6.5Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’ + All declared Imports should be used. + ``` + +# bayefdr + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/VallejosGroup/bayefdr +* Source code: https://github.com/cran/bayefdr +* Date/Publication: 2022-10-26 19:35:06 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "bayefdr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayefdr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: traceplot + > ### Title: Trace, marginal density histogram, and autocorrelation plot of + > ### MCMC draws. + > ### Aliases: traceplot + > + > ### ** Examples + > + > x <- rnorm(1000) + > traceplot(x) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: traceplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayefdr) + > + > test_check("bayefdr") + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 14 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 8. └─base::Reduce(`+`, c(list(noGeomPlot), layers)) + 9. └─ggplot2:::`+.gg`(init, x[[i]]) + 10. └─ggplot2:::add_ggplot(e1, e2, e2name) + 11. ├─ggplot2::ggplot_add(object, p, objectname) + 12. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 13. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 14 ] + Error: Test failures + Execution halted + ``` + +# bayesAB + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/FrankPortman/bayesAB +* Source code: https://github.com/cran/bayesAB +* Date/Publication: 2021-06-25 00:50:02 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "bayesAB")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayesAB) + > + > test_check("bayesAB") + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-dists.R:34:3'): Success ────────────────────────────────────── + plotNormalInvGamma(3, 1, 1, 1)$labels$y not equal to "sig_sq". + target is NULL, current is character + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 140 ] + Error: Test failures + Execution halted + ``` + +# BayesGrowth + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/jonathansmart/BayesGrowth +* Source code: https://github.com/cran/BayesGrowth +* Date/Publication: 2023-11-21 18:10:08 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "BayesGrowth")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘MCMC-example.Rmd’ + ... + > ggplot(growth_curve, aes(Age, LAA)) + geom_point(data = example_data, + + aes(Age, Length), alpha = 0.3) + geom_lineribbon(aes(ymin = .lower, + + .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + When sourcing ‘MCMC-example.R’: + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 14, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, FALSE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NUL + Execution halted + + ‘MCMC-example.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MCMC-example.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 84.8Mb + sub-directories of 1Mb or more: + data 1.5Mb + libs 82.6Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# BayesianReasoning + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/gorkang/BayesianReasoning +* Source code: https://github.com/cran/BayesianReasoning +* Date/Publication: 2023-11-14 11:33:20 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "BayesianReasoning")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(BayesianReasoning) + > + > test_check("BayesianReasoning") + + Plot created in: ./FP_10_sens_100_screening_1667_diagnostic_44.png + + ... + `names(expected)` is absent + ── Failure ('test-PPV_heatmap.R:1097:3'): Plot with line overlay ─────────────── + vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomSegment", "GeomPoint", "GeomMarkRect") (`expected`). + + `names(actual)` is a character vector ('geom_tile', 'annotate', 'annotate...3', 'geom_mark_rect') + `names(expected)` is absent + + [ FAIL 8 | WARN 56 | SKIP 4 | PASS 115 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PPV_NPV.Rmd’ + ... + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + Warning in ggforce::geom_mark_rect(aes(label = paste0(translated_labels$label_PPV_NPV, : + All aesthetics have length 1, but the data has 10201 rows. + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + + When sourcing ‘PPV_NPV.R’: + Error: object is not coercible to a unit + Execution halted + + ‘PPV_NPV.Rmd’ using ‘UTF-8’... failed + ‘introduction.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PPV_NPV.Rmd’ using rmarkdown + ``` + +# BayesMallows + +
+ +* Version: 2.2.2 +* GitHub: https://github.com/ocbe-uio/BayesMallows +* Source code: https://github.com/cran/BayesMallows +* Date/Publication: 2024-08-17 13:00:03 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "BayesMallows")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + `expected` is a character vector ('interaction(chain, cluster)') + ── Failure ('test-assess_convergence.R:217:3'): assess_convergence.BayesMallowsMixtures works ── + p$labels$colour (`actual`) not equal to "cluster" (`expected`). + + `actual` is NULL + `expected` is a character vector ('cluster') + + [ FAIL 10 | WARN 0 | SKIP 6 | PASS 435 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 23.7Mb + sub-directories of 1Mb or more: + doc 2.7Mb + libs 20.1Mb + ``` + +# bayesplay + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/bayesplay/bayesplay +* Source code: https://github.com/cran/bayesplay +* Date/Publication: 2023-04-13 12:10:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "bayesplay")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayesplay-Ex.R’ failed + The error most likely occurred in: + + > ### Name: visual_compare + > ### Title: Visually compare two models + > ### Aliases: visual_compare + > + > ### ** Examples + > + > # define two models + ... + > h1_mod <- prior(family = "normal", mean = 0, sd = 10) + > m0 <- extract_predictions(data_model * h0_mod) + > m1 <- extract_predictions(data_model * h1_mod) + > + > # visually compare the model + > visual_compare(m0, m1) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘advanced.Rmd’ + ... + > plot(posterior1, add_prior = TRUE) + labs(title = "prior and posterior distribution", + + subtitle = "for a binomial likelihood and beta prior") + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'ϴ' in 'mbcsToSbcs': dot substituted for + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'ϴ' in 'mbcsToSbcs': dot substituted for + + ... + > visual_compare(d_model1, d_model2) + + When sourcing ‘plots.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘advanced.Rmd’ using ‘UTF-8’... failed + ‘basic.Rmd’ using ‘UTF-8’... OK + ‘default_ttests.Rmd’ using ‘UTF-8’... OK + ‘plots.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘advanced.Rmd’ using rmarkdown + ``` + +# bayesplot + +
+ +* Version: 1.11.1 +* GitHub: https://github.com/stan-dev/bayesplot +* Source code: https://github.com/cran/bayesplot +* Date/Publication: 2024-02-15 05:30:11 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "bayesplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayesplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MCMC-intervals + > ### Title: Plot interval estimates from MCMC draws + > ### Aliases: MCMC-intervals mcmc_intervals mcmc_areas mcmc_areas_ridges + > ### mcmc_intervals_data mcmc_areas_data mcmc_areas_ridges_data + > + > ### ** Examples + > + ... + + $Parameter + [1] "alpha" "sigma" "beta[1]" "beta[2]" "beta[3]" "beta[4]" + + > + > color_scheme_set("brightblue") + > mcmc_intervals(x) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: mcmc_intervals ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayesplot) + This is bayesplot version 1.11.1 + - Online documentation and vignettes at mc-stan.org/bayesplot + - bayesplot theme set to bayesplot::theme_default() + * Does _not_ affect other ggplot2 plots + * See ?bayesplot_theme_set for details on theme setting + ... + 5. └─bayesplot::ppc_violin_grouped(y, yrep, group) + 6. └─ggplot2:::`+.gg`(...) + 7. └─ggplot2:::add_ggplot(e1, e2, e2name) + 8. ├─ggplot2::ggplot_add(object, p, objectname) + 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 6 | WARN 1 | SKIP 73 | PASS 994 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘plotting-mcmc-draws.Rmd’ + ... + + + > color_scheme_set("red") + + > mcmc_intervals(posterior, pars = c("cyl", "drat", + + "am", "sigma")) + + ... + > fit_cp <- sampling(schools_mod_cp, data = schools_dat, + + seed = 803214055, control = list(adapt_delta = 0.9)) + + When sourcing ‘visual-mcmc-diagnostics.R’: + Error: error in evaluating the argument 'object' in selecting a method for function 'sampling': object 'schools_mod_cp' not found + Execution halted + + ‘graphical-ppcs.Rmd’ using ‘UTF-8’... OK + ‘plotting-mcmc-draws.Rmd’ using ‘UTF-8’... failed + ‘visual-mcmc-diagnostics.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.6Mb + sub-directories of 1Mb or more: + R 4.0Mb + doc 3.8Mb + ``` + +# bayestestR + +
+ +* Version: 0.14.0 +* GitHub: https://github.com/easystats/bayestestR +* Source code: https://github.com/cran/bayestestR +* Date/Publication: 2024-07-24 14:10:02 UTC +* Number of recursive dependencies: 209 + +Run `revdepcheck::cloud_details(, "bayestestR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bayestestR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bayesfactor_restricted + > ### Title: Bayes Factors (BF) for Order Restricted Models + > ### Aliases: bayesfactor_restricted bf_restricted + > ### bayesfactor_restricted.stanreg bayesfactor_restricted.brmsfit + > ### bayesfactor_restricted.blavaan bayesfactor_restricted.emmGrid + > ### as.logical.bayesfactor_restricted + > + ... + + ) + > + > + > (b <- bayesfactor_restricted(posterior, hypothesis = hyps, prior = prior)) + Bayes Factor (Order-Restriction) + + Hypothesis P(Prior) P(Posterior) BF + A > B & B > C 0.16 0.23 1.39 + A > B & A > C 0.36 0.59 1.61 + C > A 0.46 0.34 0.742 + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(bayestestR) + > + > test_check("bayestestR") + Starting 2 test processes + [ FAIL 3 | WARN 2 | SKIP 74 | PASS 180 ] + + ... + 14. └─brms:::eval2(call, envir = args, enclos = envir) + 15. └─base::eval(expr, envir, ...) + 16. └─base::eval(expr, envir, ...) + 17. └─rstan (local) .fun(model_code = .x1) + 18. └─rstan:::cxxfunctionplus(...) + 19. └─base::sink(type = "output") + + [ FAIL 3 | WARN 2 | SKIP 74 | PASS 180 ] + Error: Test failures + Execution halted + ``` + +# BCEA + +
+ +* Version: 2.4.6 +* GitHub: https://github.com/n8thangreen/BCEA +* Source code: https://github.com/cran/BCEA +* Date/Publication: 2024-02-16 15:00:08 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "BCEA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BCEA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ceac.plot.bcea + > ### Title: Cost-Effectiveness Acceptability Curve (CEAC) Plot + > ### Aliases: ceac.plot.bcea ceac.plot + > ### Keywords: hplot + > + > ### ** Examples + > + ... + > he <- BCEA::bcea(eff, cost) + No reference selected. Defaulting to first intervention. + > ceac.plot(he) + > + > ceac.plot(he, graph = "base") + > ceac.plot(he, graph = "ggplot2") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(BCEA) + The BCEA version loaded is: 2.4.6 + + Attaching package: 'BCEA' + + The following object is masked from 'package:graphics': + ... + 3. └─BCEA:::eib_plot_ggplot(he, graph_params, ...) + 4. └─ggplot2:::`+.gg`(...) + 5. └─ggplot2:::add_ggplot(e1, e2, e2name) + 6. ├─ggplot2::ggplot_add(object, p, objectname) + 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 7 | PASS 159 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CEriskav.Rmd’ + ... + + > CEriskav(bcea_smoke) <- r + + > plot(bcea_smoke) + + > plot(bcea_smoke, graph = "ggplot") + + ... + + ‘CEriskav.Rmd’ using ‘UTF-8’... failed + ‘bcea.Rmd’ using ‘UTF-8’... failed + ‘ceac.Rmd’ using ‘UTF-8’... failed + ‘ceef.Rmd’ using ‘UTF-8’... OK + ‘ceplane.Rmd’ using ‘UTF-8’... failed + ‘contour.Rmd’ using ‘UTF-8’... failed + ‘eib.Rmd’ using ‘UTF-8’... failed + ‘paired_vs_multiple_comps.Rmd’ using ‘UTF-8’... OK + ‘Set_bcea_parameters.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘CEriskav.Rmd’ using rmarkdown + + Quitting from lines 41-46 [unnamed-chunk-3] (CEriskav.Rmd) + Error: processing vignette 'CEriskav.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘CEriskav.Rmd’ + + --- re-building ‘bcea.Rmd’ using rmarkdown + ``` + +# BDgraph + +
+ +* Version: 2.73 +* GitHub: NA +* Source code: https://github.com/cran/BDgraph +* Date/Publication: 2024-08-23 13:20:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "BDgraph")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘BDgraph-Examples.Rmd’ + ... + Sensitivity 1 0.714 0.714 + MCC 1 0.827 0.827 + + > plotroc(list(bdgraph.obj, bdgraph.mpl.obj), data.sim, + + cut = 200, labels = c("BDgraph", "BDgraph.mpl"), color = c("blue", + + "red")) + + When sourcing ‘BDgraph-Examples.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘BDgraph-Examples.Rmd’ using ‘UTF-8’... failed + ‘Introduction-BDgraph.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘BDgraph-Examples.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.3Mb + sub-directories of 1Mb or more: + libs 6.8Mb + ``` + +# BEAMR + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/annaSeffernick/BEAMR +* Source code: https://github.com/cran/BEAMR +* Date/Publication: 2024-07-27 16:00:06 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "BEAMR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BEAMR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gen_beam_plot_list + > ### Title: Generate BEAM Plot List + > ### Aliases: gen_beam_plot_list + > + > ### ** Examples + > + > data(beam_stats) + ... + + beam.specs=beam_stats$beam.specs) + > plot.list <- gen_beam_plot_list(beam.result=beam_stats, beam.specs=plot.specs, + + beam.feat.pvals=test.feat.pvals, + + number.pairs=1, set.id="ENSG00000099810", + + feat.id=NULL, title.size=11, + + pair.order="omic", endpt.order=NULL) + Error in if (new_name %in% existing) { : argument is of length zero + Error in plot.temp$plot : $ operator is invalid for atomic vectors + Calls: gen_beam_plot_list + Execution halted + ``` + +# beastt + +
+ +* Version: 0.0.1 +* GitHub: https://github.com/GSK-Biostatistics/beastt +* Source code: https://github.com/cran/beastt +* Date/Publication: 2024-06-20 15:50:16 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "beastt")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘beastt-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_dist + > ### Title: Plot Distribution + > ### Aliases: plot_dist + > + > ### ** Examples + > + > library(distributional) + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘binary.Rmd’ + ... + + > plot_dist(pwr_prior) + + When sourcing ‘binary.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ... + When sourcing ‘continuous.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, + Execution halted + + ‘binary.Rmd’ using ‘UTF-8’... failed + ‘continuous.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘binary.Rmd’ using rmarkdown + ``` + +# BeeGUTS + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/bgoussen/BeeGUTS +* Source code: https://github.com/cran/BeeGUTS +* Date/Publication: 2023-09-18 15:40:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "BeeGUTS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BeeGUTS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: traceplot + > ### Title: Plotting method for traces and densities for 'beeSurvFit' + > ### objects + > ### Aliases: traceplot traceplot.beeSurvFit + > + > ### ** Examples + > + > data(fitBetacyfluthrin_Chronic) + > traceplot(fitBetacyfluthrin_Chronic) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: traceplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + Chain 1: Elapsed Time: 137.867 seconds (Warm-up) + Chain 1: 75.093 seconds (Sampling) + Chain 1: 212.96 seconds (Total) + Chain 1: + + > traceplot(fit) + + When sourcing ‘Tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 45-58 [example] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 78.9Mb + sub-directories of 1Mb or more: + data 4.0Mb + libs 74.3Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# besthr + +
+ +* Version: 0.3.2 +* GitHub: NA +* Source code: https://github.com/cran/besthr +* Date/Publication: 2023-04-14 08:50:08 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "besthr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘besthr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.hrest + > ### Title: plots the 'hrest' object + > ### Aliases: plot.hrest + > + > ### ** Examples + > + > + > d1 <- make_data() + > hr_est <- estimate(d1, score, group) + > plot(hr_est) + Picking joint bandwidth of 0.68 + Error in as.unit(value) : object is not coercible to a unit + Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic-use.Rmd’ + ... + Confidence Intervals (0.025, 0.975) + 3.7475, 8.2525 + + 100 bootstrap resamples. + > plot(hr_est_1) + Picking joint bandwidth of 0.381 + + When sourcing ‘basic-use.R’: + Error: object is not coercible to a unit + Execution halted + + ‘basic-use.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘basic-use.Rmd’ using rmarkdown + + Quitting from lines 34-44 [unnamed-chunk-2] (basic-use.Rmd) + Error: processing vignette 'basic-use.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘basic-use.Rmd’ + + SUMMARY: processing the following file failed: + ‘basic-use.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# betaclust + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/betaclust +* Date/Publication: 2023-09-29 10:20:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "betaclust")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignettes.Rmd’ + ... + + data = pca.methylation.data[, 2:5], patient_number = 1, plot_type = "ggplot") + + > plot(threshold_out, what = "kernel density", threshold = TRUE, + + data = pca.methylation.data[, 2:5], plot_type = "ggplot") + + > plot(threshold_out, what = "uncertainty") + + When sourcing ‘vignettes.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘vignettes.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignettes.Rmd’ using rmarkdown + ``` + +# biclustermd + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/jreisner/biclustermd +* Source code: https://github.com/cran/biclustermd +* Date/Publication: 2021-06-17 15:10:06 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "biclustermd")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(biclustermd) + Loading required package: ggplot2 + Loading required package: tidyr + + Attaching package: 'tidyr' + + ... + ── Failure ('test-autoplot_biclustermd.R:6:3'): autoplot_biclustermd() correctly plots cluster lines ── + ap$data[[3]]$xintercept[-1] not equal to cumsum(colSums(sbc$P)) + 0.5. + Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' + ── Failure ('test-autoplot_biclustermd.R:7:3'): autoplot_biclustermd() correctly plots cluster lines ── + ap$data[[4]]$yintercept[-1] not equal to cumsum(colSums(sbc$Q)) + 0.5. + Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 66 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘nycflights13’ + All declared Imports should be used. + ``` + +# biodosetools + +
+ +* Version: 3.6.1 +* GitHub: https://github.com/biodosetools-team/biodosetools +* Source code: https://github.com/cran/biodosetools +* Date/Publication: 2022-11-16 16:00:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "biodosetools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(biodosetools) + > + > test_check("biodosetools") + ! Problem with `glm()` -> constraint ML optimization will be used instead + ! Problem with `glm()` -> constraint ML optimization will be used instead + number of iterations= 43 + ... + actual | expected + [2] "Estimation" | "Estimation" [2] + [3] "Dose (Gy)" | "Dose (Gy)" [3] + [4] "Translocations/cells" | "Translocations/cells" [4] + - "yield_low" [5] + - "yield_upp" [6] + + [ FAIL 4 | WARN 0 | SKIP 1 | PASS 232 ] + Error: Test failures + Execution halted + ``` + +# BioPred + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/BioPred +* Date/Publication: 2024-06-06 16:50:09 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "BioPred")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + + > tutorial_data$biogroup = ifelse(tutorial_data$x2 <= + + 0.5, "biomarker_positive", "biomarker_negative") + + > res = subgrp_perf_pred(yvar = "y.time", censorvar = "y.event", + + grpvar = "biogroup", grpname = c("biomarker_positive", "biomarker_negative"), .... [TRUNCATED] + + When sourcing ‘Tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Tutorial.Rmd’ using rmarkdown + ``` + +# BlandAltmanLeh + +
+ +* Version: 0.3.1 +* GitHub: NA +* Source code: https://github.com/cran/BlandAltmanLeh +* Date/Publication: 2015-12-23 23:32:17 +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "BlandAltmanLeh")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Intro.Rmd’ + ... + > b <- 0.02 * a + 0.3 * rnorm(150) + + > library(ggExtra) + + > print(ggMarginal(bland.altman.plot(a, b, graph.sys = "ggplot2"), + + type = "histogram", size = 4)) + + When sourcing ‘Intro.R’: + Error: argument is of length zero + Execution halted + + ‘Intro.Rmd’... failed + ``` + +# bmggum + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/Naidantu/bmggum +* Source code: https://github.com/cran/bmggum +* Date/Publication: 2021-04-09 08:50:06 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "bmggum")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘bmggum-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bayesplot + > ### Title: bayesian convergence diagnosis plotting function + > ### Aliases: bayesplot + > + > ### ** Examples + > + > Data <- c(1,4,2,3) + ... + Chain 1: + Warning: There were 3 divergent transitions after warmup. See + https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup + to find out why this is a problem and how to eliminate them. + Warning: Examine the pairs() plot to diagnose sampling problems + + > bayesplot(mod, 'alpha', 'density', inc_warmup=FALSE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: bayesplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 206.7Mb + sub-directories of 1Mb or more: + libs 206.1Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# boxly + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/Merck/boxly +* Source code: https://github.com/cran/boxly +* Date/Publication: 2023-10-24 02:40:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "boxly")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 16. ├─plotly::add_trace(...) + 17. │ └─plotly::add_data(p, data) + 18. │ └─plotly:::is.plotly(p) + 19. ├─plotly::ggplotly(p, tooltip = "text", dynamicTicks = TRUE) + 20. └─plotly:::ggplotly.ggplot(p, tooltip = "text", dynamicTicks = TRUE) + 21. └─plotly::gg2list(...) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ] + Error: Test failures + Execution halted + ``` + +# braidReports + +
+ +* Version: 0.5.4 +* GitHub: NA +* Source code: https://github.com/cran/braidReports +* Date/Publication: 2021-01-05 18:20:09 UTC +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "braidReports")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘braidReports-Ex.R’ failed + The error most likely occurred in: + + > ### Name: makeBRAIDreport + > ### Title: Make a BRAID Report Page + > ### Aliases: makeBRAIDreport + > ### Keywords: hplot + > + > ### ** Examples + > + ... + 22. │ └─grid::convertUnit(short, "cm", valueOnly = TRUE) + 23. │ ├─grid:::upgradeUnit(x) + 24. │ └─grid:::upgradeUnit.default(x) + 25. │ └─base::stop("Not a unit object") + 26. └─base::.handleSimpleError(``, "Not a unit object", base::quote(upgradeUnit.default(x))) + 27. └─rlang (local) h(simpleError(msg, call)) + 28. └─handlers[[1L]](cnd) + 29. └─cli::cli_abort(...) + 30. └─rlang::abort(...) + Execution halted + ``` + +# BRcal + +
+ +* Version: 0.0.4 +* GitHub: https://github.com/apguthrie/BRcal +* Source code: https://github.com/cran/BRcal +* Date/Publication: 2024-06-25 11:30:08 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "BRcal")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘BRcal-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lineplot + > ### Title: Lineplot for LLO-adjusted Probability Predictions + > ### Aliases: lineplot + > + > ### ** Examples + > + > + ... + > # Simulated 100 binary event outcomes using x + > y <- rbinom(100, 1, x) # By construction, x is well calibrated. + > + > # Lineplot show change in probabilities from original to MLE-recalibration to + > # specified Levels of Boldness-Recalibration via t_levels + > # Return a list with dataframe used to construct plot with return_df=TRUE + > lp1 <- lineplot(x, y, t_levels=c(0.98, 0.95), return_df=TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: lineplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘hockey_vignette.Rmd’ + ... + [841] 0.4804441 0.7670617 0.4668403 0.4104682 0.6058493 0.4249086 0.6581869 + [848] 0.7194199 0.4534938 0.7421488 0.6726924 0.3255808 0.5005185 0.6483056 + [855] 0.7210362 0.6593455 0.4586214 0.7750603 0.5841900 0.4826292 0.4080026 + [862] 0.6701504 0.6561462 0.4814185 0.7421488 0.6786381 0.3255808 0.4814569 + + > lineplot(hockey$x, hockey$y) + + When sourcing ‘hockey_vignette.R’: + Error: argument is of length zero + Execution halted + + ‘hockey_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘hockey_vignette.Rmd’ using rmarkdown + + Quitting from lines 180-181 [unnamed-chunk-11] (hockey_vignette.Rmd) + Error: processing vignette 'hockey_vignette.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘hockey_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘hockey_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# breathtestcore + +
+ +* Version: 0.8.7 +* GitHub: https://github.com/dmenne/breathtestcore +* Source code: https://github.com/cran/breathtestcore +* Date/Publication: 2024-01-24 15:02:47 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "breathtestcore")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Complete output: + > library(testthat) + > + > options(Ncpus = parallelly::availableCores(omit = 1)) + > test_check("breathtestcore") + Loading required package: breathtestcore + Starting 1 test process + [ FAIL 3 | WARN 11 | SKIP 4 | PASS 356 ] + ... + `expected`: 10 + ── Failure ('test_plot_breathtestfit.R:81:3'): Plot multiple groups data only (no fit) ── + length(p) (`actual`) not equal to length(ggplot()) (`expected`). + + `actual`: 11 + `expected`: 10 + + [ FAIL 3 | WARN 11 | SKIP 4 | PASS 356 ] + Error: Test failures + Execution halted + ``` + +# brolgar + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/njtierney/brolgar +* Source code: https://github.com/cran/brolgar +* Date/Publication: 2024-05-10 14:50:34 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "brolgar")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘brolgar-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_sample + > ### Title: Facet data into groups to facilitate exploration + > ### Aliases: facet_sample + > + > ### ** Examples + > + > library(ggplot2) + > ggplot(heights, + + aes(x = year, + + y = height_cm, + + group = country)) + + + geom_line() + + + facet_sample() + Error in if (params$as.table) { : argument is of length zero + Calls: ... -> setup -> -> compute_layout + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘exploratory-modelling.Rmd’ + ... + Warning in is.na(non_null_default_aes[[aes_param_name]]) : + is.na() applied to non-(list or vector) of type 'language' + + When sourcing ‘exploratory-modelling.R’: + Error: ℹ In index: 1. + ℹ With name: geom_line. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + ... + Error: argument is of length zero + Execution halted + + ‘exploratory-modelling.Rmd’ using ‘UTF-8’... failed + ‘finding-features.Rmd’ using ‘UTF-8’... failed + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ‘id-interesting-obs.Rmd’ using ‘UTF-8’... OK + ‘longitudinal-data-structures.Rmd’ using ‘UTF-8’... OK + ‘mixed-effects-models.Rmd’ using ‘UTF-8’... failed + ‘visualisation-gallery.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown + + Quitting from lines 47-56 [use-gg-highlight] (exploratory-modelling.Rmd) + Error: processing vignette 'exploratory-modelling.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: geom_line. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + aes_param_name]])`: + ! 'length = 2' in coercion to 'logical(1)' + --- failed re-building ‘exploratory-modelling.Rmd’ + + --- re-building ‘finding-features.Rmd’ using rmarkdown + ``` + +# calibrationband + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/marius-cp/calibrationband +* Source code: https://github.com/cran/calibrationband +* Date/Publication: 2022-08-09 14:40:02 UTC +* Number of recursive dependencies: 38 + +Run `revdepcheck::cloud_details(, "calibrationband")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘calibrationband-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.calibrationband + > ### Title: Plotting monotone confidence bands + > ### Aliases: plot.calibrationband autoplot.calibrationband + > ### autolayer.calibrationband + > + > ### ** Examples + > + ... + > p <- function(x,s){p = 1/(1+((1/x*(1-x))^(s+1)));return(p)} + > dat <- data.frame(pr=x, y=rbinom(n,1,p(x,s))) + > + > cb <- calibration_bands(x=dat$pr, y=dat$y,alpha=0.05, method="round", digits =3) + > + > #simple plotting + > plot(cb) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# cartograflow + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/fbahoken/cartogRaflow +* Source code: https://github.com/cran/cartograflow +* Date/Publication: 2023-10-17 22:40:21 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "cartograflow")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cartograflow-Ex.R’ failed + The error most likely occurred in: + + > ### Name: flowgini + > ### Title: Analysis of flow concentration (Gini coefficient) + > ### Aliases: flowgini + > + > ### ** Examples + > + > library(cartograflow) + ... + ℹ Use `flowcum` instead. + Warning: Use of `x$linkcum` is discouraged. + ℹ Use `linkcum` instead. + Warning: Use of `x$flowcum` is discouraged. + ℹ Use `flowcum` instead. + Warning: Use of `x$flowcum` is discouraged. + ℹ Use `flowcum` instead. + Error in pm[[2]] : subscript out of bounds + Calls: flowgini ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# cases + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/maxwestphal/cases +* Source code: https://github.com/cran/cases +* Date/Publication: 2023-05-18 08:30:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "cases")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘example_wdbc.Rmd’ + ... + 13 TRUE FALSE + 14 FALSE FALSE + 15 FALSE FALSE + + + > visualize(results_bm) + + ... + + regu = TRU .... [TRUNCATED] + + > visualize(results_comp) + + When sourcing ‘package_overview.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘example_wdbc.Rmd’ using ‘UTF-8’... failed + ‘package_overview.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘example_wdbc.Rmd’ using rmarkdown + data_wdbc package:cases R Documentation + + _B_r_e_a_s_t _C_a_n_c_e_r _W_i_s_c_o_n_s_i_n (_D_i_a_g_n_o_s_t_i_c) _D_a_t_a _S_e_t + + _D_e_s_c_r_i_p_t_i_o_n: + + Dataset documentation can be found at the source website and + references below. + ... + Quitting from lines 160-168 [viz_comp] (package_overview.Rmd) + Error: processing vignette 'package_overview.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘package_overview.Rmd’ + + SUMMARY: processing the following files failed: + ‘example_wdbc.Rmd’ ‘package_overview.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# cats + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/cats +* Date/Publication: 2022-03-11 10:20:07 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "cats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: trial_ocs + > ### Title: Calculates the operating characteristics of the cohort trial + > ### Aliases: trial_ocs + > + > ### ** Examples + > + > + ... + + safety_prob = safety_prob, Bayes_Sup1 = Bayes_Sup1, Bayes_Sup2 = Bayes_Sup2, + + cohort_offset = cohort_offset, sr_first_pos = sr_first_pos, + + missing_prob = missing_prob, cohort_fixed = cohort_fixed, accrual_type = accrual_type, + + accrual_param = accrual_param, hist_lag = hist_lag, analysis_times = analysis_times, + + time_trend = time_trend, cohorts_start = cohorts_start, cohorts_sim = cohorts_sim, + + iter = 2, coresnum = 1, save = FALSE, ret_list = TRUE, plot_ocs = TRUE + + ) + Error in pm[[2]] : subscript out of bounds + Calls: trial_ocs -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘epitools’ ‘forcats’ ‘purrr’ + All declared Imports should be used. + ``` + +# ceterisParibus + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/pbiecek/ceterisParibus +* Source code: https://github.com/cran/ceterisParibus +* Date/Publication: 2020-03-28 03:10:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "ceterisParibus")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ceterisParibus) + Loading required package: ggplot2 + Loading required package: gower + > + > test_check("ceterisParibus") + Welcome to DALEX (version: 2.4.3). + ... + 5. └─ceterisParibus:::plot_interactive.what_if_explainer(wi_rf_all) + 6. └─ggplot2:::`+.gg`(...) + 7. └─ggplot2:::add_ggplot(e1, e2, e2name) + 8. ├─ggplot2::ggplot_add(object, p, objectname) + 9. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 10. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 3 | SKIP 0 | PASS 29 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘knitr’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# cfda + +
+ +* Version: 0.11.0 +* GitHub: https://github.com/modal-inria/cfda +* Source code: https://github.com/cran/cfda +* Date/Publication: 2023-10-07 15:50:05 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "cfda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cfda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compute_duration + > ### Title: Compute duration of individuals + > ### Aliases: compute_duration + > + > ### ** Examples + > + > # Simulate the Jukes-Cantor model of nucleotide replacement + ... + > d_JK <- generate_Markov(n = 10, K = K, P = PJK, lambda = lambda_PJK, Tmax = 10) + > + > + > # compute duration of each individual + > duration <- compute_duration(d_JK) + > + > hist(duration) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: hist ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cfda) + Loading required package: fda + Loading required package: splines + Loading required package: fds + Loading required package: rainbow + Loading required package: MASS + ... + 7. └─cfda:::hist.njump(njump) + 8. └─ggplot2:::`+.gg`(...) + 9. └─ggplot2:::add_ggplot(e1, e2, e2name) + 10. ├─ggplot2::ggplot_add(object, p, objectname) + 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 1 | SKIP 12 | PASS 351 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cfda.Rmd’ + ... + + > head(nJump) + 1 2 3 4 5 6 + 17 9 3 13 10 13 + + > hist(nJump) + + When sourcing ‘cfda.R’: + Error: argument is of length zero + Execution halted + + ‘cfda.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cfda.Rmd’ using rmarkdown + ``` + +# cheem + +
+ +* Version: 0.4.0.0 +* GitHub: https://github.com/nspyrison/cheem +* Source code: https://github.com/cran/cheem +* Date/Publication: 2023-11-08 21:30:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "cheem")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cheem) + -------------------------------------------------------- + cheem --- version 0.4.0.0 + Please share bugs, suggestions, and feature requests at: + https://github.com/nspyrison/cheem/issues/ + -------------------------------------------------------- + ... + 13. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) + 14. │ │ └─base::stopifnot(is.list(x), is.list(val)) + 15. │ └─x %||% list() + 16. ├─plotly::ggplotly(...) + 17. └─plotly:::ggplotly.ggplot(...) + 18. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘getting-started-with-cheem.Rmd’ + ... + + > knitr::opts_chunk$set(echo = TRUE, include = TRUE, + + results = "show", eval = FALSE, message = FALSE, warning = FALSE, + + error = FALSE, co .... [TRUNCATED] + + > knitr::include_graphics("../inst/shiny_apps/cheem/www/lime_nonlinear.png") + + When sourcing ‘getting-started-with-cheem.R’: + Error: Cannot find the file(s): "../inst/shiny_apps/cheem/www/lime_nonlinear.png" + Execution halted + + ‘getting-started-with-cheem.Rmd’ using ‘UTF-8’... failed + ``` + +# chillR + +
+ +* Version: 0.75 +* GitHub: NA +* Source code: https://github.com/cran/chillR +* Date/Publication: 2023-11-27 22:20:02 UTC +* Number of recursive dependencies: 138 + +Run `revdepcheck::cloud_details(, "chillR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘chillR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_scenarios + > ### Title: Plot historic and future scenarios for climate-related metrics + > ### ('ggplot2' version) + > ### Aliases: plot_scenarios + > + > ### ** Examples + > + ... + > + > # Plot the climate scenarios + > + > plot_scenarios(climate_scenario_list, metric = 'Chill_Portions', + + add_historic = TRUE, size = 2, shape = 3, color = 'blue', + + outlier_shape = 12, historic_color = 'skyblue', + + group_by = c("Year", "Scenario")) + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# chronicle + +
+ +* Version: 0.3 +* GitHub: NA +* Source code: https://github.com/cran/chronicle +* Date/Publication: 2021-06-25 05:00:02 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "chronicle")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘chronicle-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_barplot + > ### Title: Create a bar plot from a data frame through ggplotly + > ### Aliases: make_barplot + > + > ### ** Examples + > + > make_barplot(dt = iris, bars = 'Species', value = 'Sepal.Length') + Error in pm[[2]] : subscript out of bounds + Calls: make_barplot -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘chronicle.Rmd’ + ... + + filename = "quick_demo", title = "A quick chronicle demo", + + author = .... [TRUNCATED] + + Quitting from lines 34-46 [unnamed-chunk-3] (quick_demo.Rmd) + + When sourcing ‘chronicle.R’: + Error: ℹ In index: 1. + Caused by error in `pm[[2]]`: + ! subscript out of bounds + Execution halted + + ‘chronicle.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘chronicle.Rmd’ using rmarkdown + + Quitting from lines 38-67 [unnamed-chunk-3] (chronicle.Rmd) + Error: processing vignette 'chronicle.Rmd' failed with diagnostics: + ℹ In index: 1. + Caused by error in `pm[[2]]`: + ! subscript out of bounds + --- failed re-building ‘chronicle.Rmd’ + + SUMMARY: processing the following file failed: + ‘chronicle.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’ + All declared Imports should be used. + ``` + +# CINNA + +
+ +* Version: 1.2.2 +* GitHub: NA +* Source code: https://github.com/cran/CINNA +* Date/Publication: 2023-08-08 16:40:02 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "CINNA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CINNA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pca_centralities + > ### Title: PCA Centrality Measures + > ### Aliases: pca_centralities + > + > ### ** Examples + > + > # Create a data frame with multiple observations + ... + 13. │ └─e1 %+% e2 + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CINNA.Rmd’ + ... + > calc_cent <- calculate_centralities(zachary, include = pr_cent[1:10]) + + > pca_centralities(calc_cent) + + When sourcing ‘CINNA.R’: + Error: ℹ In index: 1. + ℹ With name: contrib. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘CINNA.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CINNA.Rmd’ using rmarkdown + + Quitting from lines 231-234 [unnamed-chunk-11] (CINNA.Rmd) + Error: processing vignette 'CINNA.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: contrib. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘CINNA.Rmd’ + + SUMMARY: processing the following file failed: + ‘CINNA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘circlize’ ‘utils’ + All declared Imports should be used. + ``` + +# circhelp + +
+ +* Version: 1.1 +* GitHub: https://github.com/achetverikov/circhelp +* Source code: https://github.com/cran/circhelp +* Date/Publication: 2024-07-04 17:10:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "circhelp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘circhelp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: remove_cardinal_biases + > ### Title: Remove cardinal biases + > ### Aliases: remove_cardinal_biases + > + > ### ** Examples + > + > + > # Data in orientation domain from Pascucci et al. (2019, PLOS Bio), + > # https://doi.org/10.5281/zenodo.2544946 + > + > ex_data <- Pascucci_et_al_2019_data[observer == 4, ] + > remove_cardinal_biases(ex_data$err, ex_data$orientation, plots = "show") + Error in as.unit(value) : object is not coercible to a unit + Calls: remove_cardinal_biases ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cardinal_biases.Rmd’ + ... + + 90)) + .... [TRUNCATED] + + > ex_subj_data <- data[observer == 4, ] + + > res <- remove_cardinal_biases(ex_subj_data$err, ex_subj_data$orientation, + + plots = "show") + + When sourcing ‘cardinal_biases.R’: + Error: object is not coercible to a unit + Execution halted + + ‘cardinal_biases.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cardinal_biases.Rmd’ using rmarkdown + ``` + +# clifro + +
+ +* Version: 3.2-5 +* GitHub: https://github.com/ropensci/clifro +* Source code: https://github.com/cran/clifro +* Date/Publication: 2021-05-24 05:50:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "clifro")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Complete output: + > library(testthat) + > library(clifro) + > + > test_check("clifro") + [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ] + + ... + • On CRAN (4): 'test-cf_find_station.R:4:3', 'test-cf_last_query.R:4:3', + 'test-cf_query.R:4:3', 'test-cf_station.R:4:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-windrose.R:15:3'): windrose ────────────────────────────────── + tt$labels inherits from `'NULL'` not `'character'`. + + [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ] + Error: Test failures + Execution halted + ``` + +# clinDataReview + +
+ +* Version: 1.6.1 +* GitHub: https://github.com/openanalytics/clinDataReview +* Source code: https://github.com/cran/clinDataReview +* Date/Publication: 2024-06-18 09:10:05 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "clinDataReview")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clinDataReview-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatterplotClinData + > ### Title: Scatterplot of variables of interest for clinical data + > ### visualization. + > ### Aliases: scatterplotClinData + > + > ### ** Examples + > + ... + + data = dataPlot, + + xVar = "ADY", + + yVar = "LBSTRESN", + + aesPointVar = list(color = "TRTP", fill = "TRTP"), + + aesLineVar = list(group = "USUBJID", color = "TRTP"), + + labelVars = labelVars + + ) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: scatterplotClinData ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(clinDataReview) + > + > test_check("clinDataReview") + adding: report.html (deflated 63%) + adding: report_dependencies169f5c7b66d/ (stored 0%) + adding: report_dependencies169f5c7b66d/file169f105f2e2e.html (deflated 8%) + ... + 11. ├─base::withCallingHandlers(...) + 12. └─ggplot2:::`+.gg`(gg, do.call(layerFunction, argsGeom)) + 13. └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. ├─ggplot2::ggplot_add(object, p, objectname) + 15. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 35 | WARN 0 | SKIP 31 | PASS 453 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘clinDataReview-dataPreprocessing.Rmd’ using rmarkdown + --- finished re-building ‘clinDataReview-dataPreprocessing.Rmd’ + + --- re-building ‘clinDataReview-dataVisualization.Rmd’ using rmarkdown + + Quitting from lines 167-208 [timeProfiles] (clinDataReview-dataVisualization.Rmd) + Error: processing vignette 'clinDataReview-dataVisualization.Rmd' failed with diagnostics: + argument is of length zero + ... + --- failed re-building ‘clinDataReview-dataVisualization.Rmd’ + + --- re-building ‘clinDataReview-reporting.Rmd’ using rmarkdown + --- finished re-building ‘clinDataReview-reporting.Rmd’ + + SUMMARY: processing the following file failed: + ‘clinDataReview-dataVisualization.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.8Mb + sub-directories of 1Mb or more: + doc 4.3Mb + ``` + +# clinUtils + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/openanalytics/clinUtils +* Source code: https://github.com/cran/clinUtils +* Date/Publication: 2024-05-17 14:50:06 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "clinUtils")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘clinUtils-vignette.Rmd’ + ... + + layout + + + > listPlotsInteractiveLB <- sapply(listPlotsLB, function(ggplot) ggplotly(ggplot) %>% + + partial_bundle(), simplify = FALSE) + + When sourcing ‘clinUtils-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘clinUtils-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘clinUtils-vignette.Rmd’ using rmarkdown + ``` + +## Newly fixed + +* checking running R code from vignettes ... WARNING + ``` + Errors in running code in vignettes: + when running code in ‘clinUtils-vignette.Rmd’ + ... + + + + + + Quitting from lines 2-4 [lab-hist-interactive1] + + When sourcing ‘clinUtils-vignette.R’: + Error: there is no package called 'webshot' + Execution halted + + ‘clinUtils-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.7Mb + sub-directories of 1Mb or more: + doc 6.5Mb + ``` + +# cloneRate + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/bdj34/cloneRate +* Source code: https://github.com/cran/cloneRate +* Date/Publication: 2023-09-22 15:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "cloneRate")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cloneRate-dataAnalysis.Rmd’ + ... + + > fitColor <- colorPal[6] + + > ggplot(PD9478_long, aes(x = Age, y = VAF)) + theme_bw() + + + coord_cartesian(xlim = c(min(x), max(x)), ylim = c(-0.01, + + 0.52), expand .... [TRUNCATED] + + When sourcing ‘cloneRate-dataAnalysis.R’: + Error: `expand` must be a logical vector, not the number 0. + Execution halted + + ‘cloneRate-dataAnalysis.Rmd’ using ‘UTF-8’... failed + ‘cloneRate-simulate.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cloneRate-dataAnalysis.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 47.4Mb + sub-directories of 1Mb or more: + doc 1.0Mb + libs 45.2Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# clustEff + +
+ +* Version: 0.3.1 +* GitHub: NA +* Source code: https://github.com/cran/clustEff +* Date/Publication: 2024-01-23 08:52:55 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "clustEff")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘clustEff-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clustEff-package + > ### Title: Clusters of effects curves + > ### Aliases: clustEff-package + > ### Keywords: package + > + > ### ** Examples + > + ... + 13. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +# ClustImpute + +
+ +* Version: 0.2.4 +* GitHub: NA +* Source code: https://github.com/cran/ClustImpute +* Date/Publication: 2021-05-31 07:40:11 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "ClustImpute")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Example_on_simulated_data.Rmd’ + ... + > dat4plot$true_clust_fct <- factor(true_clust) + + > p_base <- ggplot(dat4plot, aes(x = x, y = y, color = true_clust_fct)) + + + geom_point() + + > ggExtra::ggMarginal(p_base, groupColour = TRUE, groupFill = TRUE) + + When sourcing ‘Example_on_simulated_data.R’: + Error: argument is of length zero + Execution halted + + ‘Example_on_simulated_data.Rmd’ using ‘UTF-8’... failed + ‘description_of_algorithm.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Example_on_simulated_data.Rmd’ using rmarkdown + + Quitting from lines 49-53 [unnamed-chunk-3] (Example_on_simulated_data.Rmd) + Error: processing vignette 'Example_on_simulated_data.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Example_on_simulated_data.Rmd’ + + --- re-building ‘description_of_algorithm.Rnw’ using Sweave + Error: processing vignette 'description_of_algorithm.Rnw' failed with diagnostics: + ... + l.6 \usepackage + {Sweave}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘description_of_algorithm.Rnw’ + + SUMMARY: processing the following files failed: + ‘Example_on_simulated_data.Rmd’ ‘description_of_algorithm.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# cmstatr + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/cmstatr/cmstatr +* Source code: https://github.com/cran/cmstatr +* Date/Publication: 2024-03-14 14:30:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "cmstatr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cmstatr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nested_data_plot + > ### Title: Create a plot of nested sources of variation + > ### Aliases: nested_data_plot + > + > ### ** Examples + > + > library(dplyr) + ... + + intersect, setdiff, setequal, union + + > carbon.fabric.2 %>% + + filter(test == "WT" & condition == "RTD") %>% + + nested_data_plot(strength, + + groups = c(batch, panel)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(cmstatr) + > + > test_check("cmstatr") + Starting 2 test processes + [ FAIL 6 | WARN 0 | SKIP 6 | PASS 1396 ] + ... + 6. └─cmstatr:::draw_vert_lines_to_labels(g, elm_list, vline_args) + 7. └─ggplot2:::`+.gg`(...) + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 6 | WARN 0 | SKIP 6 | PASS 1396 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cmstatr_Graphing.Rmd’ + ... + + by = "condition") %>% inner_join(a_basis_pooled_results, + + by = "condition") .... [TRUNCATED] + + > carbon.fabric.2 %>% mutate(panel = as.character(panel)) %>% + + filter(test == "WT") %>% nested_data_plot(strength, groups = c(batch, + + pane .... [TRUNCATED] + + When sourcing ‘cmstatr_Graphing.R’: + Error: argument is of length zero + Execution halted + + ‘adktest.Rmd’ using ‘UTF-8’... OK + ‘cmstatr_Graphing.Rmd’ using ‘UTF-8’... failed + ‘cmstatr_Tutorial.Rmd’ using ‘UTF-8’... OK + ‘cmstatr_Validation.Rmd’ using ‘UTF-8’... OK + ‘hk_ext.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘adktest.Rmd’ using rmarkdown + --- finished re-building ‘adktest.Rmd’ + + --- re-building ‘cmstatr_Graphing.Rmd’ using rmarkdown + ``` + +# codaredistlm + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/tystan/codaredistlm +* Source code: https://github.com/cran/codaredistlm +* Date/Publication: 2022-12-22 19:50:06 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "codaredistlm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘codaredistlm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_delta_comp + > ### Title: Plot redistributed time-use predictions from compositional ilr + > ### multiple linear regression model fit + > ### Aliases: plot_delta_comp + > + > ### ** Examples + > + ... + | | x| + |:----|------:| + |0% | 1439.9| + |25% | 1440.0| + |50% | 1440.0| + |75% | 1440.0| + |100% | 1440.1| + --- + + --- + ``` + +# coefplot + +
+ +* Version: 1.2.8 +* GitHub: NA +* Source code: https://github.com/cran/coefplot +* Date/Publication: 2022-01-14 09:42:47 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "coefplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘coefplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: buildModelCI + > ### Title: buildModelCI + > ### Aliases: buildModelCI + > + > ### ** Examples + > + > + ... + cut.C 327.4816 model1 + cut.Q -574.8626 model1 + cut.L 1187.6004 model1 + carat 7843.1229 model1 + (Intercept) -2732.2382 model1 + > coefplot(model1) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# CohortPlat + +
+ +* Version: 1.0.5 +* GitHub: NA +* Source code: https://github.com/cran/CohortPlat +* Date/Publication: 2022-02-14 09:30:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "CohortPlat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CohortPlat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_trial + > ### Title: Plots the cohort trial study overview given stage data. + > ### Aliases: plot_trial + > + > ### ** Examples + > + > + ... + + stage_data = stage_data, cohort_random = cohort_random, cohorts_max = cohorts_max, + + sr_drugs_pos = sr_drugs_pos, target_rr = target_rr, sharing_type = sharing_type, + + safety_prob = safety_prob, Bayes_Sup = Bayes_Sup, prob_rr_transform = prob_rr_transform, + + cohort_offset = cohort_offset, Bayes_Fut = Bayes_Fut, sr_first_pos = sr_first_pos + + ) + > + > plot_trial(res_list, unit = "n") + Error in pm[[2]] : subscript out of bounds + Calls: plot_trial -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘my-vignette.Rmd’ + ... + + > set.seed(50) + + > ocs1 <- trial_ocs(n_int = n_int, n_fin = n_fin, rr_comb = rr_comb, + + rr_mono = rr_mono, rr_back = rr_back, rr_plac = rr_plac, + + rr_transfo .... [TRUNCATED] + + When sourcing ‘my-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘my-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘my-vignette.Rmd’ using rmarkdown + + Quitting from lines 1043-1073 [unnamed-chunk-20] (my-vignette.Rmd) + Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘my-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘my-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# complmrob + +
+ +* Version: 0.7.0 +* GitHub: https://github.com/dakep/complmrob +* Source code: https://github.com/cran/complmrob +* Date/Publication: 2019-09-17 18:10:02 UTC +* Number of recursive dependencies: 31 + +Run `revdepcheck::cloud_details(, "complmrob")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘complmrob-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.complmrob + > ### Title: Diagnostic plots for the robust regression model with + > ### compositional covariates + > ### Aliases: plot.complmrob + > + > ### ** Examples + > + > data <- data.frame(lifeExp = state.x77[, "Life Exp"], USArrests[ , -3]) + > mUSArr <- complmrob(lifeExp ~ ., data = data) + > plot(mUSArr) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# conjoint + +
+ +* Version: 1.41 +* GitHub: NA +* Source code: https://github.com/cran/conjoint +* Date/Publication: 2018-07-26 13:00:03 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "conjoint")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘conjoint-Ex.R’ failed + The error most likely occurred in: + + > ### Name: caSegmentation + > ### Title: Function caSegmentation divides respondents on clusters + > ### Aliases: caSegmentation + > ### Keywords: multivariate + > + > ### ** Examples + > + ... + Available components: + + [1] "cluster" "centers" "totss" "withinss" "tot.withinss" + [6] "betweenss" "size" "iter" "ifault" + > util<-as.data.frame(segments$util) + > set.seed(123) + > ggplot2::autoplot(kmeans(util,3),data=util,label=TRUE,label.size=4,frame=TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# conquestr + +
+ +* Version: 1.3.4 +* GitHub: NA +* Source code: https://github.com/cran/conquestr +* Date/Publication: 2024-07-24 06:00:01 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "conquestr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘plotting.Rmd’ + ... + > myRout <- ConQuestRout() + no rout file provided, loading the example rout file instead + + > myPlot <- plotRout(myRout) + + > myPlot + + ... + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘data-cleaning-functions-in-conquestr.Rmd’ using ‘UTF-8’... OK + ‘generateResponses.Rmd’ using ‘UTF-8’... OK + ‘intro-to-conquestr.Rmd’ using ‘UTF-8’... OK + ‘itanal-in-conquestr.Rmd’ using ‘UTF-8’... OK + ‘plotting.Rmd’ using ‘UTF-8’... failed + ‘responseProbs.Rmd’ using ‘UTF-8’... OK + ‘test_item_review_sheet_markdown.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘data-cleaning-functions-in-conquestr.Rmd’ using rmarkdown + --- finished re-building ‘data-cleaning-functions-in-conquestr.Rmd’ + + --- re-building ‘generateResponses.Rmd’ using rmarkdown + ``` + +# CoreMicrobiomeR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/CoreMicrobiomeR +* Date/Publication: 2024-04-03 20:03:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "CoreMicrobiomeR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘CoreMicrobiomeR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: group_bar_plots + > ### Title: Grouped Bar Plots Based on Sample Size + > ### Aliases: group_bar_plots + > + > ### ** Examples + > + > #To run input data + ... + + top_percentage = 10 # Adjust the percentage as needed for core/non-core OTUs + + ) + Warning encountered during diversity analysis:you have empty rows: their dissimilarities may be + meaningless in method “bray” + > #To run grouped bar plot function + > plot_group_bar <- group_bar_plots(core_1$final_otu_table_bef_filter, + + core_1$final_otu_aft_filter, 10) + Error in pm[[2]] : subscript out of bounds + Calls: group_bar_plots -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# correlationfunnel + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/business-science/correlationfunnel +* Source code: https://github.com/cran/correlationfunnel +* Date/Publication: 2020-06-09 04:40:03 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "correlationfunnel")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dplyr) + + Attaching package: 'dplyr' + + The following object is masked from 'package:testthat': + + ... + ▆ + 1. ├─correlationfunnel::plot_correlation_funnel(...) at test-plot_correlation_funnel.R:23:1 + 2. └─correlationfunnel:::plot_correlation_funnel.data.frame(...) + 3. ├─plotly::ggplotly(g, tooltip = "text") + 4. └─plotly:::ggplotly.ggplot(g, tooltip = "text") + 5. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 3 | SKIP 0 | PASS 17 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘utils’ + All declared Imports should be used. + ``` + +# corrViz + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/corrViz +* Date/Publication: 2023-06-30 11:40:07 UTC +* Number of recursive dependencies: 140 + +Run `revdepcheck::cloud_details(, "corrViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘corrViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: animSolar + > ### Title: animSolar + > ### Aliases: animSolar + > + > ### ** Examples + > + > cm <- cor(mtcars) + ... + All aesthetics have length 1, but the data has 250 rows. + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + Warning in geom_text(data = solar_system, aes(x = 0, y = 0, label = sun), : + All aesthetics have length 1, but the data has 250 rows. + ℹ Please consider using `annotate()` or provide this layer with data containing + a single row. + Error in pm[[2]] : subscript out of bounds + Calls: animSolar -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘corrViz.Rmd’ + ... + > library(corrViz) + + > cm <- cor(mtcars) + + > corrHeatmap(mat = cm, display = "all", reorder = TRUE, + + pal = colorRampPalette(c("darkblue", "white", "darkred"))(100)) + + When sourcing ‘corrViz.R’: + Error: subscript out of bounds + Execution halted + + ‘corrViz.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘corrViz.Rmd’ using rmarkdown + + Quitting from lines 76-81 [heatmap] (corrViz.Rmd) + Error: processing vignette 'corrViz.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘corrViz.Rmd’ + + SUMMARY: processing the following file failed: + ‘corrViz.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.2Mb + sub-directories of 1Mb or more: + doc 6.7Mb + ``` + +# corx + +
+ +* Version: 1.0.7.2 +* GitHub: https://github.com/conig/corx +* Source code: https://github.com/cran/corx +* Date/Publication: 2023-06-16 04:10:02 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "corx")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(corx) + > + > test_check("corx") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 69 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 69 ] + Error: Test failures + Execution halted + ``` + +# cosinor2 + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/amutak/cosinor2 +* Source code: https://github.com/cran/cosinor2 +* Date/Publication: 2018-10-15 16:10:03 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "cosinor2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘cosinor2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cosinor.PR + > ### Title: Percent Rhythm + > ### Aliases: cosinor.PR + > + > ### ** Examples + > + > fit.temperature<-cosinor.lm(Temperature~time(Time), period = 24, data = temperature_zg) + ... + 1 0.9838823 0.9680243 0 + > + > fit.november<-population.cosinor.lm(data = PANAS_november, time = PANAS_time, + + period = 7) + MESOR Amplitude Acrophase + 1 1.435419 0.2662682 -5.544496 + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: population.cosinor.lm ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cosinor2.Rmd’ + ... + Loading required package: cosinor + + > fit.panas.cosinor <- population.cosinor.lm(data = PANAS_november, + + time = PANAS_time, period = 7) + MESOR Amplitude Acrophase + 1 1.435419 0.2662682 -5.544496 + + When sourcing ‘cosinor2.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘cosinor2.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘cosinor2.Rmd’ using rmarkdown + + Quitting from lines 47-48 [unnamed-chunk-2] (cosinor2.Rmd) + Error: processing vignette 'cosinor2.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘cosinor2.Rmd’ + + SUMMARY: processing the following file failed: + ‘cosinor2.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# CoSMoS + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/TycheLab/CoSMoS +* Source code: https://github.com/cran/CoSMoS +* Date/Publication: 2021-05-29 23:20:08 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "CoSMoS")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette.Rmd’ + ... + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + + > precip_ggamma <- analyzeTS(TS = precip, season = "month", + + dist = "ggamma", acsID = "weibull", lag.max = 12) + + > reportTS(aTS = precip_ggamma, method = "dist") + theme_light() + + When sourcing ‘vignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignette.Rmd’ using rmarkdown + ``` + +# countfitteR + +
+ +* Version: 1.4 +* GitHub: https://github.com/BioGenies/countfitteR +* Source code: https://github.com/cran/countfitteR +* Date/Publication: 2020-09-30 21:30:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "countfitteR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(countfitteR) + > + > test_check("countfitteR") + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 34 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('testing.R:45:3'): plot_fit ──────────────────────────────────────── + p$labels[[1]] not equal to "x". + target is NULL, current is character + + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 34 ] + Error: Test failures + Execution halted + ``` + +# coursekata + +
+ +* Version: 0.18.0 +* GitHub: https://github.com/coursekata/coursekata-r +* Source code: https://github.com/cran/coursekata +* Date/Publication: 2024-08-16 20:20:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "coursekata")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘coursekata-Ex.R’ failed + The error most likely occurred in: + + > ### Name: middle + > ### Title: Find a percentage of a distribution + > ### Aliases: middle tails lower upper + > + > ### ** Examples + > + > + ... + > tails(1:10, .5) + [1] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE + > + > sampling_distribution <- do(1000) * mean(rnorm(100, 5, 10)) + > sampling_distribution %>% + + gf_histogram(~mean, data = sampling_distribution, fill = ~ middle(mean, .68)) %>% + + gf_refine(scale_fill_manual(values = c("blue", "coral"))) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(coursekata) + Loading required package: dslabs + Loading required package: fivethirtyeight + Some larger datasets need to be installed separately, like senators and + house_district_forecast. To install these, we recommend you install the + fivethirtyeightdata package by running: + ... + • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-color.svg + • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-facet.svg + • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-color.svg + • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-facet.svg + • gf_model-visual/gf-violin-cond-mod-y-on-y.svg + • gf_model-visual/gf-violin-horizontal-mull-mod-y-on-x.svg + • gf_model-visual/gf-violin-mull-mod-y-on-x-2.svg + • gf_model-visual/gf-violin-null-mod-y-on-y.svg + Error: Test failures + Execution halted + ``` + +# covidcast + +
+ +* Version: 0.5.2 +* GitHub: https://github.com/cmu-delphi/covidcast +* Source code: https://github.com/cran/covidcast +* Date/Publication: 2023-07-12 23:40:06 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "covidcast")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(covidcast) + We encourage COVIDcast API users to register on our mailing list: + https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api + We'll send announcements about new data sources, package updates, + server maintenance, and new features. + > + ... + • plot/default-county-choropleth.svg + • plot/default-hrr-choropleth-with-include.svg + • plot/default-msa-choropleth-with-include.svg + • plot/default-state-choropleth-with-include.svg + • plot/default-state-choropleth-with-range.svg + • plot/state-choropleth-with-no-metadata.svg + • plot/state-line-graph-with-range.svg + • plot/state-line-graph-with-stderrs.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘external-data.Rmd’ + ... + Warning: Metadata for signal mean and standard deviation not available; defaulting to observed mean and standard deviation to set plot range. + Warning in ggplot2::guide_colorbar(title = NULL, horizontal = TRUE, barheight = legend_height, : + Arguments in `...` must be used. + ✖ Problematic argument: + • horizontal = TRUE + ℹ Did you misspell an argument name? + + ... + Error: Rate limit exceeded when fetching data from API anonymously. See the "API keys" section of the `covidcast_signal()` documentation for information on registering for an API key. + ℹ Message from server: + ℹ Rate limit exceeded for anonymous queries. To remove this limit, register a free API key at https://api.delphi.cmu.edu/epidata/admin/registration_form + Execution halted + + ‘correlation-utils.Rmd’ using ‘UTF-8’... OK + ‘covidcast.Rmd’ using ‘UTF-8’... OK + ‘external-data.Rmd’ using ‘UTF-8’... failed + ‘multi-signals.Rmd’ using ‘UTF-8’... OK + ‘plotting-signals.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘correlation-utils.Rmd’ using rmarkdown + --- finished re-building ‘correlation-utils.Rmd’ + + --- re-building ‘covidcast.Rmd’ using rmarkdown + + Quitting from lines 38-45 [unnamed-chunk-1] (covidcast.Rmd) + Error: processing vignette 'covidcast.Rmd' failed with diagnostics: + Rate limit exceeded when fetching data from API anonymously. See the "API keys" section of the `covidcast_signal()` documentation for information on registering for an API key. + ℹ Message from server: + ... + ℹ Message from server: + ℹ Rate limit exceeded for anonymous queries. To remove this limit, register a free API key at https://api.delphi.cmu.edu/epidata/admin/registration_form + --- failed re-building ‘plotting-signals.Rmd’ + + SUMMARY: processing the following files failed: + ‘covidcast.Rmd’ ‘external-data.Rmd’ ‘multi-signals.Rmd’ + ‘plotting-signals.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 20 marked UTF-8 strings + ``` + +# Coxmos + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/BiostatOmics/Coxmos +* Source code: https://github.com/cran/Coxmos +* Date/Publication: 2024-03-25 20:32:38 UTC +* Number of recursive dependencies: 194 + +Run `revdepcheck::cloud_details(, "Coxmos")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Coxmos-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getAutoKM + > ### Title: getAutoKM + > ### Aliases: getAutoKM + > + > ### ** Examples + > + > data("X_proteomic") + ... + > X_train <- X_proteomic[index_train,1:50] + > Y_train <- Y_proteomic[index_train,] + > X_test <- X_proteomic[-index_train,1:50] + > Y_test <- Y_proteomic[-index_train,] + > splsicox.model <- splsicox(X_train, Y_train, n.comp = 2, penalty = 0.5, x.center = TRUE, + + x.scale = TRUE) + > getAutoKM(type = "LP", model = splsicox.model) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: getAutoKM ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Coxmos-MO-pipeline.Rmd’ + ... + + $proteomic + + + > LST_KM_RES_LP <- getAutoKM(type = "LP", model = lst_models$`SB.sPLS-DRCOX`, + + comp = 1:4, top = 10, ori_data = T, BREAKTIME = NULL, only_sig = .... [TRUNCATED] + + ... + Warning in data("Y_proteomic") : data set ‘Y_proteomic’ not found + + > X <- X_proteomic + + When sourcing ‘Coxmos-pipeline.R’: + Error: object 'X_proteomic' not found + Execution halted + + ‘Coxmos-MO-pipeline.Rmd’ using ‘UTF-8’... failed + ‘Coxmos-pipeline.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 2.5Mb + doc 2.9Mb + ``` + +# cpr + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/dewittpe/cpr +* Source code: https://github.com/cran/cpr +* Date/Publication: 2024-02-15 15:40:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "cpr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cpr.Rmd’ + ... + Warning: Removed 25 rows containing missing values or values outside the scale range + (`geom_rug()`). + Warning: Removed 26 rows containing missing values or values outside the scale range + (`geom_rug()`). + Warning: Removed 38 rows containing missing values or values outside the scale range + (`geom_rug()`). + + When sourcing ‘cpr.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘cnr.Rmd’ using ‘UTF-8’... OK + ‘cpr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cnr.Rmd’ using rmarkdown + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘test-bsplineD.R’ + Running ‘test-bsplines.R’ + Running ‘test-btensor.R’ + Running ‘test-build_tensor.R’ + Running ‘test-cn.R’ + Running ‘test-cnr.R’ + Running ‘test-coef_vcov.R’ + Running the tests in ‘tests/test-coef_vcov.R’ failed. + Complete output: + > # Tests for extracting coefficients and vcov matrix from regression fits + ... + + stopifnot(identical(names(COEF_VCOV), c("theta", "coef", "vcov_theta", "vcov"))) + + stopifnot(identical(COEF_VCOV$theta, numeric(0))) + + stopifnot(identical(COEF_VCOV$coef, fixef(fit))) + + stopifnot(identical(COEF_VCOV$vcov_theta, matrix(0)[FALSE, FALSE])) + + stopifnot(identical(COEF_VCOV$vcov, as.matrix(vcov(fit)))) + + }) + Error in initializePtr() : + function 'cholmod_factor_ldetA' not provided by package 'Matrix' + Calls: with ... initialize -> -> initializePtr -> .Call + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + doc 1.6Mb + libs 4.1Mb + ``` + +# cpsvote + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/Reed-EVIC/cpsvote +* Source code: https://github.com/cran/cpsvote +* Date/Publication: 2020-11-05 16:00:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "cpsvote")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘voting.Rmd’ + ... + + .... [TRUNCATED] + + > library(usmap) + + > cps16 %>% as_survey_design(weights = turnout_weight) %>% + + mutate(state = STATE) %>% group_by(state) %>% summarize(turnout = survey_mean(hurach .... [TRUNCATED] + + When sourcing ‘voting.R’: + Error: argument is of length zero + Execution halted + + ‘add-variables.Rmd’ using ‘UTF-8’... OK + ‘background.Rmd’ using ‘UTF-8’... OK + ‘basics.Rmd’ using ‘UTF-8’... OK + ‘voting.Rmd’ using ‘UTF-8’... failed + ``` + +# crimeutils + +
+ +* Version: 0.5.1 +* GitHub: https://github.com/jacobkap/crimeutils +* Source code: https://github.com/cran/crimeutils +* Date/Publication: 2022-12-07 15:10:07 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "crimeutils")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crimeutils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scale_linetype_crim + > ### Title: A set of linetypes + > ### Aliases: scale_linetype_crim + > + > ### ** Examples + > + > ggplot2::ggplot(mtcars, ggplot2::aes(x = mpg, y = hp, linetype = as.character(cyl))) + + + ggplot2::geom_line(size = 1) + + + scale_linetype_crim() + + + theme_crim() + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# crmPack + +
+ +* Version: 1.0.6 +* GitHub: https://github.com/openpharma/crmPack +* Source code: https://github.com/cran/crmPack +* Date/Publication: 2024-06-26 15:00:14 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "crmPack")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crmPack-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DataMixture-class + > ### Title: Class for the data with mixture sharing + > ### Aliases: DataMixture-class .DataMixture + > ### Keywords: classes + > + > ### ** Examples + > + ... + + refDose = 50) + > + > nodata <- Data(doseGrid=doseGrid) + > + > priorSamples <- mcmc(nodata, model, options) + > plot(priorSamples, model, nodata) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘example.Rnw’ + ... + [1] -5.070681 + + > newDLTmodel@phi2 + [1] 1.125107 + + > print(plot(samples, model, data)) + + When sourcing ‘example.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘guidelines.Rmd’ using ‘UTF-8’... OK + ‘example.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘guidelines.Rmd’ using rmarkdown + --- finished re-building ‘guidelines.Rmd’ + + --- re-building ‘example.Rnw’ using Sweave + Loading required package: ggplot2 + Registered S3 method overwritten by 'crmPack': + method from + print.gtable gtable + Type crmPackHelp() to open help browser + ... + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + + --- failed re-building ‘example.Rnw’ + + SUMMARY: processing the following file failed: + ‘example.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# crosshap + +
+ +* Version: 1.4.0 +* GitHub: https://github.com/jacobimarsh/crosshap +* Source code: https://github.com/cran/crosshap +* Date/Publication: 2024-03-31 15:40:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "crosshap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘crosshap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: build_bot_halfeyeplot + > ### Title: Bot hap-pheno raincloud plot + > ### Aliases: build_bot_halfeyeplot + > + > ### ** Examples + > + > + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# ctrialsgov + +
+ +* Version: 0.2.5 +* GitHub: NA +* Source code: https://github.com/cran/ctrialsgov +* Date/Publication: 2021-10-18 16:00:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "ctrialsgov")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ctrialsgov) + > + > test_check("ctrialsgov") + [NCT04553939] ible Local Advanved |Bladder| Cancer + [NCT03517995] of Sulforaphane in |Bladder| Cancer Chemoprevent + [NCT04210479] Comparison of |Bladder| Filling vs. Non-Fil + ... + ▆ + 1. ├─ctrialsgov::ctgov_to_plotly(p) at test-plot.R:12:3 + 2. └─ctrialsgov:::ctgov_to_plotly.ctgov_bar_plot(p) + 3. ├─plotly::ggplotly(p, tooltip = "text") + 4. └─plotly:::ggplotly.ggplot(p, tooltip = "text") + 5. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 6 | SKIP 0 | PASS 43 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1350 marked UTF-8 strings + ``` + +# cubble + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/huizezhang-sherry/cubble +* Source code: https://github.com/cran/cubble +* Date/Publication: 2024-08-27 15:20:02 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "cubble")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cb5match.Rmd’ + ... + > p2 <- ggplot(res_tm_long, aes(x = date, y = matched, + + group = type, color = type)) + geom_line() + facet_wrap(vars(group)) + + + scale_colo .... [TRUNCATED] + + > (p1 | p2) + patchwork::plot_layout(guides = "collect") + + + plot_annotation(tag_levels = "a") & theme(legend.position = "bottom") + + ... + Error: subscript out of bounds + Execution halted + + ‘cb1class.Rmd’ using ‘UTF-8’... OK + ‘cb2create.Rmd’ using ‘UTF-8’... OK + ‘cb3tsibblesf.Rmd’ using ‘UTF-8’... OK + ‘cb4glyph.Rmd’ using ‘UTF-8’... OK + ‘cb5match.Rmd’ using ‘UTF-8’... failed + ‘cb6interactive.Rmd’ using ‘UTF-8’... failed + ‘cb7misc.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cb1class.Rmd’ using rmarkdown + --- finished re-building ‘cb1class.Rmd’ + + --- re-building ‘cb2create.Rmd’ using rmarkdown + --- finished re-building ‘cb2create.Rmd’ + + --- re-building ‘cb3tsibblesf.Rmd’ using rmarkdown + --- finished re-building ‘cb3tsibblesf.Rmd’ + + --- re-building ‘cb4glyph.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + data 3.0Mb + doc 1.4Mb + ``` + +# curtailment + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/martinlaw/curtailment +* Source code: https://github.com/cran/curtailment +* Date/Publication: 2023-10-25 15:50:04 UTC +* Number of recursive dependencies: 36 + +Run `revdepcheck::cloud_details(, "curtailment")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘curtailment-Ex.R’ failed + The error most likely occurred in: + + > ### Name: drawDiagramGeneric + > ### Title: drawDiagramGeneric + > ### Aliases: drawDiagramGeneric + > + > ### ** Examples + > + > go <- cbind(6:8, rep(8,3)) + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +# dabestr + +
+ +* Version: 2023.9.12 +* GitHub: https://github.com/ACCLAB/dabestr +* Source code: https://github.com/cran/dabestr +* Date/Publication: 2023-10-13 11:50:06 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "dabestr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tutorial_deltadelta.Rmd’ + ... + > paired_delta2.mean_diff <- load(df, x = Treatment, + + y = Measurement, experiment = Genotype, colour = Rep, delta2 = TRUE, + + idx = list(c(" ..." ... [TRUNCATED] + + > dabest_plot(paired_delta2.mean_diff, raw_marker_size = 0.5, + + raw_marker_alpha = 0.3) + + ... + Error: argument is of length zero + Execution halted + + ‘datasets.Rmd’ using ‘UTF-8’... OK + ‘plot_aesthetics.Rmd’ using ‘UTF-8’... OK + ‘tutorial_basics.Rmd’ using ‘UTF-8’... OK + ‘tutorial_deltadelta.Rmd’ using ‘UTF-8’... failed + ‘tutorial_minimeta.Rmd’ using ‘UTF-8’... failed + ‘tutorial_proportion_plots.Rmd’ using ‘UTF-8’... OK + ‘tutorial_repeated_measures.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘datasets.Rmd’ using rmarkdown + --- finished re-building ‘datasets.Rmd’ + + --- re-building ‘plot_aesthetics.Rmd’ using rmarkdown + ``` + +# DAISIEprep + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/joshwlambert/DAISIEprep +* Source code: https://github.com/cran/DAISIEprep +* Date/Publication: 2024-04-02 11:30:06 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "DAISIEprep")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(DAISIEprep) + > + > test_check("DAISIEprep") + [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2211 ] + + ══ Skipped tests (14) ══════════════════════════════════════════════════════════ + ... + ── Failure ('test-plot_phylod.R:8:3'): plot_phylod runs silent without error ─── + `plot_phylod(phylod = phylod, node_pies = FALSE)` produced warnings. + ── Failure ('test-plot_phylod.R:13:3'): plot_phylod runs silent without error ── + `plot_phylod(phylod = phylod, node_pies = TRUE)` produced warnings. + ── Failure ('test-plot_phylod.R:18:3'): plot_phylod runs silent without error ── + `plot_phylod(phylod = phylod, node_pies = TRUE)` produced warnings. + + [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2211 ] + Error: Test failures + Execution halted + ``` + +# dbmss + +
+ +* Version: 2.9-2 +* GitHub: https://github.com/EricMarcon/dbmss +* Source code: https://github.com/cran/dbmss +* Date/Publication: 2024-08-24 11:00:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "dbmss")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dbmss-Ex.R’ failed + The error most likely occurred in: + + > ### Name: DEnvelope + > ### Title: Estimation of the confidence envelope of the D function under + > ### its null hypothesis + > ### Aliases: DEnvelope + > + > ### ** Examples + > + ... + > r <- 0:30 + > NumberOfSimulations <- 20 + > Alpha <- .05 + > # Plot the envelope (after normalization by pi.r^2) + > autoplot(DEnvelope(X, r, NumberOfSimulations, Alpha, + + "V. Americana", "Q. Rosea", Intertype = TRUE), ./(pi*r^2) ~ r) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dbmss.Rmd’ + ... + + > autoplot(paracou16, labelSize = expression("Basal area (" ~ + + cm^2 ~ ")"), labelColor = "Species") + + > autoplot(Mhat(paracou16, ReferenceType = "V. Americana", + + NeighborType = "Q. Rosea"), main = "") + + When sourcing ‘dbmss.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘dbmss.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dbmss.Rmd’ using rmarkdown + ``` + +# deeptime + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/willgearty/deeptime +* Source code: https://github.com/cran/deeptime +* Date/Publication: 2024-08-19 07:00:43 UTC +* Number of recursive dependencies: 197 + +Run `revdepcheck::cloud_details(, "deeptime")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(deeptime) + > + > test_check("deeptime") + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Scale for y is already present. + ... + • patterns/geo-pattern2-new.svg + • patterns/scale-fill-geopattern-labels-new.svg + • patterns/scale-fill-geopattern-limits-new.svg + • patterns/scale-fill-geopattern-na-new.svg + • patterns/scale-fill-geopattern-na2-new.svg + • points_range/geom-points-range-aes-new.svg + • points_range/geom-points-range-bg-new.svg + • points_range/geom-points-range-h-new.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘coord_geo.Rmd’ + ... + + y = n)) + scale_x_reverse("Age (Ma)") + ylab("Coral Genera") + + + coord_geo(xlim = .... [TRUNCATED] + + > ggplot(coral_div) + geom_line(aes(x = stage_age, y = n)) + + + scale_x_reverse("Age (Ma)") + ylab("Coral Genera") + coord_geo(dat = "periods", + + .... [TRUNCATED] + + ... + Error: argument is of length zero + Execution halted + + ‘coord.Rmd’ using ‘UTF-8’... OK + ‘coord_geo.Rmd’ using ‘UTF-8’... failed + ‘geo.Rmd’ using ‘UTF-8’... OK + ‘ggarrange2.Rmd’ using ‘UTF-8’... OK + ‘phylogenies.Rmd’ using ‘UTF-8’... OK + ‘time.Rmd’ using ‘UTF-8’... failed + ‘traits.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘coord.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + R 2.8Mb + doc 1.8Mb + help 1.1Mb + ``` + +# descriptio + +
+ +* Version: 1.3 +* GitHub: https://github.com/nicolas-robette/descriptio +* Source code: https://github.com/cran/descriptio +* Date/Publication: 2024-03-07 11:00:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "descriptio")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘descriptio-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggassoc_crosstab + > ### Title: Proportional area plot + > ### Aliases: ggassoc_crosstab + > ### Keywords: multivariate aplot + > + > ### ** Examples + > + > data(Movies) + > ggassoc_crosstab(data=Movies, mapping=ggplot2::aes(Genre, Country)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggassoc_crosstab ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘FactoMineR’, ‘vcd’ + ``` + +# directlabels + +
+ +* Version: 2024.1.21 +* GitHub: https://github.com/tdhock/directlabels +* Source code: https://github.com/cran/directlabels +* Date/Publication: 2024-01-24 19:20:07 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "directlabels")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘examples.Rmd’ + ... + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + `geom_smooth()` using method = 'loess' and formula = 'y ~ x' + + When sourcing ‘examples.R’: + Error: Problem while computing stat. + ℹ Error occurred in the 3rd layer. + Caused by error in `get()`: + ! object 'last.qp' of mode 'function' was not found + Execution halted + + ‘examples.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘examples.Rmd’ using knitr + ``` + +# disto + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/talegari/disto +* Source code: https://github.com/cran/disto +* Date/Publication: 2018-08-02 12:50:02 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "disto")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘disto-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.disto + > ### Title: Plot a disto object + > ### Aliases: plot.disto + > + > ### ** Examples + > + > temp <- stats::dist(iris[,1:4]) + ... + > dio <- disto(objectname = "temp") + > plot(dio, type = "heatmap") + > plot(dio, type = "dendrogram") + Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the factoextra package. + Please report the issue at . + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette_disto.Rmd’ + ... + + > plot(dio, type = "dendrogram") + Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the factoextra package. + Please report the issue at . + + When sourcing ‘vignette_disto.R’: + Error: argument is of length zero + Execution halted + + ‘vignette_disto.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘vignette_disto.Rmd’ using rmarkdown + + Quitting from lines 42-72 [unnamed-chunk-1] (vignette_disto.Rmd) + Error: processing vignette 'vignette_disto.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘vignette_disto.Rmd’ + + SUMMARY: processing the following file failed: + ‘vignette_disto.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dplyr’ ‘proxy’ + All declared Imports should be used. + ``` + +# distributional + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/mitchelloharawild/distributional +* Source code: https://github.com/cran/distributional +* Date/Publication: 2024-02-07 13:30:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "distributional")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘distributional-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dist_truncated + > ### Title: Truncate a distribution + > ### Aliases: dist_truncated + > + > ### ** Examples + > + > dist <- dist_truncated(dist_normal(2,1), lower = 0) + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# dittoViz + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/dtm2451/dittoViz +* Source code: https://github.com/cran/dittoViz +* Date/Publication: 2024-02-02 00:00:12 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "dittoViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dittoViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: barPlot + > ### Title: Outputs a stacked bar plot to show the percent composition of + > ### samples, groups, clusters, or other groupings + > ### Aliases: barPlot + > + > ### ** Examples + > + ... + 15 3 D 12 32 0.3750000 + 16 4 D 8 32 0.2500000 + > # through hovering the cursor over the relevant parts of the plot + > if (requireNamespace("plotly", quietly = TRUE)) { + + barPlot(example_df, "clustering", group.by = "groups", + + do.hover = TRUE) + + } + Error in pm[[2]] : subscript out of bounds + Calls: barPlot -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dittoViz) + Loading required package: ggplot2 + > test_check("dittoViz") + [ FAIL 89 | WARN 2 | SKIP 0 | PASS 63 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 6. └─dittoViz:::.yPlot_add_data_y_direction(...) + 7. └─ggplot2:::`+.gg`(p, do.call(geom_boxplot, boxplot.args)) + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 89 | WARN 2 | SKIP 0 | PASS 63 ] + Error: Test failures + Execution halted + ``` + +# dotwhisker + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/fsolt/dotwhisker +* Source code: https://github.com/cran/dotwhisker +* Date/Publication: 2024-06-07 12:20:06 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "dotwhisker")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘dotwhisker-Ex.R’ failed + The error most likely occurred in: + + > ### Name: small_multiple + > ### Title: Generate a 'Small Multiple' Plot of Regression Results + > ### Aliases: small_multiple + > + > ### ** Examples + > + > library(broom) + ... + + m[[i]] <- update(m[[i-1]], paste(". ~ . +", ordered_vars[i])) + + m123456_df <- rbind(m123456_df, m[[i]] %>% tidy %>% by_2sd(mtcars) %>% + + mutate(model = paste("Model", i))) + + } + > + > # Generate a 'small multiple' plot + > small_multiple(m123456_df) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: small_multiple ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dotwhisker-vignette.Rmd’ + ... + + wt = "Weight", cyl = "Cylinders", disp = "Displacement", + + .... [TRUNCATED] + + > small_multiple(m123456_df) + theme_bw(base_size = 4) + + + ylab("Coefficient Estimate") + geom_hline(yintercept = 0, + + colour = "grey60", li .... [TRUNCATED] + + ... + + > small_multiple(results_df, show_stats = FALSE) + scale_x_discrete(limits = model_names) + + + theme_bw() + ylab("Coefficient Estimate") + geom_hl .... [TRUNCATED] + + When sourcing ‘kl2007_examples.R’: + Error: argument is of length zero + Execution halted + + ‘dotwhisker-vignette.Rmd’ using ‘UTF-8’... failed + ‘kl2007_examples.Rmd’ using ‘ASCII’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dotwhisker-vignette.Rmd’ using rmarkdown + ``` + +# DRomics + +
+ +* Version: 2.5-2 +* GitHub: https://github.com/aursiber/DRomics +* Source code: https://github.com/cran/DRomics +* Date/Publication: 2024-01-31 09:30:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "DRomics")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘DRomics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PCAdataplot + > ### Title: Performs and plots the results of a PCA on omic data + > ### Aliases: PCAdataplot + > + > ### ** Examples + > + > + ... + Number of items: 100 + Identifiers of the first 20 items: + [1] "1" "2" "3" "4" "5.1" "6.1" "7.1" "8.1" "9.1" "10.1" + [11] "11.1" "12.1" "13.1" "14.1" "15" "16.1" "17.1" "18.1" "19.1" "20.1" + Data were normalized between arrays using the following method: cyclicloess + > plot(o) + > PCAdataplot(o) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PCAdataplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘DRomics_vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘DRomics_vignette.Rmd’ + ... + [16] "ENSDARG00000100660" "ENSDARG00000113107" "ENSDARG00000099787" + [19] "ENSDARG00000112451" "ENSDARG00000070546" + Data were normalized with respect to library size and tranformed using + the following method: rlog + + > PCAdataplot(o, batch = zebraf$batch) + theme_bw() + + When sourcing ‘DRomics_vignette.R’: + Error: argument is of length zero + Execution halted + + ‘DRomics_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + doc 2.9Mb + ``` + +# dtwclust + +
+ +* Version: 6.0.0 +* GitHub: https://github.com/asardaes/dtwclust +* Source code: https://github.com/cran/dtwclust +* Date/Publication: 2024-07-23 08:50:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "dtwclust")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(dtwclust) + Loading required package: proxy + + Attaching package: 'proxy' + + The following objects are masked from 'package:stats': + + ... + 7. └─dtwclust (local) .local(x, y = y, ...) + 8. └─ggplot2:::`+.gg`(gg, do_call(ggrepel::geom_label_repel, labels)) + 9. └─ggplot2:::add_ggplot(e1, e2, e2name) + 10. ├─ggplot2::ggplot_add(object, p, objectname) + 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 0 | SKIP 15 | PASS 1930 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + --- re-building ‘parallelization-considerations.Rmd’ using rmarkdown_notangle + --- finished re-building ‘parallelization-considerations.Rmd’ + + --- re-building ‘timing-experiments.Rmd’ using rmarkdown_notangle + ``` + +* checking installed package size ... NOTE + ``` + installed size is 15.5Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 2.1Mb + libs 11.1Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# duke + +
+ +* Version: 0.0.3 +* GitHub: https://github.com/aidangildea/duke +* Source code: https://github.com/cran/duke +* Date/Publication: 2023-12-15 21:50:16 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "duke")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 2. │ └─testthat:::expect_condition_matching(...) + 3. │ └─testthat:::quasi_capture(...) + 4. │ ├─testthat (local) .capture(...) + 5. │ │ └─base::withCallingHandlers(...) + 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. └─testthat::expect_equal(ggplot2::layer_data(p3)$fill[9], "#B5B5B5") + + [ FAIL 1 | WARN 9 | SKIP 0 | PASS 27 ] + Error: Test failures + Execution halted + ``` + +# easysurv + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/Maple-Health-Group/easysurv +* Source code: https://github.com/cran/easysurv +* Date/Publication: 2024-06-21 10:30:06 UTC +* Number of recursive dependencies: 156 + +Run `revdepcheck::cloud_details(, "easysurv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘easysurv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get_km + > ### Title: Generate Kaplan-Meier estimates + > ### Aliases: get_km + > + > ### ** Examples + > + > km_results <- get_km( + ... + Poor Poor 228 145 3.101736 0.1772520 2.183562 1.978082 2.619178 + Median follow-up + Good 4.452055 + Medium 4.712329 + Poor 4.115068 + + Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = "{n.risk}", : + argument "risktable_height" is missing, with no default + Calls: ... ggsurvfit_build -> -> .construct_risktable + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘easysurv.Rmd’ + ... + Median follow-up + Tab+Vis 2.217659 + Tab->Vis 2.220397 + Tab 2.308008 + Vis 2.198494 + + + When sourcing ‘easysurv.R’: + Error: argument "risktable_height" is missing, with no default + Execution halted + + ‘easysurv.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘easysurv.Rmd’ using rmarkdown + + Quitting from lines 149-157 [km] (easysurv.Rmd) + Error: processing vignette 'easysurv.Rmd' failed with diagnostics: + argument "risktable_height" is missing, with no default + --- failed re-building ‘easysurv.Rmd’ + + SUMMARY: processing the following file failed: + ‘easysurv.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# EGAnet + +
+ +* Version: 2.0.7 +* GitHub: https://github.com/hfgolino/EGAnet +* Source code: https://github.com/cran/EGAnet +* Date/Publication: 2024-09-02 20:00:01 UTC +* Number of recursive dependencies: 190 + +Run `revdepcheck::cloud_details(, "EGAnet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EGAnet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dimensionStability + > ### Title: Dimension Stability Statistics from 'bootEGA' + > ### Aliases: dimensionStability + > + > ### ** Examples + > + > # Load data + ... + 16. │ └─e1 %+% e2 + 17. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 18. │ ├─ggplot2::ggplot_add(object, p, objectname) + 19. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 20. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 21. └─base::.handleSimpleError(...) + 22. └─purrr (local) h(simpleError(msg, call)) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 3.5Mb + ``` + +# EGM + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/shah-in-boots/EGM +* Source code: https://github.com/cran/EGM +* Date/Publication: 2024-05-23 16:10:05 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "EGM")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(EGM) + Loading required package: vctrs + Loading required package: data.table + > EGM::set_wfdb_path("/usr/local/bin") + > + > test_check("EGM") + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-ggm.R:63:2'): theming works ────────────────────────────────── + g$labels$x (`actual`) not equal to "sample" (`expected`). + + `actual` is NULL + `expected` is a character vector ('sample') + + [ FAIL 1 | WARN 0 | SKIP 19 | PASS 43 ] + Error: Test failures + Execution halted + ``` + +# emmeans + +
+ +* Version: 1.10.4 +* GitHub: https://github.com/rvlenth/emmeans +* Source code: https://github.com/cran/emmeans +* Date/Publication: 2024-08-21 03:00:01 UTC +* Number of recursive dependencies: 159 + +Run `revdepcheck::cloud_details(, "emmeans")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘emmeans-Ex.R’ failed + The error most likely occurred in: + + > ### Name: auto.noise + > ### Title: Auto Pollution Filter Noise + > ### Aliases: auto.noise + > ### Keywords: datasets + > + > ### ** Examples + > + > # (Based on belief that noise/10 is in decibel units) + > noise.lm <- lm(noise/10 ~ size * type * side, data = auto.noise) + > + > # Interaction plot of predictions + > emmip(noise.lm, type ~ size | side) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: emmip ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basics.Rmd’ + ... + 'emmGrid' object with variables: + source = fish, soy, skim + percent = 9, 12, 15, 18 + Transformation: “inverse” + + > emmip(RG4, source ~ percent, style = "factor") + + ... + ‘messy-data.Rmd’ using ‘UTF-8’... failed + ‘models.Rmd’ using ‘UTF-8’... OK + ‘predictions.Rmd’ using ‘UTF-8’... failed + ‘re-engineering-clds.rmd’ using ‘UTF-8’... OK + ‘sophisticated.Rmd’ using ‘UTF-8’... failed + ‘transformations.Rmd’ using ‘UTF-8’... failed + ‘utilities.Rmd’ using ‘UTF-8’... OK + ‘vignette-topics.Rmd’ using ‘UTF-8’... OK + ‘xplanations.Rmd’ using ‘UTF-8’... failed + ‘xtending.Rmd’ using ‘UTF-8’... OK + ``` + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'CARBayes', 'coxme', 'gee', 'geepack', 'MCMCglmm', 'MCMCpack', + 'mice', 'pscl', 'rstanarm', 'sommer' + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘AQuickStart.Rmd’ using rmarkdown + --- finished re-building ‘AQuickStart.Rmd’ + + --- re-building ‘FAQs.Rmd’ using rmarkdown + --- finished re-building ‘FAQs.Rmd’ + + --- re-building ‘basics.Rmd’ using rmarkdown + + Quitting from lines 260-262 [unnamed-chunk-13] (basics.Rmd) + Error: processing vignette 'basics.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘basics.Rmd’ + + --- re-building ‘comparisons.Rmd’ using rmarkdown + ``` + +# EMMIXmfa + +
+ +* Version: 2.0.14 +* GitHub: https://github.com/suren-rathnayake/EMMIXmfa +* Source code: https://github.com/cran/EMMIXmfa +* Date/Publication: 2024-01-25 20:30:02 UTC +* Number of recursive dependencies: 59 + +Run `revdepcheck::cloud_details(, "EMMIXmfa")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EMMIXmfa-Ex.R’ failed + The error most likely occurred in: + + > ### Name: factor_scores + > ### Title: Computes Factor Scores + > ### Aliases: factor_scores factor_scores.mcfa factor_scores.mctfa + > ### plot.emmix + > ### Keywords: cluster multivariate models + > + > ### ** Examples + ... + > Y <- iris[-c(sel_subset), -5] + > Y <- as.matrix(Y) + > clust <- predict(model, Y) + > + > fa_scores <- factor_scores(model, Y) + > # Visualizing new data in factor space + > plot_factors(fa_scores, type = "Umean", clust = clust) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_factors ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# entropart + +
+ +* Version: 1.6-15 +* GitHub: https://github.com/EricMarcon/entropart +* Source code: https://github.com/cran/entropart +* Date/Publication: 2024-08-26 19:30:09 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "entropart")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘entropart-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Accumulation + > ### Title: Diversity accumulation. + > ### Aliases: DivAC EntAC as.AccumCurve is.AccumCurve autoplot.AccumCurve + > ### plot.AccumCurve + > + > ### ** Examples + > + ... + 11. │ └─base::withCallingHandlers(...) + 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. └─l$compute_geom_2(d, theme = plot$theme) + 14. └─ggplot2 (local) compute_geom_2(..., self = self) + 15. └─self$geom$use_defaults(...) + 16. └─ggplot2 (local) use_defaults(..., self = self) + 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘entropart.Rmd’ + ... + + > autoplot(Abd18, Distribution = "lnorm") + + When sourcing ‘entropart.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (149). + ✖ Fix the following mappings: `shape`, `colour`, and `size`. + Execution halted + + ‘entropart.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘entropart.Rmd’ using rmarkdown + + Quitting from lines 53-55 [PlotN18] (entropart.Rmd) + Error: processing vignette 'entropart.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `check_aesthetics()`: + ! Aesthetics must be either length 1 or the same as the data (149). + ✖ Fix the following mappings: `shape`, `colour`, and `size`. + --- failed re-building ‘entropart.Rmd’ + + SUMMARY: processing the following file failed: + ‘entropart.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# EnvStats + +
+ +* Version: 3.0.0 +* GitHub: https://github.com/alexkowa/EnvStats +* Source code: https://github.com/cran/EnvStats +* Date/Publication: 2024-08-24 23:10:05 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "EnvStats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EnvStats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_stripchart + > ### Title: 1-D Scatter Plots with Confidence Intervals Using ggplot2 + > ### Aliases: geom_stripchart + > ### Keywords: hplot htest + > + > ### ** Examples + > + ... + > + > p + geom_stripchart() + + + labs(x = "Number of Cylinders", y = "Miles per Gallon") + Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0. + ℹ Please use the `fun` argument instead. + ℹ The deprecated feature was likely used in the EnvStats package. + Please report the issue to the authors. + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.8Mb + sub-directories of 1Mb or more: + R 3.5Mb + help 3.5Mb + ``` + +# epiCleanr + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/truenomad/epiCleanr +* Source code: https://github.com/cran/epiCleanr +* Date/Publication: 2023-09-28 12:20:05 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "epiCleanr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘epiCleanr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: handle_outliers + > ### Title: Detect and Handle Outliers in Dataset + > ### Aliases: handle_outliers + > + > ### ** Examples + > + > + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + doc 2.9Mb + help 2.5Mb + ``` + +# epiphy + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/chgigot/epiphy +* Source code: https://github.com/cran/epiphy +* Date/Publication: 2023-11-16 11:20:10 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "epiphy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘epiphy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clump + > ### Title: Regroup observational data into even clumps of individuals. + > ### Aliases: clump clump.intensity + > + > ### ** Examples + > + > my_incidence <- incidence(tomato_tswv$field_1929) + ... + 18. │ └─ggplot2 (local) setup_params(...) + 19. │ └─ggplot2:::make_summary_fun(...) + 20. │ └─rlang::as_function(fun.data) + 21. │ └─base::get(x, envir = env, mode = "function") + 22. └─base::.handleSimpleError(...) + 23. └─rlang (local) h(simpleError(msg, call)) + 24. └─handlers[[1L]](cnd) + 25. └─cli::cli_abort(...) + 26. └─rlang::abort(...) + Execution halted + ``` + +# EQUALSTATS + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/EQUALSTATS +* Date/Publication: 2024-09-06 16:10:15 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "EQUALSTATS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EQUALSTATS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: function.Survival_Analysis + > ### Title: Perform Survival Analysis + > ### Aliases: function.Survival_Analysis + > + > ### ** Examples + > + > # Create simulated data #### + ... + > rv$second_menu_choice <- NA + > rv$entry[[1]] <- "Admission to care home" + > rv$entry[[2]] <- "Follow-up" + > rv$entry[[3]] <- "Treatment" + > # Final function #### + > Results <- function.Survival_Analysis(Predefined_lists, rv) + Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", : + argument "risktable_height" is missing, with no default + Calls: function.Survival_Analysis + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘lmerTest’ + ``` + +# ergm.multi + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/statnet/ergm.multi +* Source code: https://github.com/cran/ergm.multi +* Date/Publication: 2024-02-20 23:20:05 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "ergm.multi")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ergm.multi-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gofN + > ### Title: Linear model diagnostics for multinetwork linear models + > ### Aliases: gofN [.gofN augment.gofN summary.gofN + > + > ### ** Examples + > + > data(samplk) + ... + > + > ### If 'ggplot2' and 'ggrepel' are installed, illustrate the autoplot() method. + > if(require("ggplot2") && requireNamespace("ggrepel")){ + + autoplot(fit.gof) + + } + Loading required package: ggplot2 + Loading required namespace: ggrepel + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Goeyvaerts_reproduction.Rmd’ + ... + [1] 0.9763295 + + + + > autoplot(gof.wd) + Loading required namespace: ggrepel + + When sourcing ‘Goeyvaerts_reproduction.R’: + Error: argument is of length zero + Execution halted + + ‘Goeyvaerts_reproduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Goeyvaerts_reproduction.Rmd’ using rmarkdown + + Quitting from lines 157-158 [unnamed-chunk-16] (Goeyvaerts_reproduction.Rmd) + Error: processing vignette 'Goeyvaerts_reproduction.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Goeyvaerts_reproduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘Goeyvaerts_reproduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# esci + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/rcalinjageman/esci +* Source code: https://github.com/cran/esci +* Date/Publication: 2024-07-08 21:40:10 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "esci")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘esci-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estimate_mdiff_2x2_between + > ### Title: Estimates for a 2x2 between-subjects design with a continuous + > ### outcome variable + > ### Aliases: estimate_mdiff_2x2_between + > + > ### ** Examples + > + ... + + estimates_from_summary$interaction, + + effect_size = "mean" + + ) + Warning: Using size for a discrete variable is not advised. + Warning: Using alpha for a discrete variable is not advised. + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(esci) + > + > test_check("esci") + Loading required package: Matrix + Loading required package: metadat + Loading required package: numDeriv + ... + 17. │ └─self$geom$use_defaults(...) + 18. └─base::.handleSimpleError(...) + 19. └─rlang (local) h(simpleError(msg, call)) + 20. └─handlers[[1L]](cnd) + 21. └─cli::cli_abort(...) + 22. └─rlang::abort(...) + + [ FAIL 14 | WARN 0 | SKIP 0 | PASS 3182 ] + Error: Test failures + Execution halted + ``` + +# evalITR + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/MichaelLLi/evalITR +* Source code: https://github.com/cran/evalITR +* Date/Publication: 2023-08-25 23:10:06 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "evalITR")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cv_multiple_alg.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cv_multiple_alg.Rmd’ + ... + intersect, setdiff, setequal, union + + + > load("../data/star.rda") + Warning in readChar(con, 5L, useBytes = TRUE) : + cannot open compressed file '../data/star.rda', probable reason 'No such file or directory' + + ... + Execution halted + + ‘cv_multiple_alg.Rmd’ using ‘UTF-8’... failed + ‘cv_single_alg.Rmd’ using ‘UTF-8’... failed + ‘install.Rmd’ using ‘UTF-8’... OK + ‘paper_alg1.Rmd’ using ‘UTF-8’... OK + ‘sample_split.Rmd’ using ‘UTF-8’... failed + ‘sample_split_caret.Rmd’ using ‘UTF-8’... failed + ‘user_itr.Rmd’ using ‘UTF-8’... failed + ‘user_itr_algs.Rmd’ using ‘UTF-8’... failed + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘forcats’ ‘rqPen’ ‘utils’ + All declared Imports should be used. + ``` + +# eventstudyr + +
+ +* Version: 1.1.3 +* GitHub: https://github.com/JMSLab/eventstudyr +* Source code: https://github.com/cran/eventstudyr +* Date/Publication: 2024-03-04 15:00:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "eventstudyr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(eventstudyr) + > + > test_check("eventstudyr") + Defaulting to strongest lead of differenced policy variable: proxyIV = z_fd_lead3. To specify a different proxyIV use the proxyIV argument. + Defaulting to strongest lead of differenced policy variable: proxyIV = z_fd_lead3. To specify a different proxyIV use the proxyIV argument. + Defaulting to strongest lead of differenced policy variable: proxyIV = z_fd_lead3. To specify a different proxyIV use the proxyIV argument. + ... + `expected` is a character vector ('ci_lower') + ── Failure ('test-EventStudyPlot.R:128:5'): confidence intervals are appropriately present or absent ── + p_ci$labels$ymax (`actual`) not equal to "ci_upper" (`expected`). + + `actual` is NULL + `expected` is a character vector ('ci_upper') + + [ FAIL 6 | WARN 0 | SKIP 0 | PASS 258 ] + Error: Test failures + Execution halted + ``` + +# EvoPhylo + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/tiago-simoes/EvoPhylo +* Source code: https://github.com/cran/EvoPhylo +* Date/Publication: 2022-11-03 17:00:02 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "EvoPhylo")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘EvoPhylo-Ex.R’ failed + The error most likely occurred in: + + > ### Name: make_clusters + > ### Title: Estimate and plot character partitions + > ### Aliases: make_clusters plot.cluster_df + > + > ### ** Examples + > + > # See vignette("char-part") for how to use this + ... + > # tSNE (3 dimensions; default is 2) + > cluster_df_tsne <- make_clusters(Dmatrix, k = 3, tsne = TRUE, + + tsne_dim = 2) + > + > # Plot clusters, plots divided into 2 rows, and increasing + > # overlap of text labels (default = 10) + > plot(cluster_df_tsne, nrow = 2, max.overlaps = 20) + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘char-part.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘char-part.Rmd’ + ... + + collapse = TRUE, dpi = 300) + + > devtools::load_all(".") + + When sourcing ‘char-part.R’: + Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in + '/tmp/Rtmp6FtfyP/file1a7972246c9b/vignettes'. + ... + ℹ Are you in your project directory and does your project have a 'DESCRIPTION' + file? + Execution halted + + ‘char-part.Rmd’ using ‘UTF-8’... failed + ‘data_treatment.Rmd’ using ‘UTF-8’... OK + ‘fbd-params.Rmd’ using ‘UTF-8’... failed + ‘offset_handling.Rmd’ using ‘UTF-8’... failed + ‘rates-selection_BEAST2.Rmd’ using ‘UTF-8’... failed + ‘rates-selection_MrBayes.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + data 2.5Mb + doc 1.6Mb + extdata 2.4Mb + ``` + +# expirest + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/piusdahinden/expirest +* Source code: https://github.com/cran/expirest +* Date/Publication: 2024-03-25 16:30:02 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "expirest")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(expirest) + > + > test_check("expirest") + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 1122 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + ── Failure ('test-plot_expirest_wisle.R:260:3'): plot_expirest_wisle_succeeds ── + tmp4l2[["Graph"]]$labels has length 0, not length 8. + ── Failure ('test-plot_expirest_wisle.R:264:3'): plot_expirest_wisle_succeeds ── + tmp4b1[["Graph"]]$labels has length 0, not length 5. + ── Failure ('test-plot_expirest_wisle.R:269:3'): plot_expirest_wisle_succeeds ── + tmp4b2[["Graph"]]$labels has length 0, not length 5. + + [ FAIL 9 | WARN 0 | SKIP 0 | PASS 1122 ] + Error: Test failures + Execution halted + ``` + +# explainer + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/PERSIMUNE/explainer +* Source code: https://github.com/cran/explainer +* Date/Publication: 2024-04-18 09:00:02 UTC +* Number of recursive dependencies: 183 + +Run `revdepcheck::cloud_details(, "explainer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘explainer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: eDecisionCurve + > ### Title: Decision Curve Plot + > ### Aliases: eDecisionCurve + > + > ### ** Examples + > + > library("explainer") + ... + > mylrn$train(maintask, splits$train) + > myplot <- eDecisionCurve( + + task = maintask, + + trained_model = mylrn, + + splits = splits, + + seed = seed + + ) + Error in pm[[2]] : subscript out of bounds + Calls: eDecisionCurve -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘ggpmisc’ + All declared Imports should be used. + ``` + +# exuber + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/kvasilopoulos/exuber +* Source code: https://github.com/cran/exuber +* Date/Publication: 2023-03-22 23:10:02 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "exuber")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘exuber.Rmd’ + ... + 370 1 1 1 0 + 371 1 1 0 0 + 372 1 1 0 0 + + > autoplot(est_stocks) + Using `radf_crit` for `cv`. + + ... + + > autoplot(estimation, crit_values) + + When sourcing ‘plotting.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘exuber.Rmd’ using ‘UTF-8’... failed + ‘plotting.Rmd’ using ‘UTF-8’... failed + ‘simulation.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘exuber.Rmd’ using rmarkdown + + Quitting from lines 73-74 [plot-radf] (exuber.Rmd) + Error: processing vignette 'exuber.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘exuber.Rmd’ + + --- re-building ‘plotting.Rmd’ using rmarkdown + + Quitting from lines 58-59 [autoplot-basic] (plotting.Rmd) + Error: processing vignette 'plotting.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘plotting.Rmd’ + + --- re-building ‘simulation.Rmd’ using rmarkdown + ``` + +# ezEDA + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/kviswana/ezEDA +* Source code: https://github.com/cran/ezEDA +* Date/Publication: 2021-06-29 04:40:10 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "ezEDA")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ezEDA) + > + > test_check("ezEDA") + [ FAIL 22 | WARN 0 | SKIP 0 | PASS 57 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + ── Error ('test_two_measures_relationship.R:19:3'): y axis is labeled 'hwy' ──── + Error in `expect_match(p$labels$y, "hwy")`: is.character(act$val) is not TRUE + Backtrace: + ▆ + 1. └─testthat::expect_match(p$labels$y, "hwy") at test_two_measures_relationship.R:19:3 + 2. └─base::stopifnot(is.character(act$val)) + + [ FAIL 22 | WARN 0 | SKIP 0 | PASS 57 ] + Error: Test failures + Execution halted + ``` + +# ezplot + +
+ +* Version: 0.7.13 +* GitHub: NA +* Source code: https://github.com/cran/ezplot +* Date/Publication: 2024-01-28 11:30:05 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "ezplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ezplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: model_plot + > ### Title: model_plot + > ### Aliases: model_plot + > + > ### ** Examples + > + > y = rnorm(26) + > df = data.frame(ID = 1:26, actual = y + rnorm(26), fitted = y, id = letters) + > model_plot(df, "ID", "actual", "fitted") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# fable.prophet + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/mitchelloharawild/fable.prophet +* Source code: https://github.com/cran/fable.prophet +* Date/Publication: 2020-08-20 09:30:03 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "fable.prophet")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘intro.Rmd’ + ... + 9 Domestic mdl 2019 Dec sample[5000] 5338093. + 10 Domestic mdl 2020 Jan sample[5000] 4888643. + # ℹ 62 more rows + + > fc %>% autoplot(lax_passengers) + + When sourcing ‘intro.R’: + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL + Execution halted + + ‘intro.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘intro.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# fabletools + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/tidyverts/fabletools +* Source code: https://github.com/cran/fabletools +* Date/Publication: 2024-04-22 11:22:41 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "fabletools")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fabletools-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.fbl_ts + > ### Title: Plot a set of forecasts + > ### Aliases: autoplot.fbl_ts autolayer.fbl_ts + > + > ### ** Examples + > + > ## Don't show: + ... + > library(fable) + > library(tsibbledata) + > fc <- aus_production %>% model(ets = ETS(log(Beer) ~ error("M") + trend("Ad") + + + season("A"))) %>% forecast(h = "3 years") + > fc %>% autoplot(aus_production) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(dplyr) + + Attaching package: 'dplyr' + + The following object is masked from 'package:testthat': + + ... + 28. └─ggplot2 (local) compute_geom_2(..., self = self) + 29. └─self$geom$use_defaults(...) + ── Failure ('test-graphics.R:327:3'): autoplot_dcmp_ts() ─────────────────────── + `print(p)` produced warnings. + ── Failure ('test-graphics.R:346:3'): autoplot_dcmp_ts() ─────────────────────── + `print(p)` produced warnings. + + [ FAIL 4 | WARN 5 | SKIP 1 | PASS 267 ] + Error: Test failures + Execution halted + ``` + +# factoextra + +
+ +* Version: 1.0.7 +* GitHub: https://github.com/kassambara/factoextra +* Source code: https://github.com/cran/factoextra +* Date/Publication: 2020-04-01 21:20:02 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "factoextra")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘factoextra-Ex.R’ failed + The error most likely occurred in: + + > ### Name: eclust + > ### Title: Visual enhancement of clustering analysis + > ### Aliases: eclust + > + > ### ** Examples + > + > # Load and scale data + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# fairmodels + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/ModelOriented/fairmodels +* Source code: https://github.com/cran/fairmodels +* Date/Publication: 2022-08-23 19:50:06 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "fairmodels")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(fairmodels) + > + > + > test_check("fairmodels") + Welcome to DALEX (version: 2.4.3). + Find examples and detailed introduction at: http://ema.drwhy.ai/ + ... + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 312 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test_plot_density.R:14:3'): Test plot_density ───────────────────── + plt$labels$x not equal to "probability". + target is NULL, current is character + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 312 ] + Error: Test failures + Execution halted + ``` + +# fastR2 + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/rpruim/fastR2 +* Source code: https://github.com/cran/fastR2 +* Date/Publication: 2023-11-09 06:30:03 UTC +* Number of recursive dependencies: 165 + +Run `revdepcheck::cloud_details(, "fastR2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fastR2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ACTgpa + > ### Title: ACT scores and GPA + > ### Aliases: ACTgpa + > ### Keywords: datasets + > + > ### ** Examples + > + > + > gf_point(GPA ~ ACT, data = ACTgpa) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_point ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + data 2.0Mb + snippet 3.7Mb + ``` + +# faux + +
+ +* Version: 1.2.1 +* GitHub: https://github.com/debruine/faux +* Source code: https://github.com/cran/faux +* Date/Publication: 2023-04-20 07:00:11 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "faux")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘codebook.Rmd’ using rmarkdown + --- finished re-building ‘codebook.Rmd’ + + --- re-building ‘continuous.Rmd’ using rmarkdown + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘faux-Ex.R’ failed + The error most likely occurred in: + + > ### Name: beta2norm + > ### Title: Convert beta to normal + > ### Aliases: beta2norm + > + > ### ** Examples + > + > + > x <- rbeta(10000, 2, 3) + > y <- beta2norm(x) + shape1 was set to 1.96704823352025 + shape2 was set to 2.94110338061547 + > g <- ggplot2::ggplot() + ggplot2::geom_point(ggplot2::aes(x, y)) + > ggExtra::ggMarginal(g, type = "histogram") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(faux) + + ************ + Welcome to faux. For support and examples visit: + https://debruine.github.io/faux/ + - Get and set global package options with: faux_options() + ... + 6. └─methods (local) ``(...) + 7. └─methods::new(def, ...) + 8. ├─methods::initialize(value, ...) + 9. └─methods::initialize(value, ...) + 10. └─.Object$initialize(...) + 11. └─lme4 (local) initializePtr() + + [ FAIL 20 | WARN 6 | SKIP 14 | PASS 1331 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘norta.Rmd’ + ... + + > p <- ggplot(dat, aes(uniform_var, poisson_var)) + + + geom_point() + geom_smooth() + + > ggMarginal(p, type = "histogram") + `geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")' + + ... + Error: argument is of length zero + Execution halted + + ‘codebook.Rmd’ using ‘UTF-8’... OK + ‘continuous.Rmd’ using ‘UTF-8’... OK + ‘contrasts.Rmd’ using ‘UTF-8’... OK + ‘norta.Rmd’ using ‘UTF-8’... failed + ‘rnorm_multi.Rmd’ using ‘UTF-8’... OK + ‘sim_design.Rmd’ using ‘UTF-8’... OK + ‘sim_df.Rmd’ using ‘UTF-8’... OK + ``` + +# fddm + +
+ +* Version: 1.0-2 +* GitHub: https://github.com/rtdists/fddm +* Source code: https://github.com/cran/fddm +* Date/Publication: 2024-07-02 16:00:07 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "fddm")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘benchmark.Rmd’ + ... + > mi <- min(bm_vec[, -seq_len(t_idx)]) + + > ma <- max(bm_vec[, (t_idx + 1):(ncol(bm_vec) - 4)]) + + > ggplot(mbm_vec, aes(x = factor(FuncName, levels = Names_vec), + + y = time, color = factor(FuncName, levels = Names_vec), fill = factor(FuncName, .... [TRUNCATED] + + ... + + When sourcing ‘pfddm.R’: + Error: Not a unit object + Execution halted + + ‘benchmark.Rmd’ using ‘UTF-8’... failed + ‘example.Rmd’ using ‘UTF-8’... OK + ‘math.Rmd’ using ‘UTF-8’... OK + ‘pfddm.Rmd’ using ‘UTF-8’... failed + ‘validity.Rmd’ using ‘UTF-8’... OK + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 16.6Mb + sub-directories of 1Mb or more: + doc 1.6Mb + libs 14.1Mb + ``` + +# feasts + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/tidyverts/feasts +* Source code: https://github.com/cran/feasts +* Date/Publication: 2024-03-15 09:10:02 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "feasts")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(feasts) + Loading required package: fabletools + > + > test_check("feasts") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 101 ] + + ... + ── Error ('test-graphics.R:192:3'): gg_tsdisplay() plots ─────────────────────── + Error in `p + ggplot2::labs(x = "x", y = "y", title = "title")`: non-numeric argument to binary operator + ── Failure ('test-graphics.R:273:3'): gg_arma() plots ────────────────────────── + p_built$plot$labels[c("x", "y")] not equivalent to list(x = "Re(1/root)", y = "Im(1/root)"). + Component "x": 1 string mismatch + Component "y": 1 string mismatch + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 101 ] + Error: Test failures + Execution halted + ``` + +# fergm + +
+ +* Version: 1.1.4 +* GitHub: https://github.com/benjamin-w-campbell/fergm +* Source code: https://github.com/cran/fergm +* Date/Publication: 2018-10-17 22:20:11 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "fergm")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fergm-Ex.R’ failed + The error most likely occurred in: + + > ### Name: coef_posterior_density + > ### Title: Plots the posterior density for FERGM model terms. + > ### Aliases: coef_posterior_density + > ### Keywords: FERGM interpret summary + > + > ### ** Examples + > + ... + > data("ergm.fit") + > data("fergm.fit") + > data("mesa") + > + > # rstan functions + > # Histogram of the posterior + > rstan::stan_hist(fergm.fit$stan.fit, par = "beta") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ffp + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/Reckziegel/FFP +* Source code: https://github.com/cran/ffp +* Date/Publication: 2022-09-29 15:10:06 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "ffp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ffp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scenario_density + > ### Title: Plot Scenarios + > ### Aliases: scenario_density scenario_histogram + > + > ### ** Examples + > + > x <- diff(log(EuStockMarkets))[, 1] + > p <- exp_decay(x, 0.005) + > + > scenario_density(x, p, 500) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +# fic + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/chjackson/fic +* Source code: https://github.com/cran/fic +* Date/Publication: 2019-04-13 08:32:39 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "fic")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘linear.Rnw’ + ... + + > library(ggplot2) + + > if (requireNamespace("GGally", quietly = TRUE)) { + + GGally::ggpairs(mtcars[, c("mpg", "am", "wt", "qsec", "disp", + + "hp")], aes(colour .... [TRUNCATED] + + ... + When sourcing 'linear.R': + Error: argument is of length zero + Execution halted + + ‘fic.Rnw’ using ‘UTF-8’... OK + ‘linear.Rnw’ using ‘UTF-8’... failed + ‘loss.Rnw’ using ‘UTF-8’... OK + ‘multistate.Rnw’ using ‘UTF-8’... OK + ‘skewnormal.Rnw’ using ‘UTF-8’... OK + ‘survival.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘numDeriv’ + All declared Imports should be used. + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘fic.Rnw’ using knitr + Error: processing vignette 'fic.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'fic.tex' failed. + LaTeX errors: + ! LaTeX Error: File `grfext.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + + ... + --- finished re-building ‘skewnormal.Rnw’ + + --- re-building ‘survival.Rnw’ using knitr + --- finished re-building ‘survival.Rnw’ + + SUMMARY: processing the following files failed: + ‘fic.Rnw’ ‘linear.Rnw’ ‘multistate.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# fido + +
+ +* Version: 1.1.1 +* GitHub: https://github.com/jsilve24/fido +* Source code: https://github.com/cran/fido +* Date/Publication: 2024-06-05 21:30:06 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "fido")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fido-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.pibblefit + > ### Title: Plot Summaries of Posterior Distribution of pibblefit Parameters + > ### Aliases: plot.pibblefit + > + > ### ** Examples + > + > sim <- pibble_sim(N=10, D=4, Q=3) + > fit <- pibble(sim$Y, sim$X) + > plot(fit, par="Lambda") + Scale for colour is already present. + Adding another scale for colour, which will replace the existing scale. + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(fido) + > + > #Sys.setenv(KMP_DUPLICATE_LIB_OK="TRUE") + > test_check("fido") + [1] 0.27980164 -0.69169550 -0.53205652 0.11488451 -0.42419872 2.20261388 + [7] -1.62190133 -0.90893172 0.07891428 0.75060681 0.43593605 0.26819442 + ... + 21. └─base::Map(...) + 22. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 23. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 24. └─layer$compute_geom_2(key, single_params, theme) + 25. └─ggplot2 (local) compute_geom_2(..., self = self) + 26. └─self$geom$use_defaults(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 114 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘non-linear-models.Rmd’ + ... + + The following object is masked from ‘package:dplyr’: + + select + + + When sourcing ‘non-linear-models.R’: + Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required + Execution halted + + ‘introduction-to-fido.Rmd’ using ‘UTF-8’... OK + ‘mitigating-pcrbias.Rmd’ using ‘UTF-8’... OK + ‘non-linear-models.Rmd’ using ‘UTF-8’... failed + ‘orthus.Rmd’ using ‘UTF-8’... OK + ‘picking_priors.Rmd’ using ‘UTF-8’... OK + ``` + +* checking installed package size ... NOTE + ``` + installed size is 106.5Mb + sub-directories of 1Mb or more: + data 4.0Mb + libs 100.6Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction-to-fido.Rmd’ using rmarkdown + --- finished re-building ‘introduction-to-fido.Rmd’ + + --- re-building ‘mitigating-pcrbias.Rmd’ using rmarkdown + --- finished re-building ‘mitigating-pcrbias.Rmd’ + + --- re-building ‘non-linear-models.Rmd’ using rmarkdown + ``` + +# fitdistrplus + +
+ +* Version: 1.2-1 +* GitHub: https://github.com/lbbe-software/fitdistrplus +* Source code: https://github.com/cran/fitdistrplus +* Date/Publication: 2024-07-12 12:20:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "fitdistrplus")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fitdistrplus-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CIcdfplot + > ### Title: Empirical cumulative distribution function with pointwise + > ### confidence intervals on probabilities or on quantiles + > ### Aliases: CIcdfplot + > ### Keywords: distribution + > + > ### ** Examples + ... + > f1 <- fitdist(s1, "exp") + > b1 <- bootdist(f1, niter= 11) #voluntarily low to decrease computation time + > + > # plot 95 percent bilateral confidence intervals on y values (probabilities) + > CIcdfplot(b1, CI.level= 95/100, CI.output = "probability") + > if (ggplotEx) CIcdfplot(b1, CI.level= 95/100, CI.output = "probability", plotstyle = "ggplot") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘t-CIcdfplot.R’ + Running the tests in ‘tests/t-CIcdfplot.R’ failed. + Complete output: + > library(fitdistrplus) + Loading required package: MASS + Loading required package: survival + > + > nbboot <- 201 + > nbboot <- 10 + > ggplotEx <- requireNamespace("ggplot2", quietly = TRUE) + ... + 97.5 % 2.152084 2.778622 + > + > par(mfrow=c(1,2)) + > CIcdfplot(b1, CI.level=95/100, CI.output = "probability", CI.fill="grey80", CI.col="black") + > CIcdfplot(b1, CI.level=95/100, CI.output = "quantile", datacol="blue") + > if(ggplotEx) CIcdfplot(b1, CI.level=95/100, CI.output = "probability", CI.fill="grey80", CI.col="black", plotstyle = "ggplot") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘FAQ.Rmd’ + ... + + > dcomp <- denscomp(list(fitW, fitln, fitg), legendtext = c("Weibull", + + "lognormal", "gamma"), xlab = "serving sizes (g)", xlim = c(0, + + 25 .... [TRUNCATED] + + > dcomp + ggplot2::theme_minimal() + ggplot2::ggtitle("Ground beef fits") + + When sourcing ‘FAQ.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘FAQ.Rmd’ using ‘UTF-8’... failed + ‘Optimalgo.Rmd’ using ‘UTF-8’... OK + ‘fitdistrplus_vignette.Rmd’ using ‘UTF-8’... OK + ‘starting-values.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘FAQ.Rmd’ using rmarkdown + ``` + +# fitlandr + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/Sciurus365/fitlandr +* Source code: https://github.com/cran/fitlandr +* Date/Publication: 2023-02-10 10:40:02 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "fitlandr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fitlandr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fit_2d_vf + > ### Title: Estimate a 2D vector field + > ### Aliases: fit_2d_vf + > + > ### ** Examples + > + > # generate data + > single_output_grad <- simlandr::sim_fun_grad(length = 200, seed = 1614) + > # fit the vector field + > v2 <- fit_2d_vf(single_output_grad, x = "x", y = "y", method = "MVKE") + > plot(v2) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# flexsurv + +
+ +* Version: 2.3.2 +* GitHub: https://github.com/chjackson/flexsurv +* Source code: https://github.com/cran/flexsurv +* Date/Publication: 2024-08-17 05:50:02 UTC +* Number of recursive dependencies: 147 + +Run `revdepcheck::cloud_details(, "flexsurv")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘standsurv.Rmd’ + ... + 5 0 967 Good 2.649315 68.74975 25110 1986-05-18 female Good + 6 0 629 Good 1.723288 64.53328 23570 1987-03-07 female Good + + > km <- survfit(Surv(recyrs, censrec) ~ group2, data = bc) + + > kmsurvplot <- ggsurvplot(km) + + When sourcing ‘standsurv.R’: + Error: argument is of length zero + Execution halted + + ‘standsurv.Rmd’ using ‘UTF-8’... failed + ‘flexsurv.Rnw’ using ‘UTF-8’... OK + ‘multistate.Rnw’ using ‘UTF-8’... OK + ‘distributions.Rnw’ using ‘UTF-8’... OK + ‘flexsurv-examples.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.9Mb + libs 3.4Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘standsurv.Rmd’ using rmarkdown + + Quitting from lines 113-116 [unnamed-chunk-4] (standsurv.Rmd) + Error: processing vignette 'standsurv.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘standsurv.Rmd’ + + --- re-building ‘flexsurv.Rnw’ using knitr + --- finished re-building ‘flexsurv.Rnw’ + ... + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘flexsurv-examples.Rnw’ + + SUMMARY: processing the following files failed: + ‘standsurv.Rmd’ ‘multistate.Rnw’ ‘distributions.Rnw’ + ‘flexsurv-examples.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# flipr + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/LMJL-Alea/flipr +* Source code: https://github.com/cran/flipr +* Date/Publication: 2023-08-23 09:00:02 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "flipr")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘alternative.Rmd’ using rmarkdown + --- finished re-building ‘alternative.Rmd’ + + --- re-building ‘exactness.Rmd’ using rmarkdown + + Quitting from lines 142-177 [unnamed-chunk-1] (exactness.Rmd) + Error: processing vignette 'exactness.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘exactness.Rmd’ + + --- re-building ‘flipr.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘exactness.Rmd’ + ... + + > library(flipr) + + > load("../R/sysdata.rda") + Warning in readChar(con, 5L, useBytes = TRUE) : + cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' + + ... + cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' + + When sourcing ‘plausibility.R’: + Error: cannot open the connection + Execution halted + + ‘alternative.Rmd’ using ‘UTF-8’... OK + ‘exactness.Rmd’ using ‘UTF-8’... failed + ‘flipr.Rmd’ using ‘UTF-8’... failed + ‘plausibility.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 11.2Mb + sub-directories of 1Mb or more: + doc 9.1Mb + libs 1.4Mb + ``` + +# FLOPART + +
+ +* Version: 2024.6.19 +* GitHub: NA +* Source code: https://github.com/cran/FLOPART +* Date/Publication: 2024-06-20 21:30:10 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "FLOPART")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘comparison.Rmd’ + ... + + > if (require("ggplot2")) { + + ggplot() + ggtitle("Models with label constraints (FLOPART) and without (penalty values)") + + + scale_fill_m .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + When sourcing ‘comparison.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘comparison.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘comparison.Rmd’ using knitr + ``` + +# fmesher + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/inlabru-org/fmesher +* Source code: https://github.com/cran/fmesher +* Date/Publication: 2024-07-01 13:00:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "fmesher")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fmesher-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fm_mesh_1d + > ### Title: Make a 1D mesh object + > ### Aliases: fm_mesh_1d + > + > ### ** Examples + > + > if (require("ggplot2")) { + ... + + boundary = c("neumann", "free"), + + degree = 2 + + ) + + ggplot() + + + geom_fm(data = m, xlim = c(0.5, 10.5)) + + } + Loading required package: ggplot2 + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic_use.Rmd’ + ... + + > plot(mesh2) + + > suppressPackageStartupMessages(library(ggplot2)) + + > ggplot() + geom_fm(data = mesh2) + + When sourcing ‘basic_use.R’: + Error: argument is of length zero + Execution halted + + ‘basic_use.Rmd’ using ‘UTF-8’... failed + ‘fmesher_library.Rmd’ using ‘UTF-8’... OK + ‘inla_conversion.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘basic_use.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.5Mb + sub-directories of 1Mb or more: + libs 10.5Mb + ``` + +# fmf + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/fmf +* Date/Publication: 2020-09-03 07:32:12 UTC +* Number of recursive dependencies: 175 + +Run `revdepcheck::cloud_details(, "fmf")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘fmf-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot + > ### Title: PCA Plot of the Noise Score of Each Individual + > ### Aliases: plot + > + > ### ** Examples + > + > + ... + 17. │ └─ggplot2:::`+.gg`(...) + 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 19. │ ├─ggplot2::ggplot_add(object, p, objectname) + 20. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 21. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 22. └─base::.handleSimpleError(...) + 23. └─purrr (local) h(simpleError(msg, call)) + 24. └─cli::cli_abort(...) + 25. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +# forestly + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/Merck/forestly +* Source code: https://github.com/cran/forestly +* Date/Publication: 2024-07-08 19:40:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "forestly")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘forest-plot-static.Rmd’ + ... + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for <86> + Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on 'Treatment← Favor →Placebo' in 'mbcsToSbcs': dot substituted for <92> + + When sourcing ‘forest-plot-static.R’: + Error: object is not a unit + Execution halted + + ‘forest-plot-static.Rmd’ using ‘UTF-8’... failed + ‘forestly-cran.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘forest-plot-static.Rmd’ using rmarkdown + ``` + +# FossilSim + +
+ +* Version: 2.4.0 +* GitHub: NA +* Source code: https://github.com/cran/FossilSim +* Date/Publication: 2024-09-05 19:40:02 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "FossilSim")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FossilSim-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.fbdrange + > ### Title: Plot oriented tree with stratigraphic ranges + > ### Aliases: plot.fbdrange + > + > ### ** Examples + > + > tree_file <- system.file("extdata", "fbdrange.trees", package = "FossilSim") + > fbdr <- get_fbdrange_from_file(tree_file) + > p <- plot(fbdr, smart.labels = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# FPDclustering + +
+ +* Version: 2.3.1 +* GitHub: NA +* Source code: https://github.com/cran/FPDclustering +* Date/Publication: 2024-01-30 00:10:06 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "FPDclustering")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FPDclustering-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GPDC + > ### Title: Gaussian PD-Clustering + > ### Aliases: GPDC + > + > ### ** Examples + > + > #Load the data + ... + > #Results + > table(res$label,ais$sex) + + f m + 1 95 1 + 2 5 101 + > plot(res) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# frailtyEM + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/tbalan/frailtyEM +* Source code: https://github.com/cran/frailtyEM +* Date/Publication: 2019-09-22 13:00:10 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "frailtyEM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘frailtyEM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: summary.emfrail + > ### Title: Summary for 'emfrail' objects + > ### Aliases: summary.emfrail + > + > ### ** Examples + > + > data("bladder") + ... + filter + + The following object is masked from ‘package:graphics’: + + layout + + > ggplotly(pl2) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘frailtyEM_manual.Rnw’ using Sweave + Loading required package: survival + Loading required package: gridExtra + Warning: The `` argument of `guides()` cannot be `FALSE`. Use + "none" instead as of ggplot2 3.3.4. + Warning: Removed 2 rows containing missing values or values outside + the scale range (`geom_path()`). + Warning in data("kidney") : data set ‘kidney’ not found + Warning in emfrail(Surv(time, status) ~ age + sex + cluster(id), data = kidney, : + ... + l.179 \RequirePackage{grfext}\relax + ^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘frailtyEM_manual.Rnw’ + + SUMMARY: processing the following file failed: + ‘frailtyEM_manual.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# funcharts + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/unina-sfere/funcharts +* Source code: https://github.com/cran/funcharts +* Date/Publication: 2024-07-19 12:00:31 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "funcharts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘funcharts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pca_mfd + > ### Title: Multivariate functional principal components analysis + > ### Aliases: pca_mfd + > + > ### ** Examples + > + > library(funcharts) + > mfdobj <- data_sim_mfd() + > pca_obj <- pca_mfd(mfdobj) + > plot_pca_mfd(pca_obj) + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# FunnelPlotR + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/nhs-r-community/FunnelPlotR +* Source code: https://github.com/cran/FunnelPlotR +* Date/Publication: 2024-04-12 08:40:02 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "FunnelPlotR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘FunnelPlotR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: funnel_plot + > ### Title: Funnel plots for comparing institutional performance + > ### Aliases: funnel_plot + > + > ### ** Examples + > + > # We will use the 'medpar' dataset from the 'COUNT' package. + ... + > # Draw plot, returning just the plot object + > fp<-funnel_plot(medpar, denominator=prds, numerator=los, + + group = provnum, limit=95, title="An example funnel plot") + > + > # Methods for viewing/extracting + > print(fp) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: print ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘changing_funnel_plot_options.Rmd’ + ... + + family = "poisson", data = medpar) + + > medpar$prds <- predict(mod, newdata = medpar, type = "response") + + > funnel_plot(medpar, denominator = prds, numerator = los, + + group = provnum, limit = 99, label = "outlier", draw_unadjusted = TRUE) + + ... + + group = provnum, title = "Length of Stay Funnel plot for `medpar` data", + + draw .... [TRUNCATED] + Plotting using unadjusted limits + + When sourcing ‘funnel_plots.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘changing_funnel_plot_options.Rmd’ using ‘UTF-8’... failed + ‘funnel_plots.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘changing_funnel_plot_options.Rmd’ using rmarkdown + + Quitting from lines 33-49 [dtsetup] (changing_funnel_plot_options.Rmd) + Error: processing vignette 'changing_funnel_plot_options.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘changing_funnel_plot_options.Rmd’ + + --- re-building ‘funnel_plots.Rmd’ using rmarkdown + ``` + +# genekitr + +
+ +* Version: 1.2.8 +* GitHub: https://github.com/GangLiLab/genekitr +* Source code: https://github.com/cran/genekitr +* Date/Publication: 2024-09-06 13:00:06 UTC +* Number of recursive dependencies: 202 + +Run `revdepcheck::cloud_details(, "genekitr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘genekitr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotVenn + > ### Title: Venn plot for groups of genes + > ### Aliases: plotVenn + > + > ### ** Examples + > + > k1 = requireNamespace("ComplexUpset",quietly = TRUE) + ... + + use_venn = FALSE, + + main_text_size = 15, + + legend_text_size = 8, + + legend_position = 'left' + + ) + + } + Color length should be same with venn_list, auto assign colors... + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plotVenn ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# geoheatmap + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/geoheatmap +* Date/Publication: 2024-09-05 15:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "geoheatmap")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘geoheatmap.Rmd’ + ... + + facet_col = "state", value_col = "teams", merge_col = "name_de", + + .... [TRUNCATED] + + > geoheatmap(facet_data = football_teams, grid_data = de_states_grid1, + + facet_col = "state", value_col = "teams", merge_col = "name_de", + + .... [TRUNCATED] + + When sourcing ‘geoheatmap.R’: + Error: subscript out of bounds + Execution halted + + ‘geoheatmap.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘geoheatmap.Rmd’ using rmarkdown + ``` + +# geomtextpath + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/AllanCameron/geomtextpath +* Source code: https://github.com/cran/geomtextpath +* Date/Publication: 2024-06-13 06:40:02 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "geomtextpath")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘geomtextpath-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_textsf + > ### Title: Visualise sf objects with labels + > ### Aliases: geom_textsf geom_labelsf + > + > ### ** Examples + > + > ggplot(waterways) + + ... + 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) + 20. │ └─self$draw_panel(data, panel_params, coord, na.rm = FALSE, legend = "other") + 21. │ └─geomtextpath (local) draw_panel(...) + 22. │ └─geomtextpath:::sf_textgrob(...) + 23. └─base::.handleSimpleError(...) + 24. └─rlang (local) h(simpleError(msg, call)) + 25. └─handlers[[1L]](cnd) + 26. └─cli::cli_abort(...) + 27. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(geomtextpath) + Loading required package: ggplot2 + > + > test_check("geomtextpath") + [ FAIL 1 | WARN 0 | SKIP 4 | PASS 463 ] + + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test-sf.R:91:3'): We can make grobs from sf features ──────────────── + Error in `(x$boxlinewidth %||% defaults$linewidth[type_ind]) * 3.779528`: non-numeric argument to binary operator + Backtrace: + ▆ + 1. └─geomtextpath:::sf_textgrob(river, as_textbox = TRUE) at test-sf.R:91:3 + + [ FAIL 1 | WARN 0 | SKIP 4 | PASS 463 ] + Error: Test failures + Execution halted + ``` + +# geostan + +
+ +* Version: 0.6.2 +* GitHub: https://github.com/ConnorDonegan/geostan +* Source code: https://github.com/cran/geostan +* Date/Publication: 2024-06-04 09:45:37 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "geostan")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘geostan-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.geostan_fit + > ### Title: print or plot a fitted geostan model + > ### Aliases: print.geostan_fit plot.geostan_fit + > + > ### ** Examples + > + > data(georgia) + ... + log(income) -1.013 0.001 0.019 -1.049 -1.029 -1.014 -0.998 -0.974 188 1.003 + + Samples were drawn using NUTS(diag_e) at Tue Sep 10 09:34:29 2024. + For each parameter, n_eff is a crude measure of effective sample size, + and Rhat is the potential scale reduction factor on split chains (at + convergence, Rhat=1). + > plot(fit) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 129.8Mb + sub-directories of 1Mb or more: + libs 127.7Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# GGally + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/ggobi/ggally +* Source code: https://github.com/cran/GGally +* Date/Publication: 2024-02-14 00:53:32 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "GGally")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GGally-Ex.R’ failed + The error most likely occurred in: + + > ### Name: +.gg + > ### Title: Modify a 'ggmatrix' object by adding an 'ggplot2' object to all + > ### plots + > ### Aliases: +.gg add_to_ggmatrix + > + > ### ** Examples + > + ... + > p_ <- GGally::print_if_interactive + > data(tips) + > + > pm <- ggpairs(tips[, 2:4], ggplot2::aes(color = sex)) + > ## change to black and white theme + > pm + ggplot2::theme_bw() + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (requireNamespace("testthat", quietly = TRUE)) { + + library(testthat) + + library(GGally) + + + + test_check("GGally") + + } + ... + 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 22. └─grid:::drawGrob(x) + 23. ├─grid::drawDetails(x, recording = FALSE) + 24. └─grid:::drawDetails.polyline(x, recording = FALSE) + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 20 | WARN 1 | SKIP 22 | PASS 426 ] + Error: Test failures + Execution halted + ``` + +# gganimate + +
+ +* Version: 1.0.9 +* GitHub: https://github.com/thomasp85/gganimate +* Source code: https://github.com/cran/gganimate +* Date/Publication: 2024-02-27 14:00:03 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "gganimate")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gganimate) + Loading required package: ggplot2 + > + > test_check("gganimate") + [ FAIL 1 | WARN 3 | SKIP 1 | PASS 5 ] + + ... + 3. ├─gganimate::animate(p, nframes = 2) at test-anim_save.R:14:5 + 4. └─gganimate:::animate.gganim(p, nframes = 2) + 5. └─args$renderer(frames_vars$frame_source, args$fps) + 6. └─gganimate:::png_dim(frames[1]) + 7. └─cli::cli_abort("Provided file ({file}) does not exist") + 8. └─rlang::abort(...) + + [ FAIL 1 | WARN 3 | SKIP 1 | PASS 5 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘gganimate.Rmd’ + ... + Theme element `panel.grid.major.y` is missing + Theme element `panel.grid.major.x` is missing + Warning: Failed to plot frame + Caused by error in `UseMethod()`: + ! no applicable method for 'element_grob' applied to an object of class "NULL" + + When sourcing ‘gganimate.R’: + Error: Provided file (/tmp/RtmpPBufaF/165c2292cd97/gganim_plot0001.png) does + not exist + Execution halted + + ‘gganimate.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘gganimate.Rmd’ using rmarkdown + ``` + +# ggbrain + +
+ +* Version: 0.8.1 +* GitHub: https://github.com/michaelhallquist/ggbrain +* Source code: https://github.com/cran/ggbrain +* Date/Publication: 2023-03-21 18:00:05 UTC +* Number of recursive dependencies: 74 + +Run `revdepcheck::cloud_details(, "ggbrain")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggbrain_introduction.Rmd’ + ... + + > gg_obj <- gg_base + geom_brain(definition = "underlay", + + fill_scale = scale_fill_gradient(low = "grey8", high = "grey62"), + + show_legend .... [TRUNCATED] + + > gg_obj$render() + + ... + + > plot(gg_obj) + + When sourcing ‘ggbrain_labels.R’: + Error: argument is of length zero + Execution halted + + ‘ggbrain_aesthetics.Rmd’ using ‘UTF-8’... OK + ‘ggbrain_introduction.Rmd’ using ‘UTF-8’... failed + ‘ggbrain_labels.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggbrain_aesthetics.Rmd’ using rmarkdown + --- finished re-building ‘ggbrain_aesthetics.Rmd’ + + --- re-building ‘ggbrain_introduction.Rmd’ using rmarkdown + + Quitting from lines 238-239 [unnamed-chunk-16] (ggbrain_introduction.Rmd) + Error: processing vignette 'ggbrain_introduction.Rmd' failed with diagnostics: + argument is of length zero + ... + Quitting from lines 47-54 [unnamed-chunk-2] (ggbrain_labels.Rmd) + Error: processing vignette 'ggbrain_labels.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggbrain_labels.Rmd’ + + SUMMARY: processing the following files failed: + ‘ggbrain_introduction.Rmd’ ‘ggbrain_labels.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.8Mb + sub-directories of 1Mb or more: + doc 3.0Mb + extdata 1.6Mb + libs 5.5Mb + ``` + +# ggbreak + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/YuLab-SMU/ggbreak +* Source code: https://github.com/cran/ggbreak +* Date/Publication: 2023-06-26 05:40:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "ggbreak")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggbreak-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scale_wrap + > ### Title: scale-wrap + > ### Aliases: scale_wrap + > + > ### ** Examples + > + > library(ggplot2) + > library(ggbreak) + > p <- ggplot(economics, aes(x=date, y = unemploy, colour = uempmed)) + + + geom_line() + > p + scale_wrap(n=4) + Error in identicalUnits(x) : object is not a unit + Calls: -> print.ggwrap + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggbreak.Rmd’ + ... + > p1 + p2 + + > p2 + scale_x_break(c(18, 21)) + + > p1 + scale_x_break(c(7, 17), scales = 1.5) + scale_x_break(c(18, + + 21), scales = 2) + + When sourcing ‘ggbreak.R’: + Error: second argument must be a list + Execution halted + + ‘ggbreak.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggbreak.Rmd’ using rmarkdown + ``` + +# ggcharts + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/thomas-neitmann/ggcharts +* Source code: https://github.com/cran/ggcharts +* Date/Publication: 2020-05-20 00:40:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "ggcharts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggcharts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: bar_chart + > ### Title: Bar Chart + > ### Aliases: bar_chart column_chart + > + > ### ** Examples + > + > data(biomedicalrevenue) + > revenue2018 <- biomedicalrevenue[biomedicalrevenue$year == 2018, ] + > revenue_roche <- biomedicalrevenue[biomedicalrevenue$company == "Roche", ] + > + > ## By default bar_chart() creates a horizontal and sorted plot + > bar_chart(revenue2018, company, revenue) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: bar_chart ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggcharts) + Loading required package: ggplot2 + > + > test_check("ggcharts") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ] + + ... + 4. └─ggcharts::bar_chart(revenue_2018, company, revenue) + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘customize.Rmd’ + ... + > dreaded_lang <- tibble::tribble(~language, ~pct, "VBA", + + 75.2, "Objective-C", 68.7, "Assembly", 64.4, "C", 57.5, "PHP", + + 54.2, "Erlang", .... [TRUNCATED] + + > (chart <- lollipop_chart(dreaded_lang, language, pct, + + highlight = "R")) + + ... + + > lollipop_chart(diamonds, cut, highlight = "Good") + + When sourcing ‘themes.R’: + Error: argument is of length zero + Execution halted + + ‘customize.Rmd’ using ‘UTF-8’... failed + ‘highlight.Rmd’ using ‘UTF-8’... failed + ‘themes.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘customize.Rmd’ using rmarkdown + + Quitting from lines 25-44 [unnamed-chunk-2] (customize.Rmd) + Error: processing vignette 'customize.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘customize.Rmd’ + + --- re-building ‘highlight.Rmd’ using rmarkdown + + Quitting from lines 37-44 [unnamed-chunk-2] (highlight.Rmd) + Error: processing vignette 'highlight.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘highlight.Rmd’ + + --- re-building ‘themes.Rmd’ using rmarkdown + ``` + +# ggdark + +
+ +* Version: 0.2.1 +* GitHub: NA +* Source code: https://github.com/cran/ggdark +* Date/Publication: 2019-01-11 17:30:06 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "ggdark")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggdark-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dark_mode + > ### Title: Activate dark mode on a 'ggplot2' theme + > ### Aliases: dark_mode + > + > ### ** Examples + > + > library(ggplot2) + ... + > + > p1 <- ggplot(iris, aes(Sepal.Width, Sepal.Length, color = Species)) + + + geom_point() + > + > p1 # theme returned by theme_get() + > p1 + dark_mode() # activate dark mode on theme returned by theme_get() + Error in match(x, table, nomatch = 0L) : + 'match' requires vector arguments + Calls: dark_mode -> %in% + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggdark) + > + > test_check("ggdark") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + ── Error ('test_dark_mode.R:10:1'): (code run outside of `test_that()`) ──────── + Error in `match(x, table, nomatch = 0L)`: 'match' requires vector arguments + Backtrace: + ▆ + 1. └─ggdark::dark_mode(light_theme) at test_dark_mode.R:10:1 + 2. └─geoms[["GeomPoint"]]$default_aes$colour %in% ... + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggdist + +
+ +* Version: 3.3.2 +* GitHub: https://github.com/mjskay/ggdist +* Source code: https://github.com/cran/ggdist +* Date/Publication: 2024-03-05 05:30:23 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "ggdist")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggdist-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Pr_ + > ### Title: Probability expressions in ggdist aesthetics + > ### Aliases: Pr_ p_ + > + > ### ** Examples + > + > library(ggplot2) + ... + + ) + > + > # map density onto alpha of the fill + > ggplot(df, aes(y = name, xdist = d)) + + + stat_slabinterval(aes(alpha = !!p_(x))) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + • test.stat_sample_slabinterval/nas-with-na-rm-true.svg + • test.subguide/dots-subguide-with-side-vertical.svg + • test.subguide/integer-subguide-with-zero-range.svg + • test.subguide/slab-subguide-with-inside-labels-vertical.svg + • test.subguide/slab-subguide-with-outside-labels-vert.svg + • test.subguide/slab-subguide-with-outside-labels.svg + • test.subguide/slab-subguide-with-side-vertical.svg + • test.theme_ggdist/facet-titles-on-left.svg + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dotsinterval.Rmd’ using rmarkdown + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + + Quitting from lines 49-161 [dotsinterval_components] (dotsinterval.Rmd) + Error: processing vignette 'dotsinterval.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ... + + --- re-building ‘freq-uncertainty-vis.Rmd’ using rmarkdown + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dotsinterval.Rmd’ + ... + + xdist = dist)) + geom_hline(yintercept = 0:1, color = "gray95") + + + stat_dotsin .... [TRUNCATED] + + When sourcing ‘dotsinterval.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 2nd layer. + Caused by error in `use_defaults()`: + ... + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(7, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), + Execution halted + + ‘dotsinterval.Rmd’ using ‘UTF-8’... failed + ‘freq-uncertainty-vis.Rmd’ using ‘UTF-8’... failed + ‘lineribbon.Rmd’ using ‘UTF-8’... failed + ‘slabinterval.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.3Mb + help 1.5Mb + ``` + +# ggeasy + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/jonocarroll/ggeasy +* Source code: https://github.com/cran/ggeasy +* Date/Publication: 2023-03-12 10:00:23 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "ggeasy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggeasy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: easy_labs + > ### Title: Easily add ggplot labels using label attribute of 'data.frame' + > ### column + > ### Aliases: easy_labs + > + > ### ** Examples + > + ... + + ggplot2::geom_line(ggplot2::aes(colour=Species)) + > + > p + > + > p + easy_labs() + > p + easy_labs(title = "Plot Title", subtitle = 'Plot Subtitle', x = 'x axis label') + Error in utils::modifyList(p_labs, as.list(unlist(man_labs))) : + is.list(x) is not TRUE + Calls: +.gg ... ggplot_add.easy_labs -> easy_update_labs -> -> stopifnot + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggeasy) + > + > test_check("ggeasy") + [ FAIL 6 | WARN 0 | SKIP 1 | PASS 505 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + ... + 1. └─ggeasy (local) expect_eqNe(easy_res$labels[sort(names(easy_res$labels))], hard_res$labels[sort(names(hard_res$labels))]) at test-labs.R:76:3 + 2. └─testthat::expect_equal(..., check.environment = FALSE) at test-labs.R:6:16 + + [ FAIL 6 | WARN 0 | SKIP 1 | PASS 505 ] + Deleting unused snapshots: + • labs/labels-attrib.svg + • labs/labels-manual.svg + • labs/labels-mytitle.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘shortcuts.Rmd’ + ... + + > p1 <- p + labs(title = "default labels") + + > p2 <- p + easy_labs() + labs(title = "Replace titles with column labels") + + > p3 <- p + easy_labs(x = "My x axis") + labs(title = "Manually add x axis label") + + When sourcing ‘shortcuts.R’: + Error: is.list(x) is not TRUE + Execution halted + + ‘shortcuts.Rmd’ using ‘UTF-8’... failed + ‘tests_and_coverage.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘shortcuts.Rmd’ using rmarkdown + ``` + +# ggedit + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/yonicd/ggedit +* Source code: https://github.com/cran/ggedit +* Date/Publication: 2024-03-04 14:40:02 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "ggedit")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggedit-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dput.ggedit + > ### Title: Convert ggplot object to a string call + > ### Aliases: dput.ggedit + > + > ### ** Examples + > + > + > pList$pointSmooth #original compiled plot + `geom_smooth()` using formula = 'y ~ x' + Error in compute_geom_2(..., self = self) : + unused arguments (list(6), list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, + Calls: ... get_layer_key -> Map -> mapply -> -> + Execution halted + ``` + +# ggESDA + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/kiangkiangkiang/ggESDA +* Source code: https://github.com/cran/ggESDA +* Date/Publication: 2022-08-19 08:40:10 UTC +* Number of recursive dependencies: 214 + +Run `revdepcheck::cloud_details(, "ggESDA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggESDA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: BLOOD + > ### Title: BLOOD data example + > ### Aliases: BLOOD + > ### Keywords: datasets + > + > ### ** Examples + > + > data(BLOOD) + > ggInterval_minmax(BLOOD, aes(x = Hematocrit)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggInterval_minmax ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggESDA.Rmd’ + ... + [1] "knit_image_paths" "knit_asis" + + > CONCEPT <- rep(c("FRA", "HUS", "INC", "ISA", "JPL", + + "KHA", "LOT", "PHI", "ROM"), each = 3) + + > p <- ggInterval_PCA(facedata, poly = T, concepts_group = CONCEPT) + + When sourcing ‘ggESDA.R’: + Error: argument is of length zero + Execution halted + + ‘ggESDA.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggESDA.Rmd’ using rmarkdown + + Quitting from lines 390-406 [ggInterval_PCA] (ggESDA.Rmd) + Error: processing vignette 'ggESDA.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggESDA.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggESDA.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggExtra + +
+ +* Version: 0.10.1 +* GitHub: https://github.com/daattali/ggExtra +* Source code: https://github.com/cran/ggExtra +* Date/Publication: 2023-08-21 14:40:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "ggExtra")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggExtra.Rmd’ + ... + + > p1 <- ggplot(df1, aes(x, y)) + geom_point() + theme_bw() + + > p1 + + > ggMarginal(p1) + + When sourcing ‘ggExtra.R’: + Error: argument is of length zero + Execution halted + + ‘ggExtra.Rmd’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggExtra.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘R6’ ‘scales’ ‘utils’ + All declared Imports should be used. + ``` + +# ggfacto + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/BriceNocenti/ggfacto +* Source code: https://github.com/cran/ggfacto +* Date/Publication: 2024-08-30 15:00:02 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "ggfacto")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggfacto-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MCA2 + > ### Title: Multiple Correspondence Analysis + > ### Aliases: MCA2 + > + > ### ** Examples + > + > data(tea, package = "FactoMineR") + > res.mca <- MCA2(tea, active_vars = 1:18) + > + > res.mca %>% + + ggmca(tea, sup_vars = c("SPC"), ylim = c(NA, 1.2), text_repel = TRUE) %>% + + ggi() #to make the graph interactive + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ggfixest + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/grantmcdermott/ggfixest +* Source code: https://github.com/cran/ggfixest +* Date/Publication: 2023-12-14 08:00:06 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "ggfixest")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > ## Throttle CPU threads if R CMD check (for CRAN) + > + > if (any(grepl("_R_CHECK", names(Sys.getenv()), fixed = TRUE))) { + + # fixest + + if (requireNamespace("fixest", quietly = TRUE)) { + + library(fixest) + + setFixest_nthreads(1) + ... + ----- FAILED[]: test_ggiplot.R<192--192> + call| expect_snapshot_plot(p19a, label = "ggiplot_multi_complex_kitchen_iid") + diff| 1774 + info| Diff plot saved to: _tinysnapshot_review/ggiplot_multi_complex_kitchen_iid.png + ----- FAILED[]: test_ggiplot.R<193--193> + call| expect_snapshot_plot(p19b, label = "ggiplot_multi_complex_kitchen_iid") + diff| 1774 + info| Diff plot saved to: _tinysnapshot_review/ggiplot_multi_complex_kitchen_iid.png + Error: 16 out of 101 tests failed + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggiplot.Rmd’ + ... + > iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2020)` = est_sa20_grp), + + ref.line = -1, main = "Staggered treatment: Split mutli-sample") + The degrees of freedom for the t distribution could not be deduced. Using a Normal distribution instead. + Note that you can provide the argument `df.t` directly. + + When sourcing ‘ggiplot.R’: + Error: in iplot(list(TWFE = est_twfe_grp, `Sun & Abraham (2...: + The 1st element of 'object' raises and error: + Error in nb * sd : non-numeric argument to binary operator + Execution halted + + ‘ggiplot.Rmd’ using ‘UTF-8’... failed + ``` + +# ggfocus + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/Freguglia/ggfocus +* Source code: https://github.com/cran/ggfocus +* Date/Publication: 2020-01-23 13:20:02 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::cloud_details(, "ggfocus")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction_to_ggfocus.Rmd’ + ... + + geom_point() + scale_alpha_focus(c("A", "B"), alpha_other = 0.5) + + + scale_c .... [TRUNCATED] + + > ggplot(datasets::airquality, aes(x = Day, y = Temp, + + linetype = factor(Month), group = factor(Month))) + geom_line() + + + scale_linetype_f .... [TRUNCATED] + + When sourcing ‘introduction_to_ggfocus.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘introduction_to_ggfocus.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction_to_ggfocus.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggforce + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/thomasp85/ggforce +* Source code: https://github.com/cran/ggforce +* Date/Publication: 2024-02-19 11:00:02 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "ggforce")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggforce-Ex.R’ failed + The error most likely occurred in: + + > ### Name: facet_row + > ### Title: One-dimensional facets + > ### Aliases: facet_row facet_col + > + > ### ** Examples + > + > # Standard use + > ggplot(mtcars) + + + geom_point(aes(disp, mpg)) + + + facet_col(~gear) + Error in space$x : $ operator is invalid for atomic vectors + Calls: ... -> draw_panels -> -> init_gtable + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 27.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + help 1.2Mb + libs 25.0Mb + ``` + +# ggformula + +
+ +* Version: 0.12.0 +* GitHub: https://github.com/ProjectMOSAIC/ggformula +* Source code: https://github.com/cran/ggformula +* Date/Publication: 2023-11-09 12:30:07 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "ggformula")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggformula-Ex.R’ failed + The error most likely occurred in: + + > ### Name: discrete_breaks + > ### Title: Discrete Breaks + > ### Aliases: discrete_breaks + > + > ### ** Examples + > + > x <- rbinom(100, 100, 0.4) + > p <- gf_bar( ~ x) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_bar ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggformula) + Loading required package: ggplot2 + Loading required package: scales + Loading required package: ggridges + + New to ggformula? Try the tutorials: + ... + • layer-factory/gf-text1.svg + • layer-factory/gf-text2.svg + • layer-factory/gf-tile1.svg + • layer-factory/proportions-within-all-dodge.svg + • layer-factory/proportions-within-fill-dodge.svg + • layer-factory/proportions-within-fill-facet-grid-and-group.svg + • layer-factory/proportions-within-fill-facet-grid.svg + • layer-factory/proportions-within-group-facet-grid.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggformula.Rmd’ + ... + + > theme_set(theme_light()) + + > library(ggformula) + + > gf_point(mpg ~ hp, data = mtcars) + + When sourcing ‘ggformula.R’: + Error: argument is of length zero + Execution halted + + ‘ggformula.Rmd’ using ‘UTF-8’... failed + ``` + +* checking for code/documentation mismatches ... WARNING + ``` + Codoc mismatches from documentation object 'gf_abline': + gf_hline + Code: function(object = NULL, gformula = NULL, data = NULL, ..., + yintercept, color, linetype, linewidth, alpha, xlab, + ylab, title, subtitle, caption, position = "identity", + show.legend = NA, show.help = NULL, inherit = FALSE, + environment = parent.frame()) + Docs: function(object = NULL, gformula = NULL, data = NULL, ..., + yintercept, color, linetype, linewidth, alpha, xlab, + ylab, title, subtitle, caption, show.legend = NA, + ... + xintercept, color, linetype, linewidth, alpha, xlab, + ylab, title, subtitle, caption, show.legend = NA, + show.help = NULL, inherit = FALSE, environment = + parent.frame()) + Argument names in code not in docs: + position + Mismatches in argument names (first 3): + Position: 15 Code: position Docs: show.legend + Position: 16 Code: show.legend Docs: show.help + Position: 17 Code: show.help Docs: inherit + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggformula.Rmd’ using rmarkdown + + Quitting from lines 106-109 [simple-example] (ggformula.Rmd) + Error: processing vignette 'ggformula.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggformula.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggformula.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘akima’, ‘ggforce’ + ``` + +# ggfortify + +
+ +* Version: 0.4.17 +* GitHub: https://github.com/sinhrks/ggfortify +* Source code: https://github.com/cran/ggfortify +* Date/Publication: 2024-04-17 04:30:04 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "ggfortify")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggfortify-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.cv.glmnet + > ### Title: Autoplot 'glmnet::cv.glmnet' + > ### Aliases: autoplot.cv.glmnet + > + > ### ** Examples + > + > if (requireNamespace("survival", quietly = TRUE)) { + + autoplot(glmnet::cv.glmnet(data.matrix(Orange[-3]), data.matrix(Orange[3]))) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘test-all.R’ + Running the tests in ‘tests/test-all.R’ failed. + Complete output: + > library(testthat) + > + > suppressWarnings(RNGversion("3.5.0")) + > set.seed(1, sample.kind = "Rejection") + > + > test_check('ggfortify') + Loading required package: ggfortify + ... + 3. └─ggfortify:::autoplot.ts(original.data, columns = "Data", ...) + 4. └─ggplot2:::`+.gg`(p, do.call(geom_factory, args)) + 5. └─ggplot2:::add_ggplot(e1, e2, e2name) + 6. ├─ggplot2::ggplot_add(object, p, objectname) + 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 32 | WARN 10 | SKIP 47 | PASS 358 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basics.Rmd’ + ... + + warning = FALSE) + + > library(ggfortify) + Loading required package: ggplot2 + + > autoplot(AirPassengers) + + ... + Error: argument is of length zero + Execution halted + + ‘basics.Rmd’ using ‘UTF-8’... failed + ‘plot_dist.Rmd’ using ‘UTF-8’... failed + ‘plot_lm.Rmd’ using ‘UTF-8’... OK + ‘plot_map.Rmd’ using ‘UTF-8’... failed + ‘plot_pca.Rmd’ using ‘UTF-8’... OK + ‘plot_surv.Rmd’ using ‘UTF-8’... failed + ‘plot_ts.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘basics.Rmd’ using knitr + + Attaching package: 'zoo' + + The following objects are masked from 'package:base': + + as.Date, as.Date.numeric + + + ... + + Quitting from lines 20-22 [unnamed-chunk-1] (plot_dist.Rmd) + Error: processing vignette 'plot_dist.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘plot_dist.Rmd’ + + --- re-building ‘plot_lm.Rmd’ using knitr + --- finished re-building ‘plot_lm.Rmd’ + + --- re-building ‘plot_map.Rmd’ using knitr + ``` + +# gggenomes + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/thackl/gggenomes +* Source code: https://github.com/cran/gggenomes +* Date/Publication: 2024-08-30 11:40:02 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "gggenomes")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gggenomes-Ex.R’ failed + The error most likely occurred in: + + > ### Name: flip + > ### Title: Flip bins and sequences + > ### Aliases: flip flip_seqs sync + > + > ### ** Examples + > + > library(patchwork) + ... + > p4 <- p %>% + + add_clusters(emale_cogs) %>% + + sync() + labs(caption = "shared orthologs") + Joining with `by = join_by(feat_id)` + Flipping: E4-10_086,E4-10_112,RCC970_016B + > + > p0 + p1 + p2 + p3 + p4 + plot_layout(nrow = 1, guides = "collect") + Error in as.unit(value) : object is not coercible to a unit + Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘flip.Rmd’ + ... + > p4 <- p %>% add_clusters(emale_cogs) %>% sync() + + + labs(caption = "shared orthologs") + Joining with `by = join_by(feat_id)` + Flipping: E4-10_086,E4-10_112,RCC970_016B + + > p0 + p1 + p2 + p3 + p4 + plot_layout(nrow = 1, guides = "collect") + + When sourcing ‘flip.R’: + Error: object is not coercible to a unit + Execution halted + + ‘emales.Rmd’ using ‘UTF-8’... OK + ‘flip.Rmd’ using ‘UTF-8’... failed + ‘gggenomes.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘emales.Rmd’ using rmarkdown + --- finished re-building ‘emales.Rmd’ + + --- re-building ‘flip.Rmd’ using rmarkdown + + Quitting from lines 17-44 [unnamed-chunk-2] (flip.Rmd) + Error: processing vignette 'flip.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘flip.Rmd’ + ... + virophages) + emale_tirs Terminal inverted repeats of 6 EMALE genomes + + --- finished re-building ‘gggenomes.Rmd’ + + SUMMARY: processing the following file failed: + ‘flip.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggh4x + +
+ +* Version: 0.2.8 +* GitHub: https://github.com/teunbrand/ggh4x +* Source code: https://github.com/cran/ggh4x +* Date/Publication: 2024-01-23 21:00:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "ggh4x")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggh4x) + Loading required package: ggplot2 + > + > test_check("ggh4x") + [ FAIL 1 | WARN 20 | SKIP 18 | PASS 757 ] + + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-facet_wrap2.R:64:3'): facet_wrap2() can some repeat axes ───── + sum(ctrl) (`actual`) not equal to 4L (`expected`). + + `actual`: 3 + `expected`: 4 + + [ FAIL 1 | WARN 20 | SKIP 18 | PASS 757 ] + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Facets.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Statistics.Rmd’ + ... + > incorrect$x[15] <- sqrt(2) + + > ggplot(incorrect, aes(x, colour = group)) + stat_theodensity(distri = "nbinom") + + When sourcing ‘Statistics.R’: + Error: Problem while computing stat. + ℹ Error occurred in the 1st layer. + Caused by error in `setup_params()`: + ! A discrete 'nbinom' distribution cannot be fitted to continuous data. + Execution halted + + ‘Facets.Rmd’ using ‘UTF-8’... OK + ‘Miscellaneous.Rmd’ using ‘UTF-8’... OK + ‘PositionGuides.Rmd’ using ‘UTF-8’... OK + ‘Statistics.Rmd’ using ‘UTF-8’... failed + ‘ggh4x.Rmd’ using ‘UTF-8’... OK + ``` + +# gghighlight + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/yutannihilation/gghighlight +* Source code: https://github.com/cran/gghighlight +* Date/Publication: 2023-12-16 01:00:02 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "gghighlight")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gghighlight-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gghighlight + > ### Title: Highlight Data With Predicate + > ### Aliases: gghighlight + > + > ### ** Examples + > + > d <- data.frame( + ... + 8. │ ├─purrr:::with_indexed_errors(...) + 9. │ │ └─base::withCallingHandlers(...) + 10. │ ├─purrr:::call_with_cleanup(...) + 11. │ └─gghighlight (local) .f(.x[[i]], .y[[i]], ...) + 12. │ └─gghighlight:::get_default_aes_param(nm, layer$geom, layer$mapping) + 13. └─base::.handleSimpleError(...) + 14. └─purrr (local) h(simpleError(msg, call)) + 15. └─cli::cli_abort(...) + 16. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gghighlight) + Loading required package: ggplot2 + > + > test_check("gghighlight") + label_key: type + label_key: type + ... + 15. └─cli::cli_abort(...) + 16. └─rlang::abort(...) + + [ FAIL 2 | WARN 2 | SKIP 1 | PASS 178 ] + Deleting unused snapshots: + • vdiffr/simple-bar-chart-with-facet.svg + • vdiffr/simple-line-chart.svg + • vdiffr/simple-point-chart.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘gghighlight.Rmd’ + ... + Warning in is.na(non_null_default_aes[[aes_param_name]]) : + is.na() applied to non-(list or vector) of type 'language' + + When sourcing ‘gghighlight.R’: + Error: ℹ In index: 1. + ℹ With name: geom_point. + Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[ + aes_param_name]])`: + ! 'length = 2' in coercion to 'logical(1)' + Execution halted + + ‘gghighlight.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘gghighlight.Rmd’ using rmarkdown + ``` + +# ggHoriPlot + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/rivasiker/ggHoriPlot +* Source code: https://github.com/cran/ggHoriPlot +* Date/Publication: 2022-10-11 16:22:33 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "ggHoriPlot")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggHoriPlot.Rmd’ + ... + > mid <- sum(range(dat_tab$y, na.rm = T))/2 + + > b <- plotAllLayers(dat_tab, mid, cutpoints$cuts, cutpoints$color) + + > b/a + plot_layout(guides = "collect", heights = c(6, + + 1)) + + When sourcing ‘ggHoriPlot.R’: + Error: object is not a unit + Execution halted + + ‘examples.Rmd’ using ‘UTF-8’... OK + ‘ggHoriPlot.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘examples.Rmd’ using rmarkdown + ``` + +# ggiraph + +
+ +* Version: 0.8.10 +* GitHub: https://github.com/davidgohel/ggiraph +* Source code: https://github.com/cran/ggiraph +* Date/Publication: 2024-05-17 12:10:02 UTC +* Number of recursive dependencies: 89 + +Run `revdepcheck::cloud_details(, "ggiraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggiraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotate_interactive + > ### Title: Create interactive annotations + > ### Aliases: annotate_interactive + > + > ### ** Examples + > + > # add interactive annotation to a ggplot ------- + ... + > + > gg <- ggplot(mtcars, aes(x = disp, y = qsec )) + + + geom_point(size=2) + + + annotate_interactive( + + "rect", xmin = 100, xmax = 400, fill = "red", + + data_id = "an_id", tooltip = "a tooltip", + + ymin = 18, ymax = 20, alpha = .5) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > if (requireNamespace("tinytest", quietly = TRUE)) { + + tinytest::test_package("ggiraph") + + } + + test-annotate_interactive.R... 0 tests + test-annotate_interactive.R... 0 tests + test-annotate_interactive.R... 0 tests + ... + test-geom_density_interactive.R 8 tests OK 8ms + + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 0 tests + test-geom_dotplot_interactive.R 8 tests OK Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.9Mb + sub-directories of 1Mb or more: + R 1.5Mb + libs 7.1Mb + ``` + +# ggiraphExtra + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/cardiomoon/ggiraphExtra +* Source code: https://github.com/cran/ggiraphExtra +* Date/Publication: 2020-10-06 07:00:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "ggiraphExtra")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggiraphExtra-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggAncova + > ### Title: Make an interactive plot for an ANCOVA model + > ### Aliases: ggAncova ggAncova.default ggAncova.formula ggAncova.lm + > + > ### ** Examples + > + > require(moonBook) + ... + addLabelDf, getMapping + + > require(ggplot2) + Loading required package: ggplot2 + > require(ggiraph) + Loading required package: ggiraph + > ggAncova(radial,aes(age,NTAV,color=sex),interactive=TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggAncova ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggPredict.Rmd’ + ... + + + > require(plyr) + Loading required package: plyr + + > ggPredict(fit, se = TRUE, interactive = TRUE) + + ... + + > ggPoints(aes(x = wt, y = mpg, color = am), data = mtcars, + + method = "lm", interactive = TRUE) + + When sourcing ‘introduction.R’: + Error: argument is of length zero + Execution halted + + ‘ggPredict.Rmd’ using ‘UTF-8’... failed + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggPredict.Rmd’ using rmarkdown + ``` + +# ggmatplot + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/xuan-liang/ggmatplot +* Source code: https://github.com/cran/ggmatplot +* Date/Publication: 2022-05-17 02:20:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "ggmatplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggmatplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggmatplot + > ### Title: ggmatplot + > ### Aliases: ggmatplot + > + > ### ** Examples + > + > + > # Define a data set + > iris_sub <- subset(iris, Species == "setosa") + > ggmatplot(iris_sub[, c(1, 3)], iris_sub[, c(2, 4)]) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggmatplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggmatplot) + Loading required package: ggplot2 + > library(tibble) + > library(stats) + > + > test_check("ggmatplot") + ... + • ggmatplot_parameters/single-color-scatterplot.svg + • ggmatplot_parameters/single-fill-density-plot.svg + • ggmatplot_parameters/single-linetype-line-plot.svg + • ggmatplot_parameters/single-shape-scatterplot.svg + • ggmatplot_parameters/three-color-violin-plot.svg + • ggmatplot_parameters/three-fill-color-violin-plot.svg + • ggmatplot_parameters/three-linetype-line-plot.svg + • ggmatplot_parameters/three-shape-scatterplot.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggmatplot.Rmd’ + ... + 6 -0.5325916 -0.54457006 + + > library(ggmatplot) + Loading required package: ggplot2 + + > ggmatplot(x, z) + + When sourcing ‘ggmatplot.R’: + Error: argument is of length zero + Execution halted + + ‘ggmatplot.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggmatplot.Rmd’ using rmarkdown + + Quitting from lines 47-50 [point-plot] (ggmatplot.Rmd) + Error: processing vignette 'ggmatplot.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggmatplot.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggmatplot.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggmice + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/amices/ggmice +* Source code: https://github.com/cran/ggmice +* Date/Publication: 2023-08-07 14:20:02 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "ggmice")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘old_friends.Rmd’ + ... + layout + + + > p <- plot_flux(dat) + + > ggplotly(p) + + When sourcing ‘old_friends.R’: + Error: subscript out of bounds + Execution halted + + ‘ggmice.Rmd’ using ‘UTF-8’... OK + ‘old_friends.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggmice.Rmd’ using rmarkdown + ``` + +# ggmulti + +
+ +* Version: 1.0.7 +* GitHub: NA +* Source code: https://github.com/cran/ggmulti +* Date/Publication: 2024-04-09 09:40:05 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "ggmulti")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggmulti-Ex.R’ failed + The error most likely occurred in: + + > ### Name: coord_radial + > ### Title: Radial axes + > ### Aliases: coord_radial + > + > ### ** Examples + > + > if(require("dplyr")) { + ... + + The following objects are masked from ‘package:base’: + + intersect, setdiff, setequal, union + + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > + > + > library(testthat) + > library(ggmulti) + Loading required package: ggplot2 + + Attaching package: 'ggmulti' + ... + 16. └─base::Map(...) + 17. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 18. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 19. └─layer$compute_geom_2(key, single_params, theme) + 20. └─ggplot2 (local) compute_geom_2(..., self = self) + 21. └─self$geom$use_defaults(...) + + [ FAIL 4 | WARN 5 | SKIP 0 | PASS 30 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘glyph.Rmd’ + ... + + Sepal.Width, colour = Species), serialaxes.data = iris, axes.layout = "radia ..." ... [TRUNCATED] + + When sourcing ‘glyph.R’: + Error: Base operators are not defined for quosures. Do you need to unquote the + quosure? + + # Bad: myquosure / rhs + ... + + > p + + When sourcing ‘highDim.R’: + Error: argument is of length zero + Execution halted + + ‘glyph.Rmd’ using ‘UTF-8’... failed + ‘highDim.Rmd’ using ‘UTF-8’... failed + ‘histogram-density-.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘glyph.Rmd’ using rmarkdown + ``` + +# ggpackets + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/dgkf/ggpackets +* Source code: https://github.com/cran/ggpackets +* Date/Publication: 2022-10-10 23:30:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "ggpackets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpackets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggpacket + > ### Title: A container for lazy ggplot layers + > ### Aliases: ggpacket + > + > ### ** Examples + > + > library(ggplot2) + > + > # create a ggpacket directly, setting some fixed argument settings + > ggpk_simple <- ggpacket() %+% geom_line(color = "red") %+% geom_point() + > ggplot(mtcars, aes(x = wt, y = mpg)) + ggpk_simple() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > + > library(ggplot2) + > library(ggpackets) + + Attaching package: 'ggpackets' + + ... + 10. └─ggpackets (local) f(init, x[[i]]) + 11. └─ggplot2:::`+.gg`(gg, ggpk_i) + 12. └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. ├─ggplot2::ggplot_add(object, p, objectname) + 14. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 4 | WARN 1 | SKIP 0 | PASS 27 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘composing-functions.Rmd’ + ... + + geom_point(size = 3) + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + > ggplot(Loblolly) + aes(x = age, y = height, color = Seed) + + + ggpk_my_template() + ggtitle("Growth of Loblolly Pines") + + ... + > diamonds %>% sample_frac(0.01) %>% arrange(cut) %>% + + ggplot() + aes(color = cut) + ggpk_dot_matrix(size = 3, width = 30) + + When sourcing ‘miscellaneous-examples.R’: + Error: argument is of length zero + Execution halted + + ‘composing-functions.Rmd’ using ‘UTF-8’... failed + ‘ggpackets.Rmd’ using ‘UTF-8’... failed + ‘miscellaneous-examples.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘composing-functions.Rmd’ using rmarkdown + + Quitting from lines 58-62 [simple_ggpacket_output] (composing-functions.Rmd) + Error: processing vignette 'composing-functions.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘composing-functions.Rmd’ + + --- re-building ‘ggpackets.Rmd’ using rmarkdown + ``` + +# ggparallel + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/heike/ggparallel +* Source code: https://github.com/cran/ggparallel +* Date/Publication: 2024-03-09 22:00:02 UTC +* Number of recursive dependencies: 51 + +Run `revdepcheck::cloud_details(, "ggparallel")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 12. └─self$get_layer_key(params, layers[include], data[include], theme) + 13. └─ggplot2 (local) get_layer_key(...) + 14. └─base::Map(...) + 15. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 16. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 17. └─layer$compute_geom_2(key, single_params, theme) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# ggparty + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/martin-borkovec/ggparty +* Source code: https://github.com/cran/ggparty +* Date/Publication: 2019-07-18 10:54:06 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "ggparty")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggparty-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_node_label + > ### Title: Draw (multi-line) labels at nodes + > ### Aliases: geom_node_label geom_node_info geom_node_splitvar + > + > ### ** Examples + > + > library(ggparty) + ... + 30. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 31. │ ├─ggplot2::ggplot_add(object, p, objectname) + 32. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 33. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 34. └─base::.handleSimpleError(...) + 35. └─rlang (local) h(simpleError(msg, call)) + 36. └─handlers[[1L]](cnd) + 37. └─cli::cli_abort(...) + 38. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggparty-graphic-partying.Rmd’ + ... + + 0.55 .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + When sourcing ‘ggparty-graphic-partying.R’: + Error: Problem while converting geom to grob. + ℹ Error occurred in the 5th layer. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘ggparty-graphic-partying.Rmd’ using ‘UTF-8’... failed + ‘on-the-edge.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggparty-graphic-partying.Rmd’ using rmarkdown + + Quitting from lines 42-122 [unnamed-chunk-2] (ggparty-graphic-partying.Rmd) + Error: processing vignette 'ggparty-graphic-partying.Rmd' failed with diagnostics: + Problem while converting geom to grob. + ℹ Error occurred in the 5th layer. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘ggparty-graphic-partying.Rmd’ + + --- re-building ‘on-the-edge.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘survival’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggpicrust2 + +
+ +* Version: 1.7.3 +* GitHub: https://github.com/cafferychen777/ggpicrust2 +* Source code: https://github.com/cran/ggpicrust2 +* Date/Publication: 2023-11-08 16:10:02 UTC +* Number of recursive dependencies: 231 + +Run `revdepcheck::cloud_details(, "ggpicrust2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpicrust2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pathway_pca + > ### Title: Perform Principal Component Analysis (PCA) on functional pathway + > ### abundance data and create visualizations of the PCA results. + > ### Aliases: pathway_pca + > + > ### ** Examples + > + ... + > + > # Create example metadata + > # Please ensure the sample IDs in the metadata have the column name "sample_name" + > metadata_example <- data.frame(sample_name = colnames(kegg_abundance_example), + + group = factor(rep(c("Control", "Treatment"), each = 5))) + > + > pca_plot <- pathway_pca(kegg_abundance_example, metadata_example, "group") + Error in identicalUnits(x) : object is not a unit + Calls: pathway_pca ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘ComplexHeatmap’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + R 2.1Mb + data 2.0Mb + ``` + +# ggplotlyExtra + +
+ +* Version: 0.0.1 +* GitHub: NA +* Source code: https://github.com/cran/ggplotlyExtra +* Date/Publication: 2019-12-02 16:20:06 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "ggplotlyExtra")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggplotlyExtra-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggplotly_histogram + > ### Title: Clean 'ggplot2' Histogram to be Converted to 'Plotly' + > ### Aliases: ggplotly_histogram + > + > ### ** Examples + > + > + ... + + xlab("len") + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + Warning in geom_bar(data = layerdata, mapping = aes(x = .data$x, y = .data$count, : + Ignoring unknown aesthetics: label1, label2, and label3 + > + > # convert `ggplot` object to `plotly` object + > ggplotly(p, tooltip = c("Range", "count", "density")) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggPMX + +
+ +* Version: 1.2.11 +* GitHub: https://github.com/ggPMXdevelopment/ggPMX +* Source code: https://github.com/cran/ggPMX +* Date/Publication: 2023-11-30 16:10:06 UTC +* Number of recursive dependencies: 181 + +Run `revdepcheck::cloud_details(, "ggPMX")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggPMX-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pmx_config + > ### Title: This function can be used to define the pmx configuration used + > ### in plots. e.g. Monolix/Nonmem + > ### Aliases: pmx_config + > + > ### ** Examples + > + ... + + cats = c("SEX"), + + conts = c("WT0", "AGE0"), + + strats = "STUD" + + ) + NO FINEGRID FILE: + we will use instead predictions.txt for individual plots + Warning: Duplicated aesthetics after name standardisation: colour + Error in if (new_name %in% existing) { : argument is of length zero + Calls: pmx_mlx ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggPMX-guide.Rmd’ + ... + + > work_dir <- file.path(theophylline, "Monolix") + + > input_data <- file.path(theophylline, "data_pk.csv") + + > ctr <- theophylline() + + When sourcing ‘ggPMX-guide.R’: + Error: argument is of length zero + Execution halted + + ‘ggPMX-guide.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggPMX-guide.Rmd’ using rmarkdown + + Quitting from lines 25-37 [load_package] (ggPMX-guide.Rmd) + Error: processing vignette 'ggPMX-guide.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggPMX-guide.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggPMX-guide.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘lixoftConnectors’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.9Mb + sub-directories of 1Mb or more: + doc 1.1Mb + help 2.4Mb + testdata 4.8Mb + ``` + +# ggpol + +
+ +* Version: 0.0.7 +* GitHub: https://github.com/erocoar/ggpol +* Source code: https://github.com/cran/ggpol +* Date/Publication: 2020-11-08 13:40:02 UTC +* Number of recursive dependencies: 54 + +Run `revdepcheck::cloud_details(, "ggpol")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpol-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GeomConfmat + > ### Title: Confusion Matrix + > ### Aliases: GeomConfmat geom_confmat stat_confmat + > + > ### ** Examples + > + > x <- sample(LETTERS[seq(4)], 50, replace = TRUE) + ... + 21. │ └─ggpol (local) draw_panel(...) + 22. │ └─base::lapply(GeomText$default_aes[missing_aes], rlang::eval_tidy) + 23. │ └─rlang (local) FUN(X[[i]], ...) + 24. ├─ggplot2::from_theme(fontsize) + 25. └─base::.handleSimpleError(...) + 26. └─rlang (local) h(simpleError(msg, call)) + 27. └─handlers[[1L]](cnd) + 28. └─cli::cli_abort(...) + 29. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dplyr’ ‘grDevices’ + All declared Imports should be used. + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ggprism + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/csdaw/ggprism +* Source code: https://github.com/cran/ggprism +* Date/Publication: 2024-03-21 10:50:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "ggprism")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggprism-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_pvalue + > ### Title: Add p-values to a ggplot + > ### Aliases: add_pvalue + > + > ### ** Examples + > + > library(ggplot2) + ... + + "OJ", "VC", 0.0606, 36 + + ) + > + > # boxplot (or another geom...) + > ggplot(tg, aes(x = supp, y = len)) + + + geom_boxplot() + + + add_pvalue(two.means) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("ggprism") + + } + + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + ... + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests + test-add_pvalue.R............. 0 tests Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggprism.Rmd’ + ... + + p.adj = 0.0606, y.position = 36) + + > p1 <- ggplot(ToothGrowth, aes(x = factor(supp), y = len)) + + + geom_boxplot(aes(fill = factor(supp))) + scale_fill_prism(palette = "candy_bright ..." ... [TRUNCATED] + + > p2 <- p1 + add_pvalue(df_p_val) + + ... + + When sourcing ‘pvalues.R’: + Error: argument is of length zero + Execution halted + + ‘axes.Rmd’ using ‘UTF-8’... OK + ‘colours.Rmd’ using ‘UTF-8’... OK + ‘ggprism.Rmd’ using ‘UTF-8’... failed + ‘pvalues.Rmd’ using ‘UTF-8’... failed + ‘themes.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘axes.Rmd’ using rmarkdown + ``` + +# ggpubr + +
+ +* Version: 0.6.0 +* GitHub: https://github.com/kassambara/ggpubr +* Source code: https://github.com/cran/ggpubr +* Date/Publication: 2023-02-10 16:20:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "ggpubr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggpubr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: add_summary + > ### Title: Add Summary Statistics onto a ggplot. + > ### Aliases: add_summary mean_se_ mean_sd mean_ci mean_range median_iqr + > ### median_hilow_ median_q1q3 median_mad median_range + > + > ### ** Examples + > + ... + 10. │ └─ggplot2:::`+.gg`(...) + 11. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 12. │ ├─ggplot2::ggplot_add(object, p, objectname) + 13. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 14. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 15. └─base::.handleSimpleError(...) + 16. └─purrr (local) h(simpleError(msg, call)) + 17. └─cli::cli_abort(...) + 18. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggpubr) + Loading required package: ggplot2 + > + > test_check("ggpubr") + [ FAIL 46 | WARN 3 | SKIP 0 | PASS 51 ] + + ... + 13. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 14. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 15. └─base::.handleSimpleError(...) + 16. └─purrr (local) h(simpleError(msg, call)) + 17. └─cli::cli_abort(...) + 18. └─rlang::abort(...) + + [ FAIL 46 | WARN 3 | SKIP 0 | PASS 51 ] + Error: Test failures + Execution halted + ``` + +# ggrain + +
+ +* Version: 0.0.4 +* GitHub: https://github.com/njudd/ggrain +* Source code: https://github.com/cran/ggrain +* Date/Publication: 2024-01-23 11:50:02 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "ggrain")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggrain-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_rain + > ### Title: Raincloud Plots + > ### Aliases: geom_rain + > + > ### ** Examples + > + > e1 <- ggplot(iris, aes(Species, Sepal.Width, fill = Species)) + > e1 + geom_rain() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggrain.Rmd’ + ... + > library(ggrain) + Loading required package: ggplot2 + + > ggplot(iris, aes(1, Sepal.Width)) + geom_rain() + + + theme_classic() + theme(axis.title.x = element_blank(), axis.text.x = element_blank(), + + .... [TRUNCATED] + + When sourcing ‘ggrain.R’: + Error: argument is of length zero + Execution halted + + ‘ggrain.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘ggrain.Rmd’ using rmarkdown + + Quitting from lines 36-41 [most basic raincloud possible] (ggrain.Rmd) + Error: processing vignette 'ggrain.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘ggrain.Rmd’ + + SUMMARY: processing the following file failed: + ‘ggrain.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# ggraph + +
+ +* Version: 2.2.1 +* GitHub: https://github.com/thomasp85/ggraph +* Source code: https://github.com/cran/ggraph +* Date/Publication: 2024-03-07 12:40:02 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::cloud_details(, "ggraph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggraph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_conn_bundle + > ### Title: Create hierarchical edge bundles between node connections + > ### Aliases: geom_conn_bundle geom_conn_bundle2 geom_conn_bundle0 + > + > ### ** Examples + > + > # Create a graph of the flare class system + ... + + ) + + + geom_node_point(aes(filter = leaf, colour = class)) + + + scale_edge_colour_distiller('', direction = 1, guide = 'edge_direction') + + + coord_fixed() + + + ggforce::theme_no_axes() + Error in get_layer_key(...) : + unused argument (list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, + Calls: ... -> -> process_layers -> + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Edges.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Edges.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + + ... + font family 'Arial' not found in PostScript font database + + When sourcing ‘tidygraph.R’: + Error: invalid font type + Execution halted + + ‘Edges.Rmd’ using ‘UTF-8’... failed + ‘Layouts.Rmd’ using ‘UTF-8’... failed + ‘Nodes.Rmd’ using ‘UTF-8’... failed + ‘tidygraph.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.9Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 3.9Mb + libs 2.8Mb + ``` + +# ggredist + +
+ +* Version: 0.0.2 +* GitHub: https://github.com/alarm-redist/ggredist +* Source code: https://github.com/cran/ggredist +* Date/Publication: 2022-11-23 11:20:02 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "ggredist")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggredist-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_district_text + > ### Title: Label Map Regions + > ### Aliases: geom_district_text geom_district_label + > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText + > ### Keywords: datasets + > + > ### ** Examples + ... + 22. │ └─coord$transform(data, panel_params) + 23. │ └─ggplot2 (local) transform(..., self = self) + 24. │ └─ggplot2:::sf_rescale01(...) + 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) + 26. └─base::.handleSimpleError(...) + 27. └─rlang (local) h(simpleError(msg, call)) + 28. └─handlers[[1L]](cnd) + 29. └─cli::cli_abort(...) + 30. └─rlang::abort(...) + Execution halted + ``` + +# ggRtsy + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/ggRtsy +* Date/Publication: 2023-09-15 19:12:05 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "ggRtsy")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggplot2) + > library(dplyr) + + Attaching package: 'dplyr' + + The following object is masked from 'package:testthat': + ... + 13. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) + 14. │ └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call) + 15. └─vctrs (local) ``() + 16. └─vctrs:::stop_subscript_oob(...) + 17. └─vctrs:::stop_subscript(...) + 18. └─rlang::abort(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Vignette.Rmd’ + ... + |Antique White |(238, 223, 204) |#eedfcc | + + > RectangleFiller(plotExample, c("#e32636", "#9966cc", + + "#f4c2c2", "#e16827")) + + When sourcing ‘Vignette.R’: + Error: Can't extract rows past the end. + ℹ Location 1 doesn't exist. + ℹ There are only 0 rows. + Execution halted + + ‘Vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Vignette.Rmd’ using rmarkdown + + Quitting from lines 48-49 [unnamed-chunk-2] (Vignette.Rmd) + Error: processing vignette 'Vignette.Rmd' failed with diagnostics: + Can't extract rows past the end. + ℹ Location 1 doesn't exist. + ℹ There are only 0 rows. + --- failed re-building ‘Vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘Vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 19 marked UTF-8 strings + ``` + +# ggseqplot + +
+ +* Version: 0.8.4 +* GitHub: https://github.com/maraab23/ggseqplot +* Source code: https://github.com/cran/ggseqplot +* Date/Publication: 2024-05-17 21:40:03 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "ggseqplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggseqplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggseqrfplot + > ### Title: Relative Frequency Sequence Plot + > ### Aliases: ggseqrfplot + > + > ### ** Examples + > + > # Load additional library for fine-tuning the plots + ... + [>] Pseudo/medoid-based-F statistic: 6.870317, p-value: 3.09994e-08 + > + > # ... with ggseqrfplot + > ggseqrfplot(biofam.seq, weighted = FALSE, diss = diss, k = 12, grp.meth="first") + [>] Using k=12 frequency groups with grp.meth='first' + [>] Pseudo/medoid-based-R2: 0.4620155 + [>] Pseudo/medoid-based-F statistic: 6.870317, p-value: 3.09994e-08 + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggseqplot) + Loading required package: TraMineR + + TraMineR stable version 2.2-10 (Built: 2024-05-22) + Website: http://traminer.unige.ch + Please type 'citation("TraMineR")' for citation information. + ... + Backtrace: + ▆ + 1. ├─testthat::expect_s3_class(ggseqtrplot(biofam.seq), "ggplot") at test-ggseqtrplot.R:35:3 + 2. │ └─testthat::quasi_label(enquo(object), arg = "object") + 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 4. └─ggseqplot::ggseqtrplot(biofam.seq) + + [ FAIL 1 | WARN 1045 | SKIP 0 | PASS 131 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggseqplot.Rmd’ + ... + > p1 + p2 + plot_layout(guides = "collect") & scale_fill_manual(values = canva_palettes$`Fun and tropical`[1:4]) & + + theme_ipsum(base_family = "" .... [TRUNCATED] + Scale for fill is already present. + Adding another scale for fill, which will replace the existing scale. + Scale for fill is already present. + Adding another scale for fill, which will replace the existing scale. + + When sourcing ‘ggseqplot.R’: + Error: object is not coercible to a unit + Execution halted + + ‘ggseqplot.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ggseqplot.Rmd’ using rmarkdown + ``` + +# ggside + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/jtlandis/ggside +* Source code: https://github.com/cran/ggside +* Date/Publication: 2024-03-01 09:12:37 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "ggside")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggplot2) + > library(ggside) + Registered S3 method overwritten by 'ggside': + method from + +.gg ggplot2 + > + ... + • ops_meaningful/alpha-0-5-from-function.svg + • side_layers/boxplot2.svg + • vdiff_irisScatter/collapsed-histo.svg + • vdiff_irisScatter/facetgrid-collapsed-density.svg + • vdiff_irisScatter/facetgrid-histo.svg + • vdiff_irisScatter/facetgrid-side-density.svg + • vdiff_irisScatter/stacked-side-density.svg + • vdiff_irisScatter/yside-histo.svg + Error: Test failures + Execution halted + ``` + +* checking for code/documentation mismatches ... WARNING + ``` + Codoc mismatches from documentation object 'geom_xsideabline': + geom_xsidehline + Code: function(mapping = NULL, data = NULL, position = "identity", + ..., yintercept, na.rm = FALSE, show.legend = NA) + Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = + FALSE, show.legend = NA) + Argument names in code not in docs: + position + Mismatches in argument names (first 3): + Position: 3 Code: position Docs: ... + ... + Docs: function(mapping = NULL, data = NULL, stat = "identity", + position = "identity", ..., lineend = "butt", linejoin + = "round", linemitre = 10, arrow = NULL, na.rm = + FALSE, show.legend = NA, inherit.aes = TRUE) + Argument names in code not in docs: + arrow.fill + Mismatches in argument names: + Position: 10 Code: arrow.fill Docs: na.rm + Position: 11 Code: na.rm Docs: show.legend + Position: 12 Code: show.legend Docs: inherit.aes + ``` + +# ggsmc + +
+ +* Version: 0.1.2.0 +* GitHub: https://github.com/richardgeveritt/ggsmc +* Source code: https://github.com/cran/ggsmc +* Date/Publication: 2024-07-27 17:00:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "ggsmc")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Visualising.Rmd’ + ... + 20 /tmp/RtmpuaCJEi/100d113de41a/gganim_plot0020.png + + > data(lv_output) + + > animate_reveal_time_series(lv_output, parameters = c("X", + + "Y"), alpha = 0.5, ylimits = c(0, 600), duration = 10) + + When sourcing ‘Visualising.R’: + Error: argument "theme" is missing, with no default + Execution halted + + ‘Visualising.Rmd’ using ‘UTF-8’... failed + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 175 marked UTF-8 strings + ``` + +# ggspatial + +
+ +* Version: 1.1.9 +* GitHub: https://github.com/paleolimbot/ggspatial +* Source code: https://github.com/cran/ggspatial +* Date/Publication: 2023-08-17 15:32:38 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "ggspatial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggspatial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotation_spatial_hline + > ### Title: Projected horizontal and vertical lines + > ### Aliases: annotation_spatial_hline annotation_spatial_vline + > ### GeomSpatialXline + > ### Keywords: datasets + > + > ### ** Examples + ... + 25. │ └─grid:::validGP(list(...)) + 26. │ └─grid (local) numnotnull("fontsize") + 27. │ └─grid (local) check.length(gparname) + 28. │ └─base::stop(...) + 29. └─base::.handleSimpleError(...) + 30. └─rlang (local) h(simpleError(msg, call)) + 31. └─handlers[[1L]](cnd) + 32. └─cli::cli_abort(...) + 33. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(ggspatial) + > + > test_check("ggspatial") + Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE + [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] + + ... + 33. │ └─base::stop(...) + 34. └─base::.handleSimpleError(...) + 35. └─rlang (local) h(simpleError(msg, call)) + 36. └─handlers[[1L]](cnd) + 37. └─cli::cli_abort(...) + 38. └─rlang::abort(...) + + [ FAIL 1 | WARN 1 | SKIP 22 | PASS 195 ] + Error: Test failures + Execution halted + ``` + +# ggstatsplot + +
+ +* Version: 0.12.4 +* GitHub: https://github.com/IndrajeetPatil/ggstatsplot +* Source code: https://github.com/cran/ggstatsplot +* Date/Publication: 2024-07-06 16:22:07 UTC +* Number of recursive dependencies: 174 + +Run `revdepcheck::cloud_details(, "ggstatsplot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggstatsplot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggscatterstats + > ### Title: Scatterplot with marginal distributions and statistical results + > ### Aliases: ggscatterstats + > + > ### ** Examples + > + > set.seed(123) + ... + + iris, + + x = Sepal.Width, + + y = Petal.Length, + + label.var = Species, + + label.expression = Sepal.Length > 7.6 + + ) + + + ggplot2::geom_rug(sides = "b") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggscatterstats ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ggstatsplot.Rmd’ + ... + author = {Indrajeet Patil}, + title = {{Visualizations with statistical details: The {'ggstatsplot'} approach}}, + journal = {{Journal of Open Source Software}}, + } + + > ggbetweenstats(iris, Species, Sepal.Length) + + When sourcing ‘ggstatsplot.R’: + Error: argument is of length zero + Execution halted + + ‘additional.Rmd’ using ‘UTF-8’... OK + ‘ggstatsplot.Rmd’ using ‘UTF-8’... failed + ``` + +# ggtern + +
+ +* Version: 3.5.0 +* GitHub: NA +* Source code: https://github.com/cran/ggtern +* Date/Publication: 2024-03-24 21:50:02 UTC +* Number of recursive dependencies: 42 + +Run `revdepcheck::cloud_details(, "ggtern")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggtern-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotate + > ### Title: Create an annotation layer (ggtern version). + > ### Aliases: annotate + > + > ### ** Examples + > + > ggtern() + + ... + 3. ├─ggtern::ggplot_build(x) + 4. └─ggtern:::ggplot_build.ggplot(x) + 5. └─ggtern:::layers_add_or_remove_mask(plot) + 6. └─ggint$plot_theme(plot) + 7. └─ggplot2:::validate_theme(theme) + 8. └─base::mapply(...) + 9. └─ggplot2 (local) ``(...) + 10. └─cli::cli_abort(...) + 11. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘sp’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘chemometrics’ + ``` + +# ggupset + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/const-ae/ggupset +* Source code: https://github.com/cran/ggupset +* Date/Publication: 2024-06-24 10:10:04 UTC +* Number of recursive dependencies: 46 + +Run `revdepcheck::cloud_details(, "ggupset")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ggupset-Ex.R’ failed + The error most likely occurred in: + + > ### Name: axis_combmatrix + > ### Title: Convert delimited text labels into a combination matrix axis + > ### Aliases: axis_combmatrix + > + > ### ** Examples + > + > library(ggplot2) + ... + Datsun 710 Cyl: 4_Gears: 4 + Hornet 4 Drive Cyl: 6_Gears: 3 + Hornet Sportabout Cyl: 8_Gears: 3 + Valiant Cyl: 6_Gears: 3 + > ggplot(mtcars, aes(x=combined)) + + + geom_bar() + + + axis_combmatrix(sep = "_") + Error in as.unit(e2) : object is not coercible to a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit + Execution halted + ``` + +# ggVennDiagram + +
+ +* Version: 1.5.2 +* GitHub: https://github.com/gaospecial/ggVennDiagram +* Source code: https://github.com/cran/ggVennDiagram +* Date/Publication: 2024-02-20 08:10:02 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "ggVennDiagram")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘fully-customed.Rmd’ + ... + [1] "b" "c" "e" "h" "k" "q" "s" "y" + + + > ggVennDiagram(y, show_intersect = TRUE, set_color = "black") + Warning in geom_text(aes(label = .data$count, text = .data$item), data = region_label) : + Ignoring unknown aesthetics: text + + ... + Ignoring unknown aesthetics: text + + When sourcing ‘using-ggVennDiagram.R’: + Error: subscript out of bounds + Execution halted + + ‘VennCalculator.Rmd’ using ‘UTF-8’... OK + ‘fully-customed.Rmd’ using ‘UTF-8’... failed + ‘using-ggVennDiagram.Rmd’ using ‘UTF-8’... failed + ‘using-new-shapes.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘VennCalculator.Rmd’ using rmarkdown + --- finished re-building ‘VennCalculator.Rmd’ + + --- re-building ‘fully-customed.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.1Mb + sub-directories of 1Mb or more: + doc 9.5Mb + help 1.1Mb + ``` + +# GimmeMyPlot + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/GimmeMyPlot +* Date/Publication: 2023-10-18 16:10:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "GimmeMyPlot")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GimmeMyPlot-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_violin + > ### Title: Violin plot + > ### Aliases: plot_violin + > + > ### ** Examples + > + > library(RColorBrewer) + ... + + width_text = 5, + + pch_colour = "gray30", + + pch_alpha = 0.5, + + width_title = 30, + + lwd = 1.25, + + digits = 2 + + ) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_violin ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 4. └─GimmeMyPlot::plot_violin(df) + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + > df[, 3] <- runif(10, 1, 2) + + > colnames(df) <- paste0("X", seq(3)) + + > plot_violin(df, title = "Some random variables", colour = brewer.pal(9, + + "Set1")[seq(3)]) + + When sourcing ‘Tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 24-57 [violin] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# giniVarCI + +
+ +* Version: 0.0.1-3 +* GitHub: NA +* Source code: https://github.com/cran/giniVarCI +* Date/Publication: 2024-01-08 10:30:02 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "giniVarCI")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘giniVarCI-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fcompareCI + > ### Title: Comparisons of variance estimates and confidence intervals for + > ### the Gini index in finite populations + > ### Aliases: fcompareCI + > + > ### ** Examples + > + ... + > data(eusilc, package="laeken") + > y <- eusilc$eqIncome[eusilc$db040 == "Burgenland"] + > w <- eusilc$rb050[eusilc$db040 == "Burgenland"] + > + > # Estimation of the Gini index and confidence intervals using different methods. + > fcompareCI(y, w) + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: fcompareCI + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 12.5Mb + sub-directories of 1Mb or more: + libs 12.0Mb + ``` + +# gMCPLite + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/Merck/gMCPLite +* Source code: https://github.com/cran/gMCPLite +* Date/Publication: 2024-01-11 19:30:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "gMCPLite")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘GraphicalMultiplicity.Rmd’ + ... + 0.8600 + 0.1400 + + + + > plot(os, plottype = "HR", xlab = "Events") + + When sourcing ‘GraphicalMultiplicity.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘GraphicalMultiplicity.Rmd’ using ‘UTF-8’... failed + ‘hGraph.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘GraphicalMultiplicity.Rmd’ using rmarkdown + ``` + +# gMOIP + +
+ +* Version: 1.5.2 +* GitHub: https://github.com/relund/gMOIP +* Source code: https://github.com/cran/gMOIP +* Date/Publication: 2024-02-21 21:30:05 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "gMOIP")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gMOIP-Ex.R’ failed + The error most likely occurred in: + + > ### Name: convexHull + > ### Title: Find the convex hull of a set of points. + > ### Aliases: convexHull + > + > ### ** Examples + > + > ## 1D + ... + + $pts + p1 p2 pt vtx + 1 1 1 1 TRUE + 2 2 2 1 TRUE + + > plotHull2D(pts, drawPoints = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plotHull2D ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘bi-objective_2x.Rmd’ + ... + + > b <- c(3, 27, 90) + + > obj <- matrix(c(7, -10, -10, -10), nrow = 2) + + > plotBiObj2D(A, b, obj, addTriangles = FALSE) + + ... + When sourcing ‘polytope_2d.R’: + Error: argument is of length zero + Execution halted + + ‘bi-objective_2x.Rmd’ using ‘UTF-8’... failed + ‘bi-objective_3x_ex1.Rmd’ using ‘UTF-8’... OK + ‘intro.Rmd’ using ‘UTF-8’... failed + ‘polytope_2d.Rmd’ using ‘UTF-8’... failed + ‘polytope_3d_ex1.Rmd’ using ‘UTF-8’... OK + ‘tri-objective.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘bi-objective_2x.Rmd’ using rmarkdown + + Quitting from lines 73-78 [2DLP] (bi-objective_2x.Rmd) + Error: processing vignette 'bi-objective_2x.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘bi-objective_2x.Rmd’ + + --- re-building ‘bi-objective_3x_ex1.Rmd’ using rmarkdown + ``` + +# GofCens + +
+ +* Version: 1.1 +* GitHub: NA +* Source code: https://github.com/cran/GofCens +* Date/Publication: 2024-07-29 08:40:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "GofCens")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘GofCens-Ex.R’ failed + The error most likely occurred in: + + > ### Name: kmPlot + > ### Title: Plot of the Kaplen-Meier and parametric estimations + > ### Aliases: kmPlot kmPlot.default kmPlot.formula kmPlot.probPlot + > ### kmPlot.probPlot + > + > ### ** Examples + > + ... + Scale: 10.039 + + > + > # Plots for censored data using ggplot2 + > data(colon) + Warning in data(colon) : data set ‘colon’ not found + > kmPlot(Surv(time, status) ~ 1, colon, distr= "lognormal", ggp = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: kmPlot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# greatR + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/ruthkr/greatR +* Source code: https://github.com/cran/greatR +* Date/Publication: 2024-04-09 22:40:07 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "greatR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘process-results.Rmd’ + ... + + > reg_summary$non_registered_genes + [1] "BRAA02G018970.3C" + + > plot(reg_summary, type = "registered", scatterplot_size = c(4, + + 3.5)) + + When sourcing ‘process-results.R’: + Error: object is not a unit + Execution halted + + ‘data-requirement.Rmd’ using ‘UTF-8’... OK + ‘process-results.Rmd’ using ‘UTF-8’... failed + ‘register-data-manually.Rmd’ using ‘UTF-8’... OK + ‘register-data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘data-requirement.Rmd’ using rmarkdown + --- finished re-building ‘data-requirement.Rmd’ + + --- re-building ‘process-results.Rmd’ using rmarkdown + + Quitting from lines 76-81 [plot-summary-results] (process-results.Rmd) + Error: processing vignette 'process-results.Rmd' failed with diagnostics: + object is not a unit + ... + --- finished re-building ‘register-data-manually.Rmd’ + + --- re-building ‘register-data.Rmd’ using rmarkdown + --- finished re-building ‘register-data.Rmd’ + + SUMMARY: processing the following file failed: + ‘process-results.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# Greymodels + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/havishaJ/Greymodels +* Source code: https://github.com/cran/Greymodels +* Date/Publication: 2022-12-05 12:42:35 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "Greymodels")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Greymodels-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Plots + > ### Title: plots + > ### Aliases: plots plotrm plotsmv1 plotsmv2 plotsigndgm plots_mdbgm12 + > + > ### ** Examples + > + > # Plots - EPGM (1, 1) model + ... + + geom_point(data = set4, aes(x = CI, y = y), shape = 23, color = "black") + + + geom_line(data = xy1, aes(x = x, y = y,color = "Raw Data")) + + + geom_line(data = xy2, aes(x = x, y = y,color = "Fitted&Forecasts")) + + + geom_line(data = set3, aes(x = CI, y = y,color = "LowerBound"), linetype=2) + + + geom_line(data = set4, aes(x = CI, y = y,color = "UpperBound"), linetype=2) + + + scale_color_manual(name = "Label",values = colors) + > r <- ggplotly(p) + Error in pm[[2]] : subscript out of bounds + Calls: ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# gsDesign + +
+ +* Version: 3.6.4 +* GitHub: https://github.com/keaven/gsDesign +* Source code: https://github.com/cran/gsDesign +* Date/Publication: 2024-07-26 23:20:10 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "gsDesign")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘gsDesign-Ex.R’ failed + The error most likely occurred in: + + > ### Name: summary.gsDesign + > ### Title: Bound Summary and Z-transformations + > ### Aliases: summary.gsDesign print.gsDesign gsBoundSummary xprint + > ### print.gsBoundSummary gsBValue gsDelta gsRR gsHR gsCPz + > ### Keywords: design + > + > ### ** Examples + ... + ~RR at bound 0.6605 0.6605 + P(Cross) if RR=1 0.0239 0.9761 + P(Cross) if RR=0.5 0.9000 0.1000 + > gsRR(z = xp$lower$bound, i = 1:3, xrr) + [1] 1.0732500 0.8211496 NA + > plot(xrr, plottype = "RR") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gsDesign) + > + > test_check("gsDesign") + Linear spending function with none = [ FAIL 15 | WARN 9 | SKIP 98 | PASS 1799 ] + + ══ Skipped tests (98) ══════════════════════════════════════════════════════════ + ... + 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 22. └─grid:::drawGrob(x) + 23. ├─grid::drawDetails(x, recording = FALSE) + 24. └─grid:::drawDetails.polyline(x, recording = FALSE) + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 15 | WARN 9 | SKIP 98 | PASS 1799 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ConditionalPowerPlot.Rmd’ + ... + + > cp <- gsCP(x = update, i = 1, zi = -qnorm(p), theta = theta) + + > plot(cp, xval = hr, xlab = "Future HR", ylab = "Conditional Power/Error", + + main = "Conditional probability of crossing future bound", + + o .... [TRUNCATED] + + ... + ‘PoissonMixtureModel.Rmd’ using ‘UTF-8’... OK + ‘SpendingFunctionOverview.Rmd’ using ‘UTF-8’... OK + ‘SurvivalOverview.Rmd’ using ‘UTF-8’... OK + ‘VaccineEfficacy.Rmd’ using ‘UTF-8’... OK + ‘binomialSPRTExample.Rmd’ using ‘UTF-8’... OK + ‘gsDesignPackageOverview.Rmd’ using ‘UTF-8’... failed + ‘gsSurvBasicExamples.Rmd’ using ‘UTF-8’... failed + ‘hGraph.Rmd’ using ‘UTF-8’... OK + ‘nNormal.Rmd’ using ‘UTF-8’... OK + ‘toInteger.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ConditionalErrorSpending.Rmd’ using rmarkdown + ``` + +# gtExtras + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/jthomasmock/gtExtras +* Source code: https://github.com/cran/gtExtras +* Date/Publication: 2023-09-15 22:32:06 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "gtExtras")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gtExtras) + Loading required package: gt + + Attaching package: 'gt' + + The following object is masked from 'package:testthat': + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-gt_plt_bar.R:44:3'): gt_plt_bar svg is created and has specific values ── + `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`). + + `actual`: "49.19" "32.79" "16.40" "0.00" "0.00" "0.00" + `expected`: "49.19" "32.79" "16.40" "16.40" "32.79" "49.19" + + [ FAIL 1 | WARN 14 | SKIP 23 | PASS 115 ] + Error: Test failures + Execution halted + ``` + +# HaploCatcher + +
+ +* Version: 1.0.4 +* GitHub: NA +* Source code: https://github.com/cran/HaploCatcher +* Date/Publication: 2023-04-21 23:32:39 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "HaploCatcher")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘An_Intro_to_HaploCatcher.Rmd’ + ... + > set.seed(NULL) + + > results1 <- auto_locus(geno_mat = geno_mat, gene_file = gene_comp, + + gene_name = "sst1_solid_stem", marker_info = marker_info, + + chromosom .... [TRUNCATED] + Loading required package: lattice + + When sourcing ‘An_Intro_to_HaploCatcher.R’: + Error: object is not a unit + Execution halted + + ‘An_Intro_to_HaploCatcher.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘An_Intro_to_HaploCatcher.Rmd’ using rmarkdown + + Quitting from lines 242-253 [example_models_1] (An_Intro_to_HaploCatcher.Rmd) + Error: processing vignette 'An_Intro_to_HaploCatcher.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘An_Intro_to_HaploCatcher.Rmd’ + + SUMMARY: processing the following file failed: + ‘An_Intro_to_HaploCatcher.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# healthyR + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/spsanderson/healthyR +* Source code: https://github.com/cran/healthyR +* Date/Publication: 2024-07-01 13:20:02 UTC +* Number of recursive dependencies: 146 + +Run `revdepcheck::cloud_details(, "healthyR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘getting-started.Rmd’ + ... + + .by = "month", .interactive = FALSE) + Warning: Ignoring unknown labels: + • `colour = "Legend"` + + > ts_alos_plt(.data = df_tbl, .date_col = Date, .value_col = Values, + + .by = "month", .interactive = TRUE) + + When sourcing ‘getting-started.R’: + Error: subscript out of bounds + Execution halted + + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘getting-started.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + data 2.5Mb + doc 3.7Mb + ``` + +# healthyR.ts + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/spsanderson/healthyR.ts +* Source code: https://github.com/cran/healthyR.ts +* Date/Publication: 2023-11-15 06:00:05 UTC +* Number of recursive dependencies: 200 + +Run `revdepcheck::cloud_details(, "healthyR.ts")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘healthyR.ts-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tidy_fft + > ### Title: Tidy Style FFT + > ### Aliases: tidy_fft + > + > ### ** Examples + > + > suppressPackageStartupMessages(library(dplyr)) + ... + > a <- tidy_fft( + + .data = data_tbl, + + .value_col = value, + + .date_col = date_col, + + .harmonics = 3, + + .frequency = 12 + + ) + Error in pm[[2]] : subscript out of bounds + Calls: tidy_fft -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘using-tidy-fft.Rmd’ + ... + $ value 112, 118, 132, 129, 121, 135, 148, 148, 136, 119, 104, 118, 1… + + > suppressPackageStartupMessages(library(timetk)) + + > data_tbl %>% plot_time_series(.date_var = date_col, + + .value = value) + + When sourcing ‘using-tidy-fft.R’: + Error: subscript out of bounds + Execution halted + + ‘getting-started.Rmd’ using ‘UTF-8’... OK + ‘using-tidy-fft.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘getting-started.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + sub-directories of 1Mb or more: + doc 5.2Mb + ``` + +# heatmaply + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/talgalili/heatmaply +* Source code: https://github.com/cran/heatmaply +* Date/Publication: 2023-10-06 20:50:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "heatmaply")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(heatmaply) + Loading required package: plotly + Loading required package: ggplot2 + + Attaching package: 'plotly' + + ... + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. ├─heatmaply:::predict_colors(ggplotly(g), plot_method = "ggplot") + 7. ├─plotly::ggplotly(g) + 8. └─plotly:::ggplotly.ggplot(g) + 9. └─plotly::gg2list(...) + + [ FAIL 58 | WARN 0 | SKIP 0 | PASS 193 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘heatmaply.Rmd’ + ... + + > library("heatmaply") + + > library("heatmaply") + + > heatmaply(mtcars) + + When sourcing ‘heatmaply.R’: + Error: subscript out of bounds + Execution halted + + ‘heatmaply.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘heatmaply.Rmd’ using rmarkdown + + Quitting from lines 109-111 [unnamed-chunk-5] (heatmaply.Rmd) + Error: processing vignette 'heatmaply.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘heatmaply.Rmd’ + + SUMMARY: processing the following file failed: + ‘heatmaply.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + doc 5.1Mb + ``` + +# hermiter + +
+ +* Version: 2.3.1 +* GitHub: https://github.com/MikeJaredS/hermiter +* Source code: https://github.com/cran/hermiter +* Date/Publication: 2024-03-06 23:50:02 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "hermiter")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘hermiter.Rmd’ + ... + > p2 <- ggplot(df_pdf_cdf) + geom_tile(aes(X, Y, fill = pdf_est)) + + + scale_fill_continuous_sequential(palette = "Oslo", breaks = seq(0, + + .... [TRUNCATED] + + > p1 + ggtitle("Actual PDF") + theme(legend.title = element_blank()) + + + p2 + ggtitle("Estimated PDF") + theme(legend.title = element_blank()) + .... [TRUNCATED] + + When sourcing ‘hermiter.R’: + Error: object is not a unit + Execution halted + + ‘hermiter.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘hermiter.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + R 2.6Mb + doc 1.9Mb + libs 2.0Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# heumilkr + +
+ +* Version: 0.2.0 +* GitHub: https://github.com/lschneiderbauer/heumilkr +* Source code: https://github.com/cran/heumilkr +* Date/Publication: 2024-04-01 13:50:06 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "heumilkr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘clarke_wright_performance.Rmd’ + ... + + "F", "tai"), group_desc = c("Augerat A, 1995", "Augerat B, 1995", + + "Christofides and ..." ... [TRUNCATED] + + > ggMarginal(ggplot(merge(result, description, by = "group"), + + aes(x = n_site, y = clarke_wright_perf_xi, color = group_desc)) + + + geom_poi .... [TRUNCATED] + + When sourcing ‘clarke_wright_performance.R’: + Error: argument is of length zero + Execution halted + + ‘clarke_wright_performance.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘clarke_wright_performance.Rmd’ using rmarkdown + + Quitting from lines 69-97 [perf_scale_based_graph] (clarke_wright_performance.Rmd) + Error: processing vignette 'clarke_wright_performance.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘clarke_wright_performance.Rmd’ + + SUMMARY: processing the following file failed: + ‘clarke_wright_performance.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# hilldiv + +
+ +* Version: 1.5.1 +* GitHub: https://github.com/anttonalberdi/hilldiv +* Source code: https://github.com/cran/hilldiv +* Date/Publication: 2019-10-01 14:40:02 UTC +* Number of recursive dependencies: 144 + +Run `revdepcheck::cloud_details(, "hilldiv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘hilldiv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: div_test_plot + > ### Title: Diversity test plotting + > ### Aliases: div_test_plot + > ### Keywords: chart comparison hill numbers + > + > ### ** Examples + > + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +# hmclearn + +
+ +* Version: 0.0.5 +* GitHub: NA +* Source code: https://github.com/cran/hmclearn +* Date/Publication: 2020-10-05 06:40:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "hmclearn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘hmclearn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: hmclearn-plots + > ### Title: Plotting for MCMC visualization and diagnostics provided by + > ### 'bayesplot' package + > ### Aliases: hmclearn-plots mcmc_intervals mcmc_intervals.hmclearn + > ### mcmc_areas mcmc_areas.hmclearn mcmc_hist mcmc_hist.hmclearn + > ### mcmc_hist_by_chain mcmc_hist_by_chain.hmclearn mcmc_dens + > ### mcmc_dens.hmclearn mcmc_scatter mcmc_scatter.hmclearn mcmc_hex + ... + + param = list(y=y, X=X), + + parallel=FALSE, chains=2) + > + > mcmc_trace(f, burnin=100) + > mcmc_hist(f, burnin=100) + `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. + > mcmc_intervals(f, burnin=100) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: mcmc_intervals ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# HTLR + +
+ +* Version: 0.4-4 +* GitHub: https://github.com/longhaiSK/HTLR +* Source code: https://github.com/cran/HTLR +* Date/Publication: 2022-10-22 12:47:53 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "HTLR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘simu.Rmd’ + ... + [1] "median" + + > post.t <- as.matrix(fit.t2, k = 2) + + > mcmc_intervals(post.t, pars = c("Intercept", "V1", + + "V2", "V3", "V1000")) + + When sourcing ‘simu.R’: + Error: argument is of length zero + Execution halted + + ‘simu.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘simu.Rmd’ using rmarkdown + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.8Mb + sub-directories of 1Mb or more: + data 2.0Mb + doc 1.1Mb + libs 5.4Mb + ``` + +# HVT + +
+ +* Version: 24.5.2 +* GitHub: https://github.com/Mu-Sigma/HVT +* Source code: https://github.com/cran/HVT +* Date/Publication: 2024-05-15 08:50:21 UTC +* Number of recursive dependencies: 200 + +Run `revdepcheck::cloud_details(, "HVT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘HVT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: getTransitionProbability + > ### Title: Creating Transition Probabilities list + > ### Aliases: getTransitionProbability + > ### Keywords: Transition_or_Prediction + > + > ### ** Examples + > + ... + Ignoring unknown parameters: `check_overlap` + Scale for x is already present. + Adding another scale for x, which will replace the existing scale. + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Warning in geom_polygon(data = boundaryCoords2, aes(x = bp.x, y = bp.y, : + Ignoring unknown aesthetics: text + Error in pm[[2]] : subscript out of bounds + Calls: scoreHVT -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# hypsoLoop + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/hypsoLoop +* Date/Publication: 2022-02-08 09:00:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "hypsoLoop")` for more info + +
+ +## Newly broken + +* checking whether package ‘hypsoLoop’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: replacing previous import ‘ggplot2::set_theme’ by ‘sjPlot::set_theme’ when loading ‘hypsoLoop’ + See ‘/tmp/workdir/hypsoLoop/new/hypsoLoop.Rcheck/00install.out’ for details. + ``` + +# ibdsim2 + +
+ +* Version: 2.1.1 +* GitHub: https://github.com/magnusdv/ibdsim2 +* Source code: https://github.com/cran/ibdsim2 +* Date/Publication: 2024-09-08 07:40:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "ibdsim2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ibdsim2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotSegmentDistribution + > ### Title: Scatter plots of IBD segment distributions + > ### Aliases: plotSegmentDistribution + > + > ### ** Examples + > + > + ... + Skip recomb : - + Total time used: 0.00288 secs + > + > # By default, the IBD segments of the "leaves" are computed and plotted + > plotSegmentDistribution(simPat, simMat, type = "ibd1", ids = 4:5, + + labels = c("HSpat", "HSmat")) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# ICtest + +
+ +* Version: 0.3-5 +* GitHub: NA +* Source code: https://github.com/cran/ICtest +* Date/Publication: 2022-05-18 07:30:29 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "ICtest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ICtest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggplot.ictest + > ### Title: Scatterplot Matrix for a ictest Object using ggplot2 + > ### Aliases: ggplot.ictest + > ### Keywords: hplot + > + > ### ** Examples + > + ... + > # The aesthetics variables + > mapvar <- data.frame(iris[, 5]) + > colnames(mapvar) <- "species" + > + > TestCov <- PCAasymp(X, k = 2) + > ggplot(TestCov) + > ggplot(TestCov, aes(color = species), mapvar = mapvar, which = "k") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.7Mb + sub-directories of 1Mb or more: + doc 2.5Mb + libs 2.9Mb + ``` + +# idiogramFISH + +
+ +* Version: 2.0.13 +* GitHub: NA +* Source code: https://github.com/cran/idiogramFISH +* Date/Publication: 2023-08-22 16:50:02 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "idiogramFISH")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.1Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 2.0Mb + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘index.Rmd’ + ... + > if (requireNamespace("RCurl", quietly = TRUE)) { + + v <- sub("Version: ", "", readLines("../DESCRIPTION")[3]) + + pkg <- "idiogramFISH" + + l .... [TRUNCATED] + Warning in file(con, "r") : + cannot open file '../DESCRIPTION': No such file or directory + + When sourcing ‘index.R’: + Error: cannot open the connection + Execution halted + + ‘AVignette.Rmd’ using ‘UTF-8’... OK + ‘index.Rmd’ using ‘UTF-8’... failed + ``` + +# IDMIR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/IDMIR +* Date/Publication: 2023-11-09 15:30:02 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "IDMIR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IDMIR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PlotSurvival + > ### Title: PlotSurvival + > ### Aliases: PlotSurvival + > + > ### ** Examples + > + > # Obtain the example data + ... + > GEP<-GetData_Mirna("GEP") + > survival<-GetData_Mirna("survival") + > MiRNAs<-c("hsa-miR-21-5p","hsa-miR-26a-5p","hsa-miR-369-5p","hsa-miR-1238-3p","hsa-miR-10b-5p") + > # Run the function + > SingleMiRNA_CRData<-SingleMiRNA_CRModel(GEP, + + "hsa-miR-21-5p",survival,cutoff.point=NULL) + > PlotSurvival(SingleMiRNA_CRData) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PlotSurvival ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘IDMIR.Rmd’ + ... + > survival <- GetData_Mirna("survival") + + > SingleMiRNA_CRData <- SingleMiRNA_CRModel(GEP, "hsa-miR-21-5p", + + cutoff.point = NULL, survival) + + > PlotSurvival(SingleMiRNA_CRData) + + When sourcing ‘IDMIR.R’: + Error: argument is of length zero + Execution halted + + ‘IDMIR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘IDMIR.Rmd’ using rmarkdown + + Quitting from lines 120-130 [unnamed-chunk-7] (IDMIR.Rmd) + Error: processing vignette 'IDMIR.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘IDMIR.Rmd’ + + SUMMARY: processing the following file failed: + ‘IDMIR.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# idopNetwork + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/cxzdsa2332/idopNetwork +* Source code: https://github.com/cran/idopNetwork +* Date/Publication: 2023-04-18 06:50:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "idopNetwork")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘idopNetwork_vignette.Rmd’ + ... + + > qdODE_plot_base(ode.test) + + > ode.module = test_result$d1_module + + > qdODE_plot_all(ode.module) + + When sourcing ‘idopNetwork_vignette.R’: + Error: object is not a unit + Execution halted + + ‘idopNetwork_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘idopNetwork_vignette.Rmd’ using rmarkdown + ``` + +# ihclust + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/ihclust +* Date/Publication: 2022-04-27 07:20:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "ihclust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ihclust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ihclust + > ### Title: Iterative Hierarchical Clustering (IHC) + > ### Aliases: ihclust + > + > ### ** Examples + > + > # This is an example not using the permutation approach + ... + 12. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# immunarch + +
+ +* Version: 0.9.1 +* GitHub: https://github.com/immunomind/immunarch +* Source code: https://github.com/cran/immunarch +* Date/Publication: 2024-03-18 19:10:06 UTC +* Number of recursive dependencies: 198 + +Run `revdepcheck::cloud_details(, "immunarch")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘immunarch-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geneUsageAnalysis + > ### Title: Post-analysis of V-gene and J-gene statistics: PCA, clustering, + > ### etc. + > ### Aliases: geneUsageAnalysis + > + > ### ** Examples + > + ... + 17. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 19. │ ├─ggplot2::ggplot_add(object, p, objectname) + 20. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 21. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 22. └─base::.handleSimpleError(...) + 23. └─purrr (local) h(simpleError(msg, call)) + 24. └─cli::cli_abort(...) + 25. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 5.5Mb + doc 1.6Mb + ``` + +# incidental + +
+ +* Version: 0.1 +* GitHub: NA +* Source code: https://github.com/cran/incidental +* Date/Publication: 2020-09-16 09:50:03 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "incidental")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘incidental-tutorial.Rmd’ + ... + + > data_subset = do.call("rbind", model_df_list) + + > ggplot(data_subset, aes(x = Time, y = Reported)) + + + geom_point(color = "coral2", shape = 3) + geom_line(aes(x = Time, + + y = Ihat), color .... [TRUNCATED] + + When sourcing ‘incidental-tutorial.R’: + Error: `x` must be a vector, not a object. + Execution halted + + ‘incidental-tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘incidental-tutorial.Rmd’ using rmarkdown + ``` + +# infer + +
+ +* Version: 1.0.7 +* GitHub: https://github.com/tidymodels/infer +* Source code: https://github.com/cran/infer +* Date/Publication: 2024-03-25 21:50:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "infer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘infer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: shade_confidence_interval + > ### Title: Add information about confidence interval + > ### Aliases: shade_confidence_interval shade_ci + > + > ### ** Examples + > + > # find the point estimate---mean number of hours worked per week + ... + + type = "se") + > + > + > # and plot it! + > boot_dist %>% + + visualize() + + + shade_confidence_interval(ci) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 18. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 19. │ ├─ggplot2::ggplot_add(object, p, objectname) + 20. │ └─ggplot2:::ggplot_add.list(object, p, objectname) + 21. │ ├─ggplot2::ggplot_add(o, plot, object_name) + 22. │ └─ggplot2:::ggplot_add.Layer(o, plot, object_name) + 23. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 24. └─base::.handleSimpleError(...) + 25. └─testthat (local) h(simpleError(msg, call)) + 26. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘anova.Rmd’ + ... + + generate(reps = 1000, type = "permute") %>% calculate( .... [TRUNCATED] + Dropping unused factor levels DK from the supplied explanatory variable + 'partyid'. + + > null_dist %>% visualize() + shade_p_value(observed_f_statistic, + + direction = "greater") + + ... + When sourcing ‘t_test.R’: + Error: argument is of length zero + Execution halted + + ‘anova.Rmd’ using ‘UTF-8’... failed + ‘chi_squared.Rmd’ using ‘UTF-8’... failed + ‘infer.Rmd’ using ‘UTF-8’... failed + ‘observed_stat_examples.Rmd’ using ‘UTF-8’... failed + ‘paired.Rmd’ using ‘UTF-8’... failed + ‘t_test.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘anova.Rmd’ using rmarkdown + ``` + +# injurytools + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/lzumeta/injurytools +* Source code: https://github.com/cran/injurytools +* Date/Publication: 2023-11-14 17:20:05 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "injurytools")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘model-injury-data-ii.Rmd’ + ... + n events median 0.95LCL 0.95UCL + seasonb=2017/2018 23 16 265 152 NA + seasonb=2018/2019 19 17 106 84 165 + + > ggsurvplot(fit, data = injd_sub, palette = c("#E7B800", + + "#2E9FDF")) + xlab("Time [calendar days]") + ylab(expression("Survival probability ( ..." ... [TRUNCATED] + + When sourcing ‘model-injury-data-ii.R’: + Error: argument is of length zero + Execution halted + + ‘estimate-epi-measures.Rmd’ using ‘UTF-8’... OK + ‘model-injury-data-i.Rmd’ using ‘UTF-8’... OK + ‘model-injury-data-ii.Rmd’ using ‘UTF-8’... failed + ‘prepare-injury-data.Rmd’ using ‘UTF-8’... OK + ‘visualize-injury-data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘estimate-epi-measures.Rmd’ using rmarkdown + --- finished re-building ‘estimate-epi-measures.Rmd’ + + --- re-building ‘model-injury-data-i.Rmd’ using rmarkdown + ``` + +# inlabru + +
+ +* Version: 2.11.1 +* GitHub: https://github.com/inlabru-org/inlabru +* Source code: https://github.com/cran/inlabru +* Date/Publication: 2024-07-01 23:30:02 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "inlabru")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘inlabru-Ex.R’ failed + The error most likely occurred in: + + > ### Name: seals + > ### Title: Seal pups + > ### Aliases: seals seals_sp + > ### Keywords: datasets + > + > ### ** Examples + > + > if (require(ggplot2, quietly = TRUE)) { + + ggplot() + + + geom_fm(data = seals_sp$mesh) + + + gg(seals_sp$points) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (require(testthat, quietly = TRUE)) { + + test_check("inlabru") + + } + Loading required package: inlabru + Loading required package: fmesher + Starting 2 test processes + [ FAIL 2 | WARN 0 | SKIP 49 | PASS 144 ] + ... + 9. │ └─INLA:::expand.inla.stack.responses(responses) + 10. │ └─base::lapply(...) + 11. │ └─INLA (local) FUN(X[[i]], ...) + 12. │ └─dplyr::bind_rows(...) + 13. │ └─vctrs::vec_rbind(!!!dots, .names_to = .id, .error_call = current_env()) + 14. └─rlang::abort(message = message) + + [ FAIL 2 | WARN 0 | SKIP 49 | PASS 144 ] + Error: Test failures + Execution halted + ``` + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘stars’ + ``` + +# insurancerating + +
+ +* Version: 0.7.4 +* GitHub: https://github.com/mharinga/insurancerating +* Source code: https://github.com/cran/insurancerating +* Date/Publication: 2024-05-20 11:30:03 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "insurancerating")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘insurancerating-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.univariate + > ### Title: Automatically create a ggplot for objects obtained from + > ### univariate() + > ### Aliases: autoplot.univariate + > + > ### ** Examples + > + ... + > xzip <- univariate(MTPL, x = bm, severity = amount, nclaims = nclaims, + + exposure = exposure, by = zip) + > autoplot(xzip, show_plots = 1:2) + Warning: Removed 16 rows containing missing values or values outside the scale range + (`geom_point()`). + Warning: Removed 5 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# inTextSummaryTable + +
+ +* Version: 3.3.3 +* GitHub: https://github.com/openanalytics/inTextSummaryTable +* Source code: https://github.com/cran/inTextSummaryTable +* Date/Publication: 2024-06-12 18:30:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "inTextSummaryTable")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(inTextSummaryTable) + > + > test_check("inTextSummaryTable") + [ FAIL 62 | WARN 0 | SKIP 0 | PASS 878 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 6. └─inTextSummaryTable::subjectProfileSummaryPlot(...) + 7. └─ggplot2:::`+.gg`(gg, do.call(geom_line, argsGeomLine)) + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 62 | WARN 0 | SKIP 0 | PASS 878 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘inTextSummaryTable-aesthetics.Rmd’ + ... + + > summaryTable <- data.frame(visit = c(1, 2, 1, 2), + + TRT = c("A", "A", "B", "B"), statMean = rnorm(4)) + + > subjectProfileSummaryPlot(data = summaryTable, xVar = "visit", + + colorVar = "TRT") + + ... + Error: argument is of length zero + Execution halted + + ‘inTextSummaryTable-advanced.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-aesthetics.Rmd’ using ‘UTF-8’... failed + ‘inTextSummaryTable-createTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-exportTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-introduction.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-standardTables.Rmd’ using ‘UTF-8’... OK + ‘inTextSummaryTable-visualization.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘inTextSummaryTable-advanced.Rmd’ using rmarkdown + --- finished re-building ‘inTextSummaryTable-advanced.Rmd’ + + --- re-building ‘inTextSummaryTable-aesthetics.Rmd’ using rmarkdown + + Quitting from lines 211-224 [aesthetics-defaultsVisualization] (inTextSummaryTable-aesthetics.Rmd) + Error: processing vignette 'inTextSummaryTable-aesthetics.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘inTextSummaryTable-aesthetics.Rmd’ + ... + Error: processing vignette 'inTextSummaryTable-visualization.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘inTextSummaryTable-visualization.Rmd’ + + SUMMARY: processing the following files failed: + ‘inTextSummaryTable-aesthetics.Rmd’ + ‘inTextSummaryTable-visualization.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.3Mb + sub-directories of 1Mb or more: + doc 9.7Mb + ``` + +# inventorize + +
+ +* Version: 1.1.1 +* GitHub: NA +* Source code: https://github.com/cran/inventorize +* Date/Publication: 2022-05-31 22:20:09 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "inventorize")` for more info + +
+ +## Newly broken + +* checking whether package ‘inventorize’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel -# actxps (thematic) - -# AeRobiology (unknown) - -``` -#
-# -# * Version: 2.0.1 -# * GitHub: NA -# * Source code: https://github.com/cran/AeRobiology -# * Date/Publication: 2019-06-03 06:20:03 UTC -# * Number of recursive dependencies: 98 -# -# Run `revdepcheck::cloud_details(, "AeRobiology")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘my-vignette.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘my-vignette.Rmd’ -# ... -# + export.plot = FALSE, export.result = FALSE, n.types = 3, -# + y.start = 2011, y.end = .... [TRUNCATED] -# -# > iplot_abundance(munich_pollen, interpolation = FALSE, -# + export.plot = FALSE, export.result = FALSE, n.types = 3, -# + y.start = 2011, y.end = .... [TRUNCATED] -# -# When sourcing ‘my-vignette.R’: -# Error: subscript out of bounds -# Execution halted -# -# ‘my-vignette.Rmd’ using ‘UTF-8’... failed -# ``` ``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Error in pm[[2]] : subscript out of bounds +Error: unable to load R code in package ‘inventorize’ +Execution halted +ERROR: lazy loading failed for package ‘inventorize’ +* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ -# agricolaeplotr (missing labels) - -# AnalysisLin (plotly) - -# animbook (plotly) - -# ANN2 (missing labels) - -# aplot (patchwork) - -# applicable (missing labels) - -# ASRgenomics (factoextra) - -# autoplotly (plotly) - -# autoReg (patchwork) - -# bartMan (ggnewscale) - -# bayesAB (missing labels) - -# BayesGrowth (ggdist) - -# BayesianReasoning (missing labels) - -# BayesMallows (missing labels) - -# bayesplot (missing labels) - -# bayestestR (patchwork) - -# beastt (ggdist) - -# besthr (patchwork) - -# biclustermd (xintercept/yintercept class) - -# biodosetools (missing labels) - -# boxly (plotly) - -# braidReports (annotation_logticks) - -# breathtestcore (plot slots) - -# brolgar (facet params: as.table) - -# cartograflow (plotly) - -# cartographr (unknown) ``` -#
-# -# * Version: 0.2.2 -# * GitHub: https://github.com/da-wi/cartographr -# * Source code: https://github.com/cran/cartographr -# * Date/Publication: 2024-06-28 14:50:09 UTC -# * Number of recursive dependencies: 99 -# -# Run `revdepcheck::cloud_details(, "cartographr")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > # This file is part of the standard setup for testthat. -# > # It is recommended that you do not modify it. -# > # -# > # Where should you do additional test configuration? -# > # Learn more about the roles of various files in: -# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview -# > # * https://testthat.r-lib.org/articles/special-files.html -# ... -# 21. │ └─base::stop(...) -# 22. └─base::.handleSimpleError(...) -# 23. └─rlang (local) h(simpleError(msg, call)) -# 24. └─handlers[[1L]](cnd) -# 25. └─cli::cli_abort(...) -# 26. └─rlang::abort(...) -# -# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 106 ] -# Error: Test failures -# Execution halted -# ``` -# -# ## In both -# -# * checking installed package size ... NOTE -# ``` -# installed size is 5.3Mb -# sub-directories of 1Mb or more: -# data 3.5Mb -# ``` -``` - -# cats (plotly) - -# cheem (plotly) - -# chillR (patchwork) - -# chronicle (plotly) - -# circhelp (patchwork) - -# clifro (missing labels) - -# clinDataReview (plotly) - -# clinUtils (plotly) - -# CohortPlat (plotly) - -# CoreMicrobiomeR (plotly) - -# correlationfunnel (plotly) - -# corrViz (plotly) - -# countfitteR (missing labels) - -# covidcast (unknown) - -``` -#
-# -# * Version: 0.5.2 -# * GitHub: https://github.com/cmu-delphi/covidcast -# * Source code: https://github.com/cran/covidcast -# * Date/Publication: 2023-07-12 23:40:06 UTC -# * Number of recursive dependencies: 93 -# -# Run `revdepcheck::cloud_details(, "covidcast")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(covidcast) -# We encourage COVIDcast API users to register on our mailing list: -# https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api -# We'll send announcements about new data sources, package updates, -# server maintenance, and new features. -# > -# ... -# • plot/default-county-choropleth.svg -# • plot/default-hrr-choropleth-with-include.svg -# • plot/default-msa-choropleth-with-include.svg -# • plot/default-state-choropleth-with-include.svg -# • plot/default-state-choropleth-with-range.svg -# • plot/state-choropleth-with-no-metadata.svg -# • plot/state-line-graph-with-range.svg -# • plot/state-line-graph-with-stderrs.svg -# Error: Test failures -# Execution halted -# ``` -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘plotting-signals.Rmd’ -# ... -# > knitr::opts_chunk$set(fig.width = 6, fig.height = 4) -# -# > plot(dv) -# -# When sourcing ‘plotting-signals.R’: -# Error: Problem while setting up geom aesthetics. -# ℹ Error occurred in the 6th layer. -# Caused by error in `$<-.data.frame`: -# ! replacement has 1 row, data has 0 -# Execution halted -# -# ‘correlation-utils.Rmd’ using ‘UTF-8’... OK -# ‘covidcast.Rmd’ using ‘UTF-8’... OK -# ‘external-data.Rmd’ using ‘UTF-8’... OK -# ‘multi-signals.Rmd’ using ‘UTF-8’... OK -# ‘plotting-signals.Rmd’ using ‘UTF-8’... failed -# ``` -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘correlation-utils.Rmd’ using rmarkdown -# --- finished re-building ‘correlation-utils.Rmd’ -# -# --- re-building ‘covidcast.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking data for non-ASCII characters ... NOTE -# ``` -# Note: found 20 marked UTF-8 strings -# ``` -``` - -# crosshap (plotly) - -# cubble (patchwork) - -# deeptime (ggnewscale) - -# distributional (ggdist) - -# dittoViz (plotly) - -# EGM (missing labels) - -# entropart (default access) - -# epiCleanr (ggdist) - -# esci (ggdist) - -# evalITR (unknown) - -``` -#
-# -# * Version: 1.0.0 -# * GitHub: https://github.com/MichaelLLi/evalITR -# * Source code: https://github.com/cran/evalITR -# * Date/Publication: 2023-08-25 23:10:06 UTC -# * Number of recursive dependencies: 167 -# -# Run `revdepcheck::cloud_details(, "evalITR")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘cv_multiple_alg.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘cv_multiple_alg.Rmd’ -# ... -# intersect, setdiff, setequal, union -# -# -# > load("../data/star.rda") -# Warning in readChar(con, 5L, useBytes = TRUE) : -# cannot open compressed file '../data/star.rda', probable reason 'No such file or directory' -# -# ... -# Execution halted -# -# ‘cv_multiple_alg.Rmd’ using ‘UTF-8’... failed -# ‘cv_single_alg.Rmd’ using ‘UTF-8’... failed -# ‘install.Rmd’ using ‘UTF-8’... OK -# ‘paper_alg1.Rmd’ using ‘UTF-8’... OK -# ‘sample_split.Rmd’ using ‘UTF-8’... failed -# ‘sample_split_caret.Rmd’ using ‘UTF-8’... failed -# ‘user_itr.Rmd’ using ‘UTF-8’... failed -# ‘user_itr_algs.Rmd’ using ‘UTF-8’... failed -# ``` -# -# * checking dependencies in R code ... NOTE -# ``` -# Namespaces in Imports field not imported from: -# ‘forcats’ ‘rqPen’ ‘utils’ -# All declared Imports should be used. -# ``` -``` - -# eventstudyr (missing labels) - -# EvoPhylo (patchwork) - -# expirest (missing labels) - -# explainer (plotly) - -# ezEDA (missing labels) - -# ezplot (0-length width) - -# fable.prophet (ggdist) - -# fabletools (ggdist) +### CRAN -# factoextra (0-length width) - -# fairmodels (missing labels) - -# fddm (ggforce) - -# feasts (missing labels) - -# ffp (ggdist) - -# fido (ggdist) - -# flipr (unknown) - -``` -#
-# -# * Version: 0.3.3 -# * GitHub: https://github.com/LMJL-Alea/flipr -# * Source code: https://github.com/cran/flipr -# * Date/Publication: 2023-08-23 09:00:02 UTC -# * Number of recursive dependencies: 106 -# -# Run `revdepcheck::cloud_details(, "flipr")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘alternative.Rmd’ using rmarkdown -# --- finished re-building ‘alternative.Rmd’ -# -# --- re-building ‘exactness.Rmd’ using rmarkdown -# -# Quitting from lines 142-177 [unnamed-chunk-1] (exactness.Rmd) -# Error: processing vignette 'exactness.Rmd' failed with diagnostics: -# subscript out of bounds -# --- failed re-building ‘exactness.Rmd’ -# -# --- re-building ‘flipr.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘exactness.Rmd’ -# ... -# -# > library(flipr) -# -# > load("../R/sysdata.rda") -# Warning in readChar(con, 5L, useBytes = TRUE) : -# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' -# -# ... -# cannot open compressed file '../R/sysdata.rda', probable reason 'No such file or directory' -# -# When sourcing ‘plausibility.R’: -# Error: cannot open the connection -# Execution halted -# -# ‘alternative.Rmd’ using ‘UTF-8’... OK -# ‘exactness.Rmd’ using ‘UTF-8’... failed -# ‘flipr.Rmd’ using ‘UTF-8’... failed -# ‘plausibility.Rmd’ using ‘UTF-8’... failed -# ``` -# -# * checking installed package size ... NOTE -# ``` -# installed size is 11.0Mb -# sub-directories of 1Mb or more: -# doc 9.1Mb -# libs 1.2Mb -# ``` -``` - -# foqat (ggnewscale) - -# forestly (patchwork) - -# frailtyEM (plotly) - -# funcharts (patchwork) - -# geomtextpath (default access) - -# GGally (missing labels) - -# gganimate (gganimate) - -# ggbrain (ggnewscale) - -# ggbreak (patchwork) - -# ggdark (default access) - -# ggdist (ggdist) - -# ggDoubleHeat (ggnewscale) - -# ggeasy (missing labels) - -# ggedit (saved to disk) - -# ggESDA (passing NULL aesthetic mapping) - -# ggfixest (visual differences) - -# ggforce (ggforce) - -Note: facet_zoom/facet_col/facet_row - -# ggformula (docs) - -# ggfortify (tests) - -# gggenomes (patchwork) - -# ggh4x (unknown) - -``` -#
-# -# * Version: 0.2.8 -# * GitHub: https://github.com/teunbrand/ggh4x -# * Source code: https://github.com/cran/ggh4x -# * Date/Publication: 2024-01-23 21:00:02 UTC -# * Number of recursive dependencies: 77 -# -# Run `revdepcheck::cloud_details(, "ggh4x")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘ggh4x-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: guide_stringlegend -# > ### Title: String legend -# > ### Aliases: guide_stringlegend -# > -# > ### ** Examples -# > -# > p <- ggplot(mpg, aes(displ, hwy)) + -# + geom_point(aes(colour = manufacturer)) -# > -# > # String legend can be set in the `guides()` function -# > p + guides(colour = guide_stringlegend(ncol = 2)) -# Error in (function (layer, df) : -# argument "theme" is missing, with no default -# Calls: ... use_defaults -> eval_from_theme -> %||% -> calc_element -# Execution halted -# ``` -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(ggh4x) -# Loading required package: ggplot2 -# > -# > test_check("ggh4x") -# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] -# -# ... -# 25. └─ggplot2 (local) compute_geom_2(..., self = self) -# 26. └─self$geom$use_defaults(...) -# 27. └─ggplot2 (local) use_defaults(..., self = self) -# 28. └─ggplot2:::eval_from_theme(default_aes, theme) -# 29. ├─calc_element("geom", theme) %||% .default_geom_element -# 30. └─ggplot2::calc_element("geom", theme) -# -# [ FAIL 2 | WARN 20 | SKIP 18 | PASS 753 ] -# Error: Test failures -# Execution halted -# ``` -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘Facets.Rmd’ using rmarkdown -# ``` -# -# ## In both -# -# * checking running R code from vignettes ... ERROR -# ``` -# Errors in running code in vignettes: -# when running code in ‘Miscellaneous.Rmd’ -# ... -# -# > ggplot(diamonds, aes(price, carat, colour = clarity)) + -# + geom_point(shape = ".") + scale_colour_brewer(palette = "Dark2", -# + guide = "stri ..." ... [TRUNCATED] -# Warning: The S3 guide system was deprecated in ggplot2 3.5.0. -# ℹ It has been replaced by a ggproto system that can be extended. -# -# ... -# ℹ Error occurred in the 1st layer. -# Caused by error in `setup_params()`: -# ! A discrete 'nbinom' distribution cannot be fitted to continuous data. -# Execution halted -# -# ‘Facets.Rmd’ using ‘UTF-8’... OK -# ‘Miscellaneous.Rmd’ using ‘UTF-8’... failed -# ‘PositionGuides.Rmd’ using ‘UTF-8’... OK -# ‘Statistics.Rmd’ using ‘UTF-8’... failed -# ‘ggh4x.Rmd’ using ‘UTF-8’... OK -# ``` -``` - -# gghighlight (default access) - -# ggHoriPlot (patchwork) - -# ggiraph (additional params) - -# ggiraphExtra (additional params) - -# ggmice (plotly) - -# ggmulti (custom use_defaults) - -# ggnewscale (ggnewscale) - -# ggparallel (unknown) - -``` -#
-# -# * Version: 0.4.0 -# * GitHub: https://github.com/heike/ggparallel -# * Source code: https://github.com/cran/ggparallel -# * Date/Publication: 2024-03-09 22:00:02 UTC -# * Number of recursive dependencies: 51 -# -# Run `revdepcheck::cloud_details(, "ggparallel")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > # This file is part of the standard setup for testthat. -# > # It is recommended that you do not modify it. -# > # -# > # Where should you do additional test configuration? -# > # Learn more about the roles of various files in: -# > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview -# > # * https://testthat.r-lib.org/articles/special-files.html -# ... -# 12. └─self$get_layer_key(params, layers[include], data[include], theme) -# 13. └─ggplot2 (local) get_layer_key(...) -# 14. └─base::Map(...) -# 15. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) -# 16. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) -# 17. └─layer$compute_geom_2(key, single_params, theme) -# -# [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] -# Error: Test failures -# Execution halted -# ``` -``` - -# ggpicrust2 (patchwork) - -# ggpie (ggnewscale) - -# ggplotlyExtra (plotly) - -# ggpol (default access) - -# ggpubr (update tests) - -# ggraph (guide theme passing) - -# ggredist (unknown) - -``` -#
-# -# * Version: 0.0.2 -# * GitHub: https://github.com/alarm-redist/ggredist -# * Source code: https://github.com/cran/ggredist -# * Date/Publication: 2022-11-23 11:20:02 UTC -# * Number of recursive dependencies: 67 -# -# Run `revdepcheck::cloud_details(, "ggredist")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘ggredist-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: geom_district_text -# > ### Title: Label Map Regions -# > ### Aliases: geom_district_text geom_district_label -# > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText -# > ### Keywords: datasets -# > -# > ### ** Examples -# ... -# 22. │ └─coord$transform(data, panel_params) -# 23. │ └─ggplot2 (local) transform(..., self = self) -# 24. │ └─ggplot2:::sf_rescale01(...) -# 25. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2])) -# 26. └─base::.handleSimpleError(...) -# 27. └─rlang (local) h(simpleError(msg, call)) -# 28. └─handlers[[1L]](cnd) -# 29. └─cli::cli_abort(...) -# 30. └─rlang::abort(...) -# Execution halted -# ``` -``` - -# ggRtsy (missing labels) - -# ggseqplot (length 0 width) - -# ggside (unknown) - -``` -#
-# -# * Version: 0.3.1 -# * GitHub: https://github.com/jtlandis/ggside -# * Source code: https://github.com/cran/ggside -# * Date/Publication: 2024-03-01 09:12:37 UTC -# * Number of recursive dependencies: 76 -# -# Run `revdepcheck::cloud_details(, "ggside")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(ggplot2) -# > library(ggside) -# Registered S3 method overwritten by 'ggside': -# method from -# +.gg ggplot2 -# > -# ... -# • ops_meaningful/alpha-0-5-from-function.svg -# • side_layers/boxplot2.svg -# • vdiff_irisScatter/collapsed-histo.svg -# • vdiff_irisScatter/facetgrid-collapsed-density.svg -# • vdiff_irisScatter/facetgrid-histo.svg -# • vdiff_irisScatter/facetgrid-side-density.svg -# • vdiff_irisScatter/stacked-side-density.svg -# • vdiff_irisScatter/yside-histo.svg -# Error: Test failures -# Execution halted -# ``` -# -# * checking for code/documentation mismatches ... WARNING -# ``` -# Codoc mismatches from documentation object 'geom_xsideabline': -# geom_xsidehline -# Code: function(mapping = NULL, data = NULL, position = "identity", -# ..., yintercept, na.rm = FALSE, show.legend = NA) -# Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm = -# FALSE, show.legend = NA) -# Argument names in code not in docs: -# position -# Mismatches in argument names (first 3): -# Position: 3 Code: position Docs: ... -# ... -# Docs: function(mapping = NULL, data = NULL, stat = "identity", -# position = "identity", ..., lineend = "butt", linejoin -# = "round", linemitre = 10, arrow = NULL, na.rm = -# FALSE, show.legend = NA, inherit.aes = TRUE) -# Argument names in code not in docs: -# arrow.fill -# Mismatches in argument names: -# Position: 10 Code: arrow.fill Docs: na.rm -# Position: 11 Code: na.rm Docs: show.legend -# Position: 12 Code: show.legend Docs: inherit.aes -# ``` -``` - -# ggspatial (missing defaults) - -# ggtern (ggtern) - -# ggupset (unknown) - -``` -#
-# -# * Version: 0.4.0 -# * GitHub: https://github.com/const-ae/ggupset -# * Source code: https://github.com/cran/ggupset -# * Date/Publication: 2024-06-24 10:10:04 UTC -# * Number of recursive dependencies: 46 -# -# Run `revdepcheck::cloud_details(, "ggupset")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘ggupset-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: axis_combmatrix -# > ### Title: Convert delimited text labels into a combination matrix axis -# > ### Aliases: axis_combmatrix -# > -# > ### ** Examples -# > -# > library(ggplot2) -# ... -# Datsun 710 Cyl: 4_Gears: 4 -# Hornet 4 Drive Cyl: 6_Gears: 3 -# Hornet Sportabout Cyl: 8_Gears: 3 -# Valiant Cyl: 6_Gears: 3 -# > ggplot(mtcars, aes(x=combined)) + -# + geom_bar() + -# + axis_combmatrix(sep = "_") -# Error in as.unit(e2) : object is not coercible to a unit -# Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit -# Execution halted -# ``` ``` +* installing *source* package ‘inventorize’ ... +** package ‘inventorize’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** byte-compile and prepare package for lazy loading +Warning in qgamma(service_level, alpha, beta) : NaNs produced +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (inventorize) -# ggVennDiagram (plotly) - -# greatR (patchwork) - -# Greymodels (plotly) - -# gtExtras (unknown) ``` -#
-# -# * Version: 0.5.0 -# * GitHub: https://github.com/jthomasmock/gtExtras -# * Source code: https://github.com/cran/gtExtras -# * Date/Publication: 2023-09-15 22:32:06 UTC -# * Number of recursive dependencies: 105 -# -# Run `revdepcheck::cloud_details(, "gtExtras")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(gtExtras) -# Loading required package: gt -# -# Attaching package: 'gt' -# -# The following object is masked from 'package:testthat': -# ... -# ══ Failed tests ════════════════════════════════════════════════════════════════ -# ── Failure ('test-gt_plt_bar.R:44:3'): gt_plt_bar svg is created and has specific values ── -# `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`). -# -# `actual`: "49.19" "32.79" "16.40" "0.00" "0.00" "0.00" -# `expected`: "49.19" "32.79" "16.40" "16.40" "32.79" "49.19" -# -# [ FAIL 1 | WARN 14 | SKIP 23 | PASS 115 ] -# Error: Test failures -# Execution halted -# ``` -``` - -# HaploCatcher (patchwork) - -# healthyR (plotly) - -# healthyR.ts (plotly) - -# heatmaply (plotly) - -# hermiter (patchwork) - -# hesim (missing labels) - -# hidecan (ggnewscale) - -# HVT (plotly) - -# hypsoLoop (namespace conflict) - -# ICvectorfields (ggnewscale) - -# idopNetwork (patchwork) - -# inferCSN (plotly) - -# insurancerating (patchwork) +# IPV + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/NilsPetras/IPV +* Source code: https://github.com/cran/IPV +* Date/Publication: 2022-09-30 15:00:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "IPV")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IPV-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nested_chart + > ### Title: Nested Chart + > ### Aliases: nested_chart + > + > ### ** Examples + > + > # as simple as that + ... + 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) + 8. └─vctrs::vec_as_names(names, repair = "check_unique") + 9. └─vctrs (local) ``() + 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 11. └─vctrs:::stop_names_cannot_be_empty(names, call = call) + 12. └─vctrs:::stop_names(...) + 13. └─vctrs:::stop_vctrs(...) + 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ipv-vignette.Rmd’ + ... + Facet circle radius set to 0.211 based on the data. + cor_spacing set to 0.193 based on the data. + Relative scaling set to 3.78 based on the data. + Axis tick set to 0.1 based on the data. + dist_construct_label set to 0.5 based on the data. + + When sourcing ‘ipv-vignette.R’: + Error: Names can't be empty. + ✖ Empty name found at location 4. + Execution halted + + ‘ipv-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ipv-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.0Mb + sub-directories of 1Mb or more: + data 7.0Mb + ``` + +# IRon + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/nunompmoniz/IRon +* Source code: https://github.com/cran/IRon +* Date/Publication: 2023-01-20 07:20:06 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "IRon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘IRon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sera + > ### Title: Squared Error-Relevance Area (SERA) + > ### Aliases: sera + > + > ### ** Examples + > + > library(IRon) + ... + 16. │ └─self$stat$setup_params(data, self$stat_params) + 17. │ └─ggplot2 (local) setup_params(...) + 18. │ └─base::match.fun(method) + 19. │ └─base::get(as.character(FUN), mode = "function", envir = envir) + 20. └─base::.handleSimpleError(...) + 21. └─rlang (local) h(simpleError(msg, call)) + 22. └─handlers[[1L]](cnd) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.7Mb + sub-directories of 1Mb or more: + data 6.5Mb + ``` + +# irt + +
+ +* Version: 0.2.9 +* GitHub: https://github.com/egonulates/irt +* Source code: https://github.com/cran/irt +* Date/Publication: 2024-02-20 20:40:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "irt")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘irt-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_distractor_icc + > ### Title: Plot Empirical Item or Test characteristic curve + > ### Aliases: plot_distractor_icc + > + > ### ** Examples + > + > n_item <- 10 # sample(8:12, 1) + ... + > raw_resp <- matrix(sample(LETTERS[1:4], n_item * n_theta, replace = TRUE), + + nrow = n_theta, ncol = n_item, + + dimnames = list(paste0("Examinee-", 1:n_theta), + + paste0("Item_", 1:n_item))) + > key <- sample(LETTERS[1:4], n_item, replace = TRUE) + > plot_distractor_icc(raw_resp, 3, key) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plot_distractor_icc ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 20.3Mb + sub-directories of 1Mb or more: + R 1.5Mb + libs 18.0Mb + ``` + +# isoorbi + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/isoverse/isoorbi +* Source code: https://github.com/cran/isoorbi +* Date/Publication: 2024-08-27 05:10:03 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "isoorbi")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dual_inlet.Rmd’ + ... + |20230518_05_USGS32_vs_USGS34 | 16| 7|reference |changeover | NA| 10695| 11020| 65.019| 66.994| + |20230518_05_USGS32_vs_USGS34 | 17| 7|reference |data | NA| 11025| 12335| 67.025| 74.985| + + > orbi_plot_raw_data(df_w_blocks, isotopocules = "15N", + + y = ions.incremental) + + When sourcing ‘dual_inlet.R’: + ... + + When sourcing ‘shot_noise.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘dual_inlet.Rmd’ using ‘UTF-8’... failed + ‘flow_injection.Rmd’ using ‘UTF-8’... OK + ‘isoxl_demo.Rmd’ using ‘UTF-8’... OK + ‘quick_start.Rmd’ using ‘UTF-8’... OK + ‘shot_noise.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘dual_inlet.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + doc 2.0Mb + extdata 3.3Mb + ``` + +# ivDiag + +
+ +* Version: 1.0.6 +* GitHub: NA +* Source code: https://github.com/cran/ivDiag +* Date/Publication: 2023-09-17 06:00:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "ivDiag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ivDiag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ltz + > ### Title: Local-to-Zero Test + > ### Aliases: ltz + > + > ### ** Examples + > + > data(ivDiag) + > controls <- c('altitudine', 'escursione', 'costal', 'nearsea', 'population', + + 'pop2', 'gini_land', 'gini_income') + > ltz_out <- ltz(data = gsz, Y = "totassoc_p", D = "libero_comune_allnord", + + Z = "bishopcity", controls = controls, weights = "population", + + prior = c(0.178, 0.137)) + > plot_ltz(ltz_out) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_ltz ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ivreg + +
+ +* Version: 0.6-3 +* GitHub: https://github.com/zeileis/ivreg +* Source code: https://github.com/cran/ivreg +* Date/Publication: 2024-04-20 15:22:35 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "ivreg")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ivreg.Rmd’ + ... + | F | 204.932 | | + +----------------------+-----------+---------+ + | RMSE | 0.37 | 0.40 | + +----------------------+-----------+---------+ + + > modelplot(m_list, coef_omit = "Intercept|experience") + + When sourcing ‘ivreg.R’: + Error: argument is of length zero + Execution halted + + ‘Diagnostics-for-2SLS-Regression.Rmd’ using ‘UTF-8’... OK + ‘ivreg.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Diagnostics-for-2SLS-Regression.Rmd’ using rmarkdown + ``` + +# jarbes + +
+ +* Version: 2.2.1 +* GitHub: NA +* Source code: https://github.com/cran/jarbes +* Date/Publication: 2024-06-07 09:20:02 UTC +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "jarbes")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘hmr.Rmd’ + ... + Warning: Contour data has duplicated x, y coordinates. + ℹ 15940 duplicated rows have been dropped. + Warning: Removed 161 rows containing non-finite outside the scale range + (`stat_contour()`). + Warning: Removed 92 rows containing missing values or values outside the scale range + (`geom_point()`). + + When sourcing ‘hmr.R’: + Error: argument is of length zero + Execution halted + + ‘bmeta.Rmd’ using ‘UTF-8’... OK + ‘hmr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘bmeta.Rmd’ using rmarkdown + ``` + +# karel + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/mpru/karel +* Source code: https://github.com/cran/karel +* Date/Publication: 2022-03-26 21:50:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "karel")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘karel-Ex.R’ failed + The error most likely occurred in: + + > ### Name: acciones + > ### Title: Acciones que Karel puede realizar + > ### Aliases: acciones avanzar girar_izquierda poner_coso juntar_coso + > ### girar_derecha darse_vuelta + > + > ### ** Examples + > + ... + 1. └─karel::ejecutar_acciones() + 2. ├─base::suppressWarnings(...) + 3. │ └─base::withCallingHandlers(...) + 4. ├─gganimate::animate(...) + 5. └─gganimate:::animate.gganim(...) + 6. └─args$renderer(frames_vars$frame_source, args$fps) + 7. └─gganimate:::png_dim(frames[1]) + 8. └─cli::cli_abort("Provided file ({file}) does not exist") + 9. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(karel) + > + > test_check("karel") + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 5. ├─gganimate::animate(...) + 6. └─gganimate:::animate.gganim(...) + 7. └─args$renderer(frames_vars$frame_source, args$fps) + 8. └─gganimate:::png_dim(frames[1]) + 9. └─cli::cli_abort("Provided file ({file}) does not exist") + 10. └─rlang::abort(...) + + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘gifski’ + All declared Imports should be used. + ``` + +# kDGLM + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/silvaneojunior/kDGLM +* Source code: https://github.com/cran/kDGLM +* Date/Publication: 2024-05-25 09:50:03 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "kDGLM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘kDGLM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: forecast.fitted_dlm + > ### Title: Auxiliary function for forecasting + > ### Aliases: forecast.fitted_dlm + > + > ### ** Examples + > + > + ... + > forecast(fitted.data, 24, + + chickenPox = list(Total = rep(175, 24)), # Optional + + Vaccine.1.Covariate = rep(TRUE, 24), + + Vaccine.2.Covariate = rep(TRUE, 24) + + ) + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Error in pm[[2]] : subscript out of bounds + Calls: forecast ... lapply -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘fitting.Rmd’ + ... + > outcome <- Multinom(p = c("p.1", "p.2"), data = chickenPox[, + + c(2, 3, 5)]) + + > fitted.model <- fit_model(structure * 2, chickenPox = outcome) + + > forecast(fitted.model, t = 24, plot = "base") + + When sourcing ‘fitting.R’: + Error: Error: Missing extra argument: Vaccine.1.Covariate + Execution halted + + ‘example1.Rmd’ using ‘UTF-8’... OK + ‘fitting.Rmd’ using ‘UTF-8’... failed + ‘intro.Rmd’ using ‘UTF-8’... OK + ‘outcomes.Rmd’ using ‘UTF-8’... OK + ‘structures.Rmd’ using ‘UTF-8’... OK + ``` + +# KMEANS.KNN + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/KMEANS.KNN +* Date/Publication: 2024-05-17 09:20:12 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "KMEANS.KNN")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘KMEANS.KNN-Ex.R’ failed + The error most likely occurred in: + + > ### Name: KMEANS_FUNCTION + > ### Title: KMEANS_FUNCTION + > ### Aliases: KMEANS_FUNCTION + > + > ### ** Examples + > + > data(iris) + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ] + Error: Test failures + Execution halted + ``` + +# latentcor + +
+ +* Version: 2.0.1 +* GitHub: NA +* Source code: https://github.com/cran/latentcor +* Date/Publication: 2022-09-05 20:50:02 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "latentcor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘latentcor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: latentcor + > ### Title: Estimate latent correlation for mixed types. + > ### Aliases: latentcor + > + > ### ** Examples + > + > # Example 1 - truncated data type, same type for all variables + ... + > R_approx = latentcor(X = X, types = "tru", method = "approx")$R + > proc.time() - start_time + user system elapsed + 0.027 0.000 0.027 + > # Heatmap for latent correlation matrix. + > Heatmap_R_approx = latentcor(X = X, types = "tru", method = "approx", + + showplot = TRUE)$plotR + Error in pm[[2]] : subscript out of bounds + Calls: latentcor ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# lcars + +
+ +* Version: 0.3.8 +* GitHub: https://github.com/leonawicz/lcars +* Source code: https://github.com/cran/lcars +* Date/Publication: 2023-09-10 04:10:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "lcars")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lcars-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lcars_border + > ### Title: LCARS border plot + > ### Aliases: lcars_border + > + > ### ** Examples + > + > lcars_border() + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + invalid font type + Calls: lcars_border ... drawDetails -> drawDetails.text -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘lcars.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family '0.5' not found in PostScript font database + + When sourcing ‘lcars.R’: + Error: invalid font type + Execution halted + + ‘lcars.Rmd’ using ‘UTF-8’... failed + ``` + +# lemon + +
+ +* Version: 0.4.9 +* GitHub: https://github.com/stefanedwards/lemon +* Source code: https://github.com/cran/lemon +* Date/Publication: 2024-02-08 08:00:08 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "lemon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lemon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: annotate_y_axis + > ### Title: Annotations on the axis + > ### Aliases: annotate_y_axis annotate_x_axis + > + > ### ** Examples + > + > library(ggplot2) + > + > p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point() + > + > l <- p + annotate_y_axis('mark at', y=200, tick=TRUE) + > l + Error in identicalUnits(x) : object is not a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> identicalUnits + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(lemon) + > + > + > if (TRUE) { + + test_check("lemon") + + } #else { + ... + 17. ├─grid::unit.c(unit(1, "npc"), unit(1, "npc") - tick.length) + 18. └─grid:::Ops.unit(unit(1, "npc"), tick.length) + 19. └─grid:::as.unit(e2) + + [ FAIL 1 | WARN 0 | SKIP 3 | PASS 138 ] + Deleting unused snapshots: + • facet/facet-rep-wrap-spacing.svg + • facet_aux/facet-rep-wrap.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘capped-axes.Rmd’ + ... + > p + coord_capped_cart(bottom = "right") + + > p + coord_capped_cart(bottom = "right", left = "none") + + > ggplot(dat1, aes(gp, y)) + geom_point(position = position_jitter(width = 0.2, + + height = 0)) + coord_capped_cart(left = "none", bottom = bracke .... [TRUNCATED] + + ... + When sourcing ‘legends.R’: + Error: Could not find panel named `panel-1-5`. + Execution halted + + ‘capped-axes.Rmd’ using ‘UTF-8’... failed + ‘facet-rep-labels.Rmd’ using ‘UTF-8’... failed + ‘geoms.Rmd’ using ‘UTF-8’... OK + ‘gtable_show_lemonade.Rmd’ using ‘UTF-8’... OK + ‘legends.Rmd’ using ‘UTF-8’... failed + ‘lemon_print.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘capped-axes.Rmd’ using rmarkdown + ``` + +# lfproQC + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/lfproQC +* Date/Publication: 2024-09-06 13:00:02 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "lfproQC")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lfproQC-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Boxplot_data + > ### Title: Creating Boxplot for a dataset + > ### Aliases: Boxplot_data + > + > ### ** Examples + > + > Boxplot_data(yeast_data) + Using Majority protein IDs as id variables + Warning: Removed 269 rows containing non-finite outside the scale range + (`stat_boxplot()`). + Error in pm[[2]] : subscript out of bounds + Calls: Boxplot_data -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘user_guide.Rmd’ + ... + > yeast$`Best combinations` + PCV_best_combination PEV_best_combination PMAD_best_combination + 1 knn_rlr lls_vsn lls_rlr + + > Boxplot_data(yeast$knn_rlr_data) + Using Majority protein IDs as id variables + + When sourcing ‘user_guide.R’: + Error: subscript out of bounds + Execution halted + + ‘user_guide.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘user_guide.Rmd’ using rmarkdown + + Quitting from lines 53-54 [unnamed-chunk-8] (user_guide.Rmd) + Error: processing vignette 'user_guide.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘user_guide.Rmd’ + + SUMMARY: processing the following file failed: + ‘user_guide.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + doc 5.8Mb + ``` + +# lgpr + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/jtimonen/lgpr +* Source code: https://github.com/cran/lgpr +* Date/Publication: 2023-09-24 06:50:02 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "lgpr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # Short tests + > # - focus on testing that everything runs + > # - should take less than minute + > library(testthat) + > library(lgpr) + Attached lgpr 1.2.4, using rstan 2.32.6. Type ?lgpr to get started. + > + ... + 3. └─bayesplot::mcmc_areas(sf, regex_pars = regex_pars, ...) + 4. └─ggplot2:::`+.gg`(...) + 5. └─ggplot2:::add_ggplot(e1, e2, e2name) + 6. ├─ggplot2::ggplot_add(object, p, objectname) + 7. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 8. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 3 | WARN 1 | SKIP 0 | PASS 434 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 156.9Mb + sub-directories of 1Mb or more: + R 1.5Mb + libs 155.0Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# LightLogR + +
+ +* Version: 0.3.8 +* GitHub: https://github.com/tscnlab/LightLogR +* Source code: https://github.com/cran/LightLogR +* Date/Publication: 2024-07-04 17:00:02 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "LightLogR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘LightLogR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: aggregate_Date + > ### Title: Aggregate dates to a single day + > ### Aliases: aggregate_Date + > + > ### ** Examples + > + > library(ggplot2) + > #gg_days without aggregation + > sample.data.environment %>% + + gg_days() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# LMoFit + +
+ +* Version: 0.1.7 +* GitHub: NA +* Source code: https://github.com/cran/LMoFit +* Date/Publication: 2024-05-14 07:33:23 UTC +* Number of recursive dependencies: 62 + +Run `revdepcheck::cloud_details(, "LMoFit")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LMoFit.Rmd’ + ... + + > lspace_BrIII + + When sourcing ‘LMoFit.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `compute_geom_2()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, + c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, + Execution halted + + ‘LMoFit.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘LMoFit.Rmd’ using rmarkdown + + Quitting from lines 236-237 [unnamed-chunk-15] (LMoFit.Rmd) + Error: processing vignette 'LMoFit.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `compute_geom_2()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, + ... + NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), list(), 11, list("white", NA, NULL, NULL, TRUE), list(), 5.5, NULL, NULL, list("grey92", NULL, NULL, NULL, FALSE, TRUE), list(), list(), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, + 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, c(5.5, 5.5, 5.5, 5.5), list("white", "black", 2, NULL, TRUE), NULL, NULL, "inherit", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, + NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75, list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5))) + --- failed re-building ‘LMoFit.Rmd’ + + SUMMARY: processing the following file failed: + ‘LMoFit.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.0Mb + sub-directories of 1Mb or more: + data 6.5Mb + ``` + +# lnmixsurv + +
+ +* Version: 3.1.6 +* GitHub: NA +* Source code: https://github.com/cran/lnmixsurv +* Date/Publication: 2024-09-03 15:20:08 UTC +* Number of recursive dependencies: 196 + +Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + Error in `pm[[2]]`: subscript out of bounds + Backtrace: + ▆ + 1. └─testthat::expect_snapshot(plot(mod1)) at test-survival_ln_mixture_em-methods.R:25:3 + 2. └─rlang::cnd_signal(state$error) + + [ FAIL 1 | WARN 0 | SKIP 7 | PASS 50 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘expectation_maximization.Rmd’ + ... + + x, data = data, iter = 200, starting_seed = 20, number_em_search = 0) + + > gg <- plot_fit_on_data(model_em, data)$ggplot + + > plot(model_em) + Loading required namespace: plotly + + When sourcing ‘expectation_maximization.R’: + Error: subscript out of bounds + Execution halted + + ‘compare.Rmd’ using ‘UTF-8’... OK + ‘expectation_maximization.Rmd’ using ‘UTF-8’... failed + ‘intercept_only.Rmd’ using ‘UTF-8’... OK + ‘lnmixsurv.Rmd’ using ‘UTF-8’... OK + ‘parallel_computation.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘compare.Rmd’ using rmarkdown + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + ... + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + + warning: solve(): system is singular; attempting approx solution + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.0Mb + sub-directories of 1Mb or more: + doc 4.0Mb + libs 5.7Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘purrr’ ‘readr’ + All declared Imports should be used. + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘rstanarm’ + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# LocalControl + +
+ +* Version: 1.1.4 +* GitHub: https://github.com/OHDSI/LocalControl +* Source code: https://github.com/cran/LocalControl +* Date/Publication: 2024-09-04 22:30:18 UTC +* Number of recursive dependencies: 41 + +Run `revdepcheck::cloud_details(, "LocalControl")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LocalControl-jss-2020.Rnw’ + ... + Warning: A numeric `legend.position` argument in `theme()` was deprecated in + ggplot2 3.5.0. + ℹ Please use the `legend.position.inside` argument of `theme()` + instead. + + > grid.arrange(plotz$rad_1, plotz$rad_11, ncol = 1) + + When sourcing 'LocalControl-jss-2020.R': + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘LocalControl-jss-2020.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + doc 2.0Mb + libs 2.7Mb + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘LocalControl-jss-2020.Rnw’ using Sweave + Loading required package: data.table + Loading required package: colorspace + Loading required package: RColorBrewer + Loading required package: gridExtra + Loading required package: ggplot2 + Loading required package: rpart + Loading required package: rpart.plot + Loading required package: LocalControl + ... + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + + --- failed re-building 'LocalControl-jss-2020.Rnw' + + SUMMARY: processing the following file failed: + 'LocalControl-jss-2020.Rnw' + + Error: Vignette re-building failed. + Execution halted + ``` + +# LocalCop + +
+ +* Version: 0.0.1 +* GitHub: https://github.com/mlysy/LocalCop +* Source code: https://github.com/cran/LocalCop +* Date/Publication: 2024-03-21 14:50:06 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "LocalCop")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘LocalCop-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LocalCop-vignette.Rmd’ + ... + > tibble(x = x0, True = BiCopEta2Tau(family, eta = eta_fun(x0)), + + Fitted = BiCopEta2Tau(fitseq$eta, family = family)) %>% pivot_longer(True:Fitt .... [TRUNCATED] + Warning: Removed 51 rows containing missing values or values outside the scale range + (`geom_line()`). + Warning: Removed 51 rows containing missing values or values outside the scale range + (`geom_point()`). + + When sourcing ‘LocalCop-vignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘LocalCop-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 55.7Mb + sub-directories of 1Mb or more: + libs 55.3Mb + ``` + +# LongDat + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/CCY-dev/LongDat +* Source code: https://github.com/cran/LongDat +* Date/Publication: 2023-07-17 05:40:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "LongDat")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LongDat_cont_tutorial.Rmd’ + ... + + > test_plot <- cuneiform_plot(result_table = test_cont[[1]], + + title_size = 15) + [1] "Finished plotting successfully!" + + > test_plot + + ... + [1] "Finished plotting successfully!" + + > test_plot + + When sourcing ‘LongDat_disc_tutorial.R’: + Error: object is not coercible to a unit + Execution halted + + ‘LongDat_cont_tutorial.Rmd’ using ‘UTF-8’... failed + ‘LongDat_disc_tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘LongDat_cont_tutorial.Rmd’ using rmarkdown + Warning in eng_r(options) : + Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason: + Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. + + Warning in eng_r(options) : + Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason: + Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored. + + ... + Quitting from lines 181-182 [unnamed-chunk-11] (LongDat_disc_tutorial.Rmd) + Error: processing vignette 'LongDat_disc_tutorial.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘LongDat_disc_tutorial.Rmd’ + + SUMMARY: processing the following files failed: + ‘LongDat_cont_tutorial.Rmd’ ‘LongDat_disc_tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# longreadvqs + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/NakarinP/longreadvqs +* Source code: https://github.com/cran/longreadvqs +* Date/Publication: 2024-08-26 19:30:05 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "longreadvqs")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘longreadvqs-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vqscompare + > ### Title: Comparing viral quasispecies profile and operational taxonomic + > ### unit (OTU) classified by k-means clustering between samples + > ### Aliases: vqscompare + > + > ### ** Examples + > + ... + 13. │ └─ggplot2:::`+.gg`(...) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘longreadvqs-vignette.Rmd’ + ... + + > comp <- vqscompare(samplelist = list(s1, s2, s3, s4_fix), + + lab_name = "Sample", kmeans.n = 10) + + When sourcing ‘longreadvqs-vignette.R’: + Error: ℹ In index: 1. + ℹ With name: Dim.2. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘longreadvqs-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘longreadvqs-vignette.Rmd’ using rmarkdown + ``` + +# lpdensity + +
+ +* Version: 2.4 +* GitHub: NA +* Source code: https://github.com/cran/lpdensity +* Date/Publication: 2023-01-21 23:50:02 UTC +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "lpdensity")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lpdensity-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lpdensity + > ### Title: Local Polynomial Density Estimation and Inference + > ### Aliases: lpdensity + > + > ### ** Examples + > + > # Generate a random sample + ... + 18 1.2878 0.6298 457 0.1749 0.0097 0.1222 , 0.2179 + 19 1.5768 0.6298 299 0.1221 0.0086 0.0863 , 0.1719 + ============================================================================= + > + > # Plot the estimates and confidence intervals + > plot(est1, legendTitle="My Plot", legendGroups=c("X")) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# lspartition + +
+ +* Version: 0.4 +* GitHub: NA +* Source code: https://github.com/cran/lspartition +* Date/Publication: 2019-08-08 22:40:06 UTC +* Number of recursive dependencies: 34 + +Run `revdepcheck::cloud_details(, "lspartition")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘lspartition-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lsprobust.plot + > ### Title: Graphic Presentation of Results for 'lspartition' Package + > ### Aliases: lsprobust.plot + > + > ### ** Examples + > + > x <- runif(500) + > y <- sin(4*x)+rnorm(500) + > est <- lsprobust(y, x) + > lsprobust.plot(est) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# LSTbook + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/dtkaplan/LSTbook +* Source code: https://github.com/cran/LSTbook +* Date/Publication: 2024-02-23 19:20:15 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "LSTbook")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + [ FAIL 1 | WARN 1 | SKIP 4 | PASS 73 ] + Deleting unused snapshots: + • model_plot/four-facets.png + • pointplot/1-var-plot.png + • pointplot/bird-logistic-plot.png + • pointplot/color-and-facet-na.png + • pointplot/logistic-fun-plot.png + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘DAGs.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘DAGs.Rmd’ + ... + 3 -1.35 -11.9 + 4 0.429 0.171 + 5 0.622 5.85 + 6 2.35 16.5 + + > Wrong_way <- datasim_make(x = rnorm(n, mean = 0, sd = 2)) + + ... + + > model_plot(height_model) + + When sourcing ‘modeling.R’: + Error: argument is of length zero + Execution halted + + ‘DAGs.Rmd’ using ‘UTF-8’... failed + ‘LSTbook.Rmd’ using ‘UTF-8’... OK + ‘modeling.Rmd’ using ‘UTF-8’... failed + ``` + +* checking loading without being on the library search path ... WARNING + ``` + Error: package or namespace load failed for ‘LSTbook’: + .onLoad failed in loadNamespace() for 'LSTbook', details: + call: loadNamespace(name) + error: there is no package called ‘mosaicData’ + Execution halted + + It looks like this package has a loading problem when not on .libPaths: + see the messages for details. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 20 marked UTF-8 strings + ``` + +# manydata + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/globalgov/manydata +* Source code: https://github.com/cran/manydata +* Date/Publication: 2024-05-06 19:00:02 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "manydata")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(manydata) + manydata 0.9.3 + Please see manydata.ch for more information. + Type 'citation("manydata")' for citing this R package in publications. + > + > test_check("manydata") + ... + ── Failure ('test_compare.R:8:3'): plot for compare_categories returns the correct output format ── + Names of `db` ('data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout', 'labels') don't match 'data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout' + ── Failure ('test_compare.R:74:3'): compare_missing() and plot_missing() returns the correct output format ── + `pl` has length 11, not length 10. + ── Failure ('test_compare.R:76:3'): compare_missing() and plot_missing() returns the correct output format ── + Names of `pl` ('data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout', 'labels') don't match 'data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout' + + [ FAIL 4 | WARN 0 | SKIP 3 | PASS 121 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 3 marked UTF-8 strings + ``` + +# manymome + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/sfcheung/manymome +* Source code: https://github.com/cran/manymome +* Date/Publication: 2024-06-05 23:30:03 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "manymome")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘manymome-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_effect_vs_w + > ### Title: Plot an Effect Against a Moderator + > ### Aliases: plot_effect_vs_w + > + > ### ** Examples + > + > + ... + + y = "y", + + m = "m", + + fit = fit_lm, + + sd_from_mean = seq(-2, 2, length.out = 10), + + boot_ci = TRUE, + + boot_out = boot_out_lm) + > p <- plot_effect_vs_w(out_lm) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_effect_vs_w ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# mapbayr + +
+ +* Version: 0.10.0 +* GitHub: https://github.com/FelicienLL/mapbayr +* Source code: https://github.com/cran/mapbayr +* Date/Publication: 2023-07-17 08:20:02 UTC +* Number of recursive dependencies: 68 + +Run `revdepcheck::cloud_details(, "mapbayr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mapbayr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mapbayr_plot + > ### Title: Make mapbayr plot + > ### Aliases: mapbayr_plot + > + > ### ** Examples + > + > aug <- data.frame( + ... + > obs <- data.frame( + + ID = 1, time = c(6, 20), evid = 0, + + mdv = c(0,1), DV = c(0.5, 5), cmt = 2 + + ) + > + > mapbayr_plot(aug, obs) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# MBNMAdose + +
+ +* Version: 0.4.3 +* GitHub: NA +* Source code: https://github.com/cran/MBNMAdose +* Date/Publication: 2024-04-18 12:42:47 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "MBNMAdose")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘outputs-4.Rmd’ + ... + + > plot(trip.emax) + + When sourcing ‘outputs-4.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ... + Execution halted + + ‘consistencychecking-3.Rmd’ using ‘UTF-8’... OK + ‘dataexploration-1.Rmd’ using ‘UTF-8’... OK + ‘mbnmadose-overview.Rmd’ using ‘UTF-8’... OK + ‘metaregression-6.Rmd’ using ‘UTF-8’... OK + ‘nma_in_mbnmadose.Rmd’ using ‘UTF-8’... OK + ‘outputs-4.Rmd’ using ‘UTF-8’... failed + ‘predictions-5.Rmd’ using ‘UTF-8’... OK + ‘runmbnmadose-2.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘consistencychecking-3.Rmd’ using rmarkdown + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 6 marked Latin-1 strings + ``` + +# MBNMAtime + +
+ +* Version: 0.2.4 +* GitHub: NA +* Source code: https://github.com/cran/MBNMAtime +* Date/Publication: 2023-10-14 15:20:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "MBNMAtime")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘consistencychecking-3.Rmd’ using rmarkdown + + Quitting from lines 141-146 [unnamed-chunk-8] (consistencychecking-3.Rmd) + Error: processing vignette 'consistencychecking-3.Rmd' failed with diagnostics: + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, + NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, 2.2, 0, 2.2), NULL, TRUE), list("grey20", NULL, NULL, NULL, FALSE, "grey20", TRUE), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, + NULL, NULL, NULL, NULL, list("transparent", NA, NULL, NULL, FALSE), NULL, 2, NULL, NULL, list("transparent", NA, NULL, NULL, FALSE), 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list(), list(NULL, "grey20", NULL, NULL, TRUE), NULL, NULL, + NULL, list("grey92", NULL, NULL, NULL, FALSE, "grey92", TRUE), list("grey95", NULL, NULL, NULL, FALSE, "grey95", FALSE), list("grey95", 0.5, NULL, NULL, FALSE, "grey95", FALSE), NULL, NULL, NULL, NULL, FALSE, list("white", NA, NULL, NULL, FALSE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list( + NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, NULL, list("lightsteelblue1", "black", NULL, NULL, FALSE), NULL, NULL, "on", "inside", list(NULL, NULL, "black", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, FALSE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + --- failed re-building ‘consistencychecking-3.Rmd’ + + --- re-building ‘dataexploration-1.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘consistencychecking-3.Rmd’ + ... + |-> direct | | 0.228| -0.213| 0.684| + |-> indirect | | -0.515| -0.891| -0.137| + | | | | | | + + > plot(nodesplit, plot.type = "forest") + + When sourcing ‘consistencychecking-3.R’: + ... + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, + Execution halted + + ‘consistencychecking-3.Rmd’ using ‘UTF-8’... failed + ‘dataexploration-1.Rmd’ using ‘UTF-8’... failed + ‘mbnmatime-overview.Rmd’ using ‘UTF-8’... OK + ‘outputs-4.Rmd’ using ‘UTF-8’... failed + ‘predictions-5.Rmd’ using ‘UTF-8’... OK + ‘runmbnmatime-2.Rmd’ using ‘UTF-8’... OK + ``` + +# mecoturn + +
+ +* Version: 0.3.0 +* GitHub: https://github.com/ChiLiubio/mecoturn +* Source code: https://github.com/cran/mecoturn +* Date/Publication: 2023-09-10 13:40:02 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "mecoturn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mecoturn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: betaturn + > ### Title: Analyze the 'turnover' of microbial communities. + > ### Aliases: betaturn + > + > ### ** Examples + > + > + ... + 13. │ └─ggplot2:::`+.gg`(...) + 14. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. │ ├─ggplot2::ggplot_add(object, p, objectname) + 16. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 17. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 18. └─base::.handleSimpleError(...) + 19. └─purrr (local) h(simpleError(msg, call)) + 20. └─cli::cli_abort(...) + 21. └─rlang::abort(...) + Execution halted + ``` + +# MetaNet + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/Asa12138/MetaNet +* Source code: https://github.com/cran/MetaNet +* Date/Publication: 2024-03-25 20:40:07 UTC +* Number of recursive dependencies: 151 + +Run `revdepcheck::cloud_details(, "MetaNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MetaNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.ggig + > ### Title: Transfer an igraph object to a ggig + > ### Aliases: as.ggig + > + > ### ** Examples + > + > as.ggig(co_net, coors = c_net_layout(co_net)) -> ggig + > plot(ggig) + Warning: Removed 446 rows containing missing values or values outside the scale range + (`geom_text()`). + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +# metR + +
+ +* Version: 0.15.0 +* GitHub: https://github.com/eliocamp/metR +* Source code: https://github.com/cran/metR +* Date/Publication: 2024-02-09 00:40:02 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "metR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘metR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_contour_tanaka + > ### Title: Illuminated contours + > ### Aliases: geom_contour_tanaka GeomContourTanaka + > ### Keywords: datasets + > + > ### ** Examples + > + ... + 19. │ ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params)) + 20. │ └─self$draw_panel(...) + 21. │ └─metR (local) draw_panel(...) + 22. │ └─metR:::stopf(...) + 23. │ └─base::stop(e) + 24. └─rlang (local) ``(``) + 25. └─handlers[[1L]](cnd) + 26. └─cli::cli_abort(...) + 27. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(metR) + > # library(vdiffr) + > + > on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false"))) + > if (on_cran) data.table::setDTthreads(2) + > + ... + • vis-streamline/streamline-ywrapped.svg + • vis-text-contour/labels-text.svg + • vis-text-contour/minsize.svg + • vis-text-contour/placement-fraction.svg + • vis-text-contour/placement-minmax-horizontal.svg + • vis-text-contour/placement-minmax-vertical.svg + • vis-text-contour/placement-n.svg + • vis-text-contour/text-contour-norotate.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Visualization-tools.Rmd’ + ... + + > ggplot(temperature[lev == 300], aes(lon, lat, z = air.z)) + + + geom_contour_fill() + geom_contour_tanaka() + scale_fill_divergent() + + When sourcing ‘Visualization-tools.R’: + Error: Problem while converting geom to grob. + ℹ Error occurred in the 2nd layer. + Caused by error: + ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. + Execution halted + + ‘Visualization-tools.Rmd’ using ‘UTF-8’... failed + ‘Working-with-data.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Visualization-tools.Rmd’ using knitr + + Quitting from lines 241-245 [unnamed-chunk-16] (Visualization-tools.Rmd) + Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics: + Problem while converting geom to grob. + ℹ Error occurred in the 2nd layer. + Caused by error: + ! geom_path: If you are using dotted or dashed lines, colour, size and linetype must be constant over the line. + ... + --- failed re-building ‘Visualization-tools.Rmd’ + + --- re-building ‘Working-with-data.Rmd’ using knitr + --- finished re-building ‘Working-with-data.Rmd’ + + SUMMARY: processing the following file failed: + ‘Visualization-tools.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 2.0Mb + doc 1.8Mb + ``` + +# metrica + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/adriancorrendo/metrica +* Source code: https://github.com/cran/metrica +* Date/Publication: 2024-06-30 14:20:02 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "metrica")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘regression_case.Rmd’ + ... + + mutate(Year = seq(2001, 2020, by = 1)) + + > wheat_time %>% ggplot2::ggplot(aes(x = Year)) + geom_point(aes(y = pred, + + fill = "Predicted", shape = "Predicted")) + geom_point(aes(y = obs, .... [TRUNCATED] + Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. + ℹ Please use `linewidth` instead. + + ... + Execution halted + + ‘Cheatsheet.Rmd’ using ‘UTF-8’... OK + ‘JOSS_publication.Rmd’ using ‘UTF-8’... OK + ‘Shinyapp.Rmd’ using ‘UTF-8’... OK + ‘apsim_open.Rmd’ using ‘UTF-8’... OK + ‘available_metrics_classification.Rmd’ using ‘UTF-8’... OK + ‘available_metrics_regression.Rmd’ using ‘UTF-8’... OK + ‘classification_case.Rmd’ using ‘UTF-8’... OK + ‘regression_case.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Cheatsheet.Rmd’ using rmarkdown + --- finished re-building ‘Cheatsheet.Rmd’ + + --- re-building ‘JOSS_publication.Rmd’ using rmarkdown + --- finished re-building ‘JOSS_publication.Rmd’ + + --- re-building ‘Shinyapp.Rmd’ using rmarkdown + --- finished re-building ‘Shinyapp.Rmd’ + + ... + --- re-building ‘apsim_open.Rmd’ using rmarkdown + --- finished re-building ‘apsim_open.Rmd’ + + --- re-building ‘available_metrics_classification.Rmd’ using rmarkdown + --- finished re-building ‘available_metrics_classification.Rmd’ + + --- re-building ‘available_metrics_regression.Rmd’ using rmarkdown + --- finished re-building ‘available_metrics_regression.Rmd’ + + --- re-building ‘classification_case.Rmd’ using rmarkdown + ``` + +# miceRanger + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/FarrellDay/miceRanger +* Source code: https://github.com/cran/miceRanger +* Date/Publication: 2021-09-06 15:20:02 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::cloud_details(, "miceRanger")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘usingMiceRanger.Rmd’ + ... + > plotList <- lapply(plotVars, function(x) { + + missIndx <- is.na(ampIris[, get(x)]) + + impVsAmp <- data.table(originalData = iris[missIndx, x], .... [TRUNCATED] + + When sourcing ‘usingMiceRanger.R’: + Error: ℹ In index: 1. + ℹ With name: imputedData. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘diagnosticPlotting.Rmd’ using ‘UTF-8’... OK + ‘miceAlgorithm.Rmd’ using ‘UTF-8’... OK + ‘usingMiceRanger.Rmd’ using ‘UTF-8’... failed + ``` + +# microbial + +
+ +* Version: 0.0.21 +* GitHub: NA +* Source code: https://github.com/cran/microbial +* Date/Publication: 2024-05-15 18:20:02 UTC +* Number of recursive dependencies: 179 + +Run `revdepcheck::cloud_details(, "microbial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘microbial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotalpha + > ### Title: plot alpha diversity + > ### Aliases: plotalpha + > + > ### ** Examples + > + > { + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘microbial.Rmd’ + ... + > plotbar(phy, level = "Phylum") + + > plotalpha(physeq, group = "group") + + When sourcing ‘microbial.R’: + Error: ℹ In index: 1. + ℹ With name: val. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘microbial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘microbial.Rmd’ using knitr + ``` + +# MicrobiomeSurv + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/N-T-Huyen/MicrobiomeSurv +* Source code: https://github.com/cran/MicrobiomeSurv +* Date/Publication: 2023-10-12 06:20:02 UTC +* Number of recursive dependencies: 158 + +Run `revdepcheck::cloud_details(, "MicrobiomeSurv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MicrobiomeSurv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: EstimateHR + > ### Title: Classification, Survival Estimation and Visualization + > ### Aliases: EstimateHR + > + > ### ** Examples + > + > # Prepare data + ... + + Mean = TRUE) + > + > # Using the function + > est_HR_fam_shan_w3 = EstimateHR(Risk.Scores = lasso_fam_shan_w3$Risk.Scores, + + Data.Survival = lasso_fam_shan_w3$Data.Survival, + + Prognostic = prog_fam_shan_w3, Plots = TRUE, + + Mean = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: EstimateHR ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# migraph + +
+ +* Version: 1.4.2 +* GitHub: https://github.com/stocnet/migraph +* Source code: https://github.com/cran/migraph +* Date/Publication: 2024-09-04 12:00:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "migraph")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(manynet) + > library(migraph) + > + > test_check("migraph") + Starting 2 test processes + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 46 ] + ... + `expected` is a character vector ('Statistic') + ── Failure ('test-model_tests.R:73:3'): qap plot works ───────────────────────── + qapplot$labels$x (`actual`) not identical to "Statistic" (`expected`). + + `actual` is NULL + `expected` is a character vector ('Statistic') + + [ FAIL 2 | WARN 2 | SKIP 0 | PASS 46 ] + Error: Test failures + Execution halted + ``` + +# mikropml + +
+ +* Version: 1.6.1 +* GitHub: https://github.com/SchlossLab/mikropml +* Source code: https://github.com/cran/mikropml +* Date/Publication: 2023-08-21 15:10:05 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::cloud_details(, "mikropml")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mikropml) + > test_check("mikropml") + Fraction of data in the training set: 0.778 + Groups in the training set: A C D + Groups in the testing set: B + Fraction of data in the training set: 0.778 + ... + `names(expected)` is absent + ── Failure ('test-plot.R:140:3'): plot_mean_prc uses geom ribbon, line, and hline ── + ... %>% unlist() (`actual`) not equal to c(...) (`expected`). + + `names(actual)` is a character vector ('geom_ribbon1', 'geom_ribbon2', 'geom_ribbon3', 'geom_ribbon4', 'geom_line1', ...) + `names(expected)` is absent + + [ FAIL 2 | WARN 19 | SKIP 12 | PASS 314 ] + Error: Test failures + Execution halted + ``` + +# MiMIR + +
+ +* Version: 1.5 +* GitHub: NA +* Source code: https://github.com/cran/MiMIR +* Date/Publication: 2024-02-01 08:50:02 UTC +* Number of recursive dependencies: 191 + +Run `revdepcheck::cloud_details(, "MiMIR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MiMIR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: LOBOV_accuracies + > ### Title: LOBOV_accuracies + > ### Aliases: LOBOV_accuracies + > + > ### ** Examples + > + > require(pROC) + ... + 56 metabolites x 500 samples + | Pruning samples on5SD: + 56 metabolites x 500 samples + | Performing scaling ... DONE! + | Imputation ... DONE! + > p_avail<-colnames(b_p)[c(1:5)] + > LOBOV_accuracies(sur$surrogates, b_p, p_avail, MiMIR::acc_LOBOV) + Error in pm[[2]] : subscript out of bounds + Calls: LOBOV_accuracies -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# miRetrieve + +
+ +* Version: 1.3.4 +* GitHub: NA +* Source code: https://github.com/cran/miRetrieve +* Date/Publication: 2021-09-18 17:30:02 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "miRetrieve")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(miRetrieve) + > + > test_check("miRetrieve") + [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + Backtrace: + ▆ + 1. └─miRetrieve::compare_mir_terms_scatter(df_merged, "miR-21", title = "Test_title") at test-comparemirterms.R:56:1 + 2. ├─plotly::ggplotly(plot) + 3. └─plotly:::ggplotly.ggplot(plot) + 4. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 11 | SKIP 0 | PASS 202 ] + Error: Test failures + Execution halted + ``` + +# MiscMetabar + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/adrientaudiere/MiscMetabar +* Source code: https://github.com/cran/MiscMetabar +* Date/Publication: 2024-09-09 09:20:01 UTC +* Number of recursive dependencies: 420 + +Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MiscMetabar-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggscatt_pq + > ### Title: Scatterplot with marginal distributions and statistical results + > ### against Hill diversity of phyloseq object + > ### Aliases: ggscatt_pq + > + > ### ** Examples + > + ... + + ) + + } + Loading required namespace: ggstatsplot + Taxa are now in columns. + Cleaning suppress 0 taxa and 0 samples. + Taxa are now in rows. + Joining with `by = join_by(Sample)` + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggscatt_pq ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(MiscMetabar) + Loading required package: phyloseq + Loading required package: ggplot2 + Loading required package: dada2 + Loading required package: Rcpp + Loading required package: dplyr + ... + 14. └─ggplot2:::add_ggplot(e1, e2, e2name) + 15. ├─ggplot2::ggplot_add(object, p, objectname) + 16. └─ggplot2:::ggplot_add.list(object, p, objectname) + 17. ├─ggplot2::ggplot_add(o, plot, object_name) + 18. └─ggplot2:::ggplot_add.Layer(o, plot, object_name) + 19. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 0 | SKIP 76 | PASS 82 ] + Error: Test failures + Execution halted + ``` + +# misspi + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/misspi +* Date/Publication: 2023-10-17 09:50:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "misspi")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘misspi-Ex.R’ failed + The error most likely occurred in: + + > ### Name: evaliq + > ### Title: Evaluate the Imputation Quality + > ### Aliases: evaliq + > + > ### ** Examples + > + > # A very quick example + ... + > # Default plot + > er.eval <- evaliq(x.true[na.idx], x.est[na.idx]) + `geom_smooth()` using formula = 'y ~ x' + > + > # Interactive plot + > er.eval <- evaliq(x.true[na.idx], x.est[na.idx], interactive = TRUE) + `geom_smooth()` using formula = 'y ~ x' + Error in pm[[2]] : subscript out of bounds + Calls: evaliq -> print -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# mixpoissonreg + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/vpnsctl/mixpoissonreg +* Source code: https://github.com/cran/mixpoissonreg +* Date/Publication: 2021-03-10 19:50:06 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "mixpoissonreg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mixpoissonreg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.mixpoissonreg + > ### Title: Autoplot Method for 'mixpoissonreg' Objects + > ### Aliases: autoplot.mixpoissonreg autoplot + > + > ### ** Examples + > + > daysabs_prog <- mixpoissonregML(daysabs ~ prog, data = Attendance) + > autoplot(daysabs_prog) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: autoplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mixpoissonreg) + > + > test_check("mixpoissonreg") + + Negative Binomial Regression - Expectation-Maximization Algorithm + + ... + 2. └─mixpoissonreg:::autoplot.mixpoissonreg(fit_ml1, nrow = 2) + 3. └─ggplot2:::`+.gg`(...) + 4. └─ggplot2:::add_ggplot(e1, e2, e2name) + 5. ├─ggplot2::ggplot_add(object, p, objectname) + 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 28 | SKIP 0 | PASS 35 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘influence-mixpoissonreg.Rmd’ + ... + 5 2.747544 -0.2460342 -0.006644830 -0.4252217 -1.269154 + 6 2.746786 -0.2443429 -0.006641383 -0.4268347 -1.269387 + + > plot(fit, which = c(3, 4, 5)) + + > autoplot(fit, which = c(3, 4, 5)) + + ... + + When sourcing ‘tutorial-mixpoissonreg.R’: + Error: argument is of length zero + Execution halted + + ‘influence-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ‘intervals-mixpoissonreg.Rmd’ using ‘UTF-8’... OK + ‘ml-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ‘tidyverse-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ‘tutorial-mixpoissonreg.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘influence-mixpoissonreg.Rmd’ using rmarkdown + ``` + +# mizer + +
+ +* Version: 2.5.1 +* GitHub: https://github.com/sizespectrum/mizer +* Source code: https://github.com/cran/mizer +* Date/Publication: 2024-03-08 23:10:02 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "mizer")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mizer) + > + > test_check("mizer") + [ FAIL 10 | WARN 0 | SKIP 5 | PASS 1251 ] + + ... + • plots/plot-spectra.svg + • plots/plot-yield-by-gear.svg + • plots/plot-yield.svg + • plots/plotfishing-mortality.svg + • plots/plotfmort-truncated.svg + • plots/plotpredation-mortality.svg + • plots/plotpredmort-truncated.new.svg + • plots/plotpredmort-truncated.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + doc 1.5Mb + help 1.8Mb + ``` + +# mlr3spatiotempcv + +
+ +* Version: 2.3.1 +* GitHub: https://github.com/mlr-org/mlr3spatiotempcv +* Source code: https://github.com/cran/mlr3spatiotempcv +* Date/Publication: 2024-04-17 12:10:05 UTC +* Number of recursive dependencies: 167 + +Run `revdepcheck::cloud_details(, "mlr3spatiotempcv")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mlr3spatiotempcv-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.ResamplingCustomCV + > ### Title: Visualization Functions for Non-Spatial CV Methods. + > ### Aliases: autoplot.ResamplingCustomCV plot.ResamplingCustomCV + > + > ### ** Examples + > + > if (mlr3misc::require_namespaces(c("sf", "patchwork"), quietly = TRUE)) { + ... + + + + autoplot(resampling, task) + + + ggplot2::scale_x_continuous(breaks = seq(-79.085, -79.055, 0.01)) + + autoplot(resampling, task, fold_id = 1) + + autoplot(resampling, task, fold_id = c(1, 2)) * + + ggplot2::scale_x_continuous(breaks = seq(-79.085, -79.055, 0.01)) + + } + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘spatiotemp-viz.Rmd’ + ... + + > knitr::opts_chunk$set(collapse = TRUE, comment = "#>") + + > knitr::include_graphics("../man/figures/sptcv_cstf_multiplot.png") + + When sourcing ‘spatiotemp-viz.R’: + Error: Cannot find the file(s): "../man/figures/sptcv_cstf_multiplot.png" + Execution halted + + ‘mlr3spatiotempcv.Rmd’ using ‘UTF-8’... OK + ‘spatiotemp-viz.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.9Mb + sub-directories of 1Mb or more: + data 3.5Mb + ``` + +# mlr3viz + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/mlr-org/mlr3viz +* Source code: https://github.com/cran/mlr3viz +* Date/Publication: 2024-07-01 12:30:02 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "mlr3viz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mlr3viz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: autoplot.OptimInstanceBatchSingleCrit + > ### Title: Plots for Optimization Instances + > ### Aliases: autoplot.OptimInstanceBatchSingleCrit + > + > ### ** Examples + > + > if (requireNamespace("mlr3") && requireNamespace("bbotk") && requireNamespace("patchwork")) { + ... + INFO [09:22:56.650] [bbotk] 5.884797 2.2371095 -32.51896 + INFO [09:22:56.650] [bbotk] -7.841127 -0.8872557 -91.31148 + INFO [09:22:56.668] [bbotk] Finished optimizing after 20 evaluation(s) + INFO [09:22:56.669] [bbotk] Result: + INFO [09:22:56.670] [bbotk] x1 x2 x_domain y + INFO [09:22:56.670] [bbotk] + INFO [09:22:56.670] [bbotk] 2.582281 -2.940254 9.657379 + Error in identicalUnits(x) : object is not a unit + Calls: print ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (requireNamespace("testthat", quietly = TRUE)) { + + library("testthat") + + library("mlr3viz") + + test_check("mlr3viz") + + } + Starting 2 test processes + [ FAIL 4 | WARN 1 | SKIP 24 | PASS 84 ] + ... + • TuningInstanceSingleCrit/tisc-surface-grid-50.svg + • TuningInstanceSingleCrit/tisc-surface-regr-lm.svg + • TuningInstanceSingleCrit/tisc-surface.svg + • plot_learner_prediction/learner-prediction-1d-se.svg + • plot_learner_prediction/learner-prediction-binary-prob.svg + • plot_learner_prediction/learner-prediction-binary-response.svg + • plot_learner_prediction/learner-prediction-categorical.svg + • plot_learner_prediction/learner-prediction-prob.svg + Error: Test failures + Execution halted + ``` + +# modeltime.resample + +
+ +* Version: 0.2.3 +* GitHub: https://github.com/business-science/modeltime.resample +* Source code: https://github.com/cran/modeltime.resample +* Date/Publication: 2023-04-12 15:50:02 UTC +* Number of recursive dependencies: 227 + +Run `revdepcheck::cloud_details(, "modeltime.resample")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > + > # Machine Learning + > library(tidymodels) + ── Attaching packages ────────────────────────────────────── tidymodels 1.2.0 ── + ✔ broom 1.0.6 ✔ recipes 1.1.0 + ✔ dials 1.3.0 ✔ rsample 1.2.1 + ... + ▆ + 1. ├─m750_models_resample %>% ... at test-modeltime_fit_resamples.R:116:5 + 2. └─modeltime.resample::plot_modeltime_resamples(., .interactive = TRUE) + 3. ├─plotly::ggplotly(g) + 4. └─plotly:::ggplotly.ggplot(g) + 5. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 16 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’ + All declared Imports should be used. + ``` + +# moreparty + +
+ +* Version: 0.4 +* GitHub: NA +* Source code: https://github.com/cran/moreparty +* Date/Publication: 2023-11-22 14:30:02 UTC +* Number of recursive dependencies: 165 + +Run `revdepcheck::cloud_details(, "moreparty")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Titanic_example.Rmd’ + ... + 24 Age 57 0.3187270 + 25 Embarked Cherbourg 0.4603041 + [ reached 'max' / getOption("max.print") -- omitted 2 rows ] + + > ggForestEffects(pdep, vline = mean(pred_foret), xlab = "Probability of survival") + + + xlim(c(0, 1)) + + When sourcing ‘Titanic_example.R’: + Error: `x` must be a vector, not a object. + Execution halted + + ‘Titanic_example.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Titanic_example.Rmd’ using rmarkdown + ``` + +# mosaicCalc + +
+ +* Version: 0.6.4 +* GitHub: https://github.com/ProjectMOSAIC/mosaicCalc +* Source code: https://github.com/cran/mosaicCalc +* Date/Publication: 2024-07-26 15:50:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "mosaicCalc")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mosaicCalc-Ex.R’ failed + The error most likely occurred in: + + > ### Name: box_set + > ### Title: Evenly spaced samples across a one- or two-dim domain + > ### Aliases: box_set + > + > ### ** Examples + > + > box_set(x*y ~ x & y, domain(x=0:1, y=0:1), n = 4) + ... + [1] 0 + > # a polygon + > poly <- tibble(x = c(1:9, 8:1), y = c(1, 2*(5:3), 2, -1, 17, 9, 8, 2:9)) + > boxes <- box_set(1 ~ x & y, poly, dx = 1) + > gf_polygon(y ~ x, data = poly, color="blue", fill="blue", alpha=0.2) %>% + + gf_rect((y - dy/3) + (y + dy/3) ~ (x - dx/3) + (x + dx/3), + + data = boxes) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Calculus_with_R.Rmd’ + ... + + > soln <- integrateODE(SIR, bounds(t = 0:20)) + Solution containing functions S(t), I(t). + + > traj_plot(S(t) ~ I(t), soln, color = "blue") %>% vectorfield_plot(SIR, + + bounds(I = 0:75, S = 60:400), transform = I, npts = 20, alpha = 0.6) + + ... + + > gf_point(flipper_length_mm ~ body_mass_g, data = palmerpenguins::penguins) + + When sourcing ‘quick-reference.R’: + Error: argument is of length zero + Execution halted + + ‘Calculus_with_R.Rmd’ using ‘UTF-8’... failed + ‘Instructors.Rmd’ using ‘UTF-8’... failed + ‘quick-reference.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Calculus_with_R.Rmd’ using rmarkdown + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 56 marked UTF-8 strings + ``` + +# mosaicData + +
+ +* Version: 0.20.4 +* GitHub: https://github.com/ProjectMOSAIC/mosaicData +* Source code: https://github.com/cran/mosaicData +* Date/Publication: 2023-11-05 05:50:02 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "mosaicData")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mosaicData-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Birthdays + > ### Title: US Births in 1969 - 1988 + > ### Aliases: Birthdays + > + > ### ** Examples + > + > data(Birthdays) + ... + IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test, + quantile, sd, t.test, var + + The following objects are masked from ‘package:base’: + + max, mean, min, prod, range, sample, sum + + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_point ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 7 marked UTF-8 strings + ``` + +# mosaicModel + +
+ +* Version: 0.3.0 +* GitHub: NA +* Source code: https://github.com/cran/mosaicModel +* Date/Publication: 2017-09-22 16:21:41 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "mosaicModel")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Basics.Rmd’ + ... + + out.width = "45%") + + > mtcars <- mtcars %>% mutate(transmission = ifelse(am, + + "manual", "automatic")) + + > gf_point(mpg ~ hp, color = ~transmission, data = mtcars) + + When sourcing ‘Basics.R’: + Error: argument is of length zero + Execution halted + + ‘Basics.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Basics.Rmd’ using rmarkdown + + Quitting from lines 66-68 [fuel_intro] (Basics.Rmd) + Error: processing vignette 'Basics.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Basics.Rmd’ + + SUMMARY: processing the following file failed: + ‘Basics.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’ + All declared Imports should be used. + ``` + +# mppR + +
+ +* Version: 1.5.0 +* GitHub: https://github.com/vincentgarin/mppR +* Source code: https://github.com/cran/mppR +* Date/Publication: 2024-02-22 17:20:02 UTC +* Number of recursive dependencies: 69 + +Run `revdepcheck::cloud_details(, "mppR")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘MPP_ME_QTL_detect.Rmd’ + ... + F2 -2.9970560 0.18508863 -0.00806081 0.1266095 + F283 10.2417600 1.78749082 -0.04223259 2.0862106 + DK105 0.1792433 0.03829626 NA NA + + > plot_QxEC(Qeff, EC = EC, env_id = c("CIAM", "TUM", + + "INRA", "KWS"), QTL = 2, EC_id = "cum rain", trait_id = "DMY") + + When sourcing ‘MPP_ME_QTL_detect.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘MPP_ME_QTL_detect.Rmd’ using ‘UTF-8’... failed + ‘mppR_gen_vignette.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MPP_ME_QTL_detect.Rmd’ using rmarkdown + ``` + +# MSCMT + +
+ +* Version: 1.4.0 +* GitHub: NA +* Source code: https://github.com/cran/MSCMT +* Date/Publication: 2024-03-19 10:20:02 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "MSCMT")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘WorkingWithMSCMT.Rmd’ + ... + (Predictor weights V are standardized by sum(V)=1) + + + > library(ggplot2) + + > ggplot(res, type = "comparison") + + When sourcing ‘WorkingWithMSCMT.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘CheckingSynth.Rmd’ using ‘UTF-8’... OK + ‘UsingTimeSeries.Rmd’ using ‘UTF-8’... OK + ‘WorkingWithMSCMT.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘CheckingSynth.Rmd’ using rmarkdown + --- finished re-building ‘CheckingSynth.Rmd’ + + --- re-building ‘UsingTimeSeries.Rmd’ using rmarkdown + --- finished re-building ‘UsingTimeSeries.Rmd’ + + --- re-building ‘WorkingWithMSCMT.Rmd’ using rmarkdown + + ... + Quitting from lines 156-158 [unnamed-chunk-8] (WorkingWithMSCMT.Rmd) + Error: processing vignette 'WorkingWithMSCMT.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘WorkingWithMSCMT.Rmd’ + + SUMMARY: processing the following file failed: + ‘WorkingWithMSCMT.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# mstate + +
+ +* Version: 0.3.3 +* GitHub: https://github.com/hputter/mstate +* Source code: https://github.com/cran/mstate +* Date/Publication: 2024-07-11 21:30:06 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "mstate")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mstate-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.Cuminc + > ### Title: Plot method for Cuminc objects + > ### Aliases: plot.Cuminc + > + > ### ** Examples + > + > library(ggplot2) + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘visuals_demo.Rmd’ + ... + + > msf.WW <- msfit(object = c1, newdata = WW, trans = tmat) + + > plot(msf.WW) + + > plot(msf.WW, use.ggplot = TRUE) + + When sourcing ‘visuals_demo.R’: + Error: `expand` must be a logical vector, not the number 0. + Execution halted + + ‘visuals_demo.Rmd’ using ‘UTF-8’... failed + ‘Tutorial.Rnw’ using ‘UTF-8’... OK + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘visuals_demo.Rmd’ using rmarkdown + ``` + +# mtb + +
+ +* Version: 0.1.8 +* GitHub: https://github.com/yh202109/mtb +* Source code: https://github.com/cran/mtb +* Date/Publication: 2022-10-20 17:22:35 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "mtb")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(mtb) + > + > test_check("mtb") + [ FAIL 2 | WARN 13 | SKIP 0 | PASS 56 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + - "yend" [6] + - "xmin" [7] + - "xmax" [8] + - "ymin" [9] + - "ymax" [10] + ... ... ... and 3 more ... + + [ FAIL 2 | WARN 13 | SKIP 0 | PASS 56 ] + Error: Test failures + Execution halted + ``` + +# mulgar + +
+ +* Version: 1.0.2 +* GitHub: https://github.com/dicook/mulgar +* Source code: https://github.com/cran/mulgar +* Date/Publication: 2023-08-25 22:00:02 UTC +* Number of recursive dependencies: 43 + +Run `revdepcheck::cloud_details(, "mulgar")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘mulgar-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggmcbic + > ### Title: Produces an mclust summary plot with ggplot + > ### Aliases: ggmcbic + > + > ### ** Examples + > + > require(mclust) + ... + Type 'citation("mclust")' for citing this R package in publications. + > data(clusters) + > clusters_BIC <- mclustBIC(clusters[,1:5], G=2:6) + > ggmcbic(clusters_BIC) + Warning: Removed 5 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.8Mb + sub-directories of 1Mb or more: + data 8.5Mb + ``` + +# MultivariateAnalysis + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/MultivariateAnalysis +* Date/Publication: 2024-04-08 18:40:03 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::cloud_details(, "MultivariateAnalysis")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘MultivariateAnalysis-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ContribuicaoRelativa + > ### Title: Contribuicao das variaveis independentes para o agrupamento + > ### Aliases: ContribuicaoRelativa + > + > ### ** Examples + > + > + ... + 12. │ └─ggplot2:::`+.gg`(p, do.call(geom_line, option)) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# mxfda + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/julia-wrobel/mxfda +* Source code: https://github.com/cran/mxfda +* Date/Publication: 2024-05-08 11:00:02 UTC +* Number of recursive dependencies: 221 + +Run `revdepcheck::cloud_details(, "mxfda")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + data 4.0Mb + ``` + +# neatmaps + +
+ +* Version: 2.1.0 +* GitHub: https://github.com/PhilBoileau/neatmaps +* Source code: https://github.com/cran/neatmaps +* Date/Publication: 2019-05-12 19:10:03 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "neatmaps")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neatmaps-Ex.R’ failed + The error most likely occurred in: + + > ### Name: consClustResTable + > ### Title: Consensus Cluster Results in a Table + > ### Aliases: consClustResTable + > + > ### ** Examples + > + > # create the data frame using the network, node and edge attributes + ... + > df <- netsDataFrame(network_attr_df, + + node_attr_df, + + edge_df) + > + > # run the neatmap code on df + > neat_res <- neatmap(df, scale_df = "ecdf", max_k = 3, reps = 100, + + xlab = "vars", ylab = "nets", xlab_cex = 1, ylab_cex = 1) + Error in pm[[2]] : subscript out of bounds + Calls: neatmap ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.3Mb + ``` + +# neatStats + +
+ +* Version: 1.13.3 +* GitHub: https://github.com/gasparl/neatstats +* Source code: https://github.com/cran/neatStats +* Date/Publication: 2022-12-07 20:50:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "neatStats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neatStats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: peek_neat + > ### Title: Cursory Summaries and Plots per Group + > ### Aliases: peek_neat + > + > ### ** Examples + > + > + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +# netcom + +
+ +* Version: 2.1.7 +* GitHub: https://github.com/langendorfr/netcom +* Source code: https://github.com/cran/netcom +* Date/Publication: 2024-06-04 17:50:05 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "netcom")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tutorial.Rmd’ + ... + > networks <- c(networks_undisturbed, networks_disturbed) + + > comparisons <- netcom::compare(networks, method = "align") + + > stats::prcomp(comparisons) %>% ggplot2::autoplot(data = tibble(Kind = c(rep("Undisturbed", + + num_networks), rep("Disturbed", num_networks))), c .... [TRUNCATED] + + When sourcing ‘tutorial.R’: + Error: argument is of length zero + Execution halted + + ‘tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘tutorial.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’ + All declared Imports should be used. + ``` + +# NetFACS + +
+ +* Version: 0.5.0 +* GitHub: NA +* Source code: https://github.com/cran/NetFACS +* Date/Publication: 2022-12-06 17:32:35 UTC +* Number of recursive dependencies: 101 + +Run `revdepcheck::cloud_details(, "NetFACS")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NetFACS-Ex.R’ failed + The error most likely occurred in: + + > ### Name: network_conditional + > ### Title: Create a network based on conditional probabilities of dyads of + > ### elements + > ### Aliases: network_conditional + > + > ### ** Examples + > + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + invalid font type + Calls: ... drawDetails -> drawDetails.text -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘netfacs_tutorial.Rmd’ + ... + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + font family 'Arial Narrow' not found in PostScript font database + + When sourcing ‘netfacs_tutorial.R’: + Error: invalid font type + Execution halted + + ‘netfacs_tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +# neuroUp + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/eduardklap/neuroUp +* Source code: https://github.com/cran/neuroUp +* Date/Publication: 2024-08-28 08:20:05 UTC +* Number of recursive dependencies: 82 + +Run `revdepcheck::cloud_details(, "neuroUp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘neuroUp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: estim_corr + > ### Title: Estimate correlations + > ### Aliases: estim_corr + > + > ### ** Examples + > + > data_gambling <- gambling + ... + 8 100 -0.0787 -0.271 0.120 2 NA + 9 140 -0.0555 -0.219 0.111 2 NA + 10 221 -0.0405 -0.172 0.0920 2 NA + # ℹ 45 more rows + + $fig_corr + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 10 ] + Deleting unused snapshots: + • estim_corr/create-fig-corr-nozero.svg + • estim_diff/create-fig-cohen-s-d.svg + • estim_diff/create-fig-d-nozero.svg + • estim_diff/create-fig-nozero.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘neuroUp.Rmd’ + ... + > set.seed(1234) + + > feedback_estim <- estim_diff(feedback_data, c("mfg_learning", + + "mfg_application"), 20:271, 20, "Feedback middle frontal gyrus") + + > feedback_estim$fig_diff + + When sourcing ‘neuroUp.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘neuroUp.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘neuroUp.Rmd’ using rmarkdown + + Quitting from lines 92-93 [unnamed-chunk-5] (neuroUp.Rmd) + Error: processing vignette 'neuroUp.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘neuroUp.Rmd’ + + SUMMARY: processing the following file failed: + ‘neuroUp.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# NHSRplotthedots + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/NHSRplotthedots +* Date/Publication: 2021-11-03 20:20:10 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "NHSRplotthedots")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(NHSRplotthedots) + > + > test_check("NHSRplotthedots") + [ FAIL 1 | WARN 733 | SKIP 3 | PASS 431 ] + + ... + + `actual$type` is absent + `expected$type` is a character vector ('type') + + `actual$text` is absent + `expected$text` is a character vector ('text') + + [ FAIL 1 | WARN 733 | SKIP 3 | PASS 431 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘NHSRdatasets’ ‘grid’ ‘utils’ + All declared Imports should be used. + ``` + +# nichetools + +
+ +* Version: 0.3.1 +* GitHub: https://github.com/benjaminhlina/nichetools +* Source code: https://github.com/cran/nichetools +* Date/Publication: 2024-09-06 17:00:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "nichetools")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘using-nichetools-with-the-package-SIBER.Rmd’ + ... + + option = "A", alpha = 0.75) + + > ggplot() + stat_pointinterval(data = bays_95_overlap, + + aes(x = group_1, y = prop_overlap, point_fill = group_2), + + interval_colour = "gre ..." ... [TRUNCATED] + + When sourcing ‘using-nichetools-with-the-package-SIBER.R’: + Error: unused argument (theme = list(list("black", 0.681818181818182, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.681818181818182, 1, TRUE), list("", "plain", "black", 15, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.681818181818182, 0.681818181818182, 1, 1, "", 5.27189705271897, 2.04545454545455, 19, TRUE), 7.5, c(7.5, 7.5, 7.5, 7.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, + NULL, c(3.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 3.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 3.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(3, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, + Execution halted + + ‘using-nichetools-with-the-package-SIBER.Rmd’ using ‘UTF-8’... failed + ‘using-nichetools-with-the-package-nicheROVER.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘using-nichetools-with-the-package-SIBER.Rmd’ using rmarkdown + ``` + +# NIMAA + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/jafarilab/NIMAA +* Source code: https://github.com/cran/NIMAA +* Date/Publication: 2022-04-11 14:12:45 UTC +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "NIMAA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘NIMAA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: extractSubMatrix + > ### Title: Extract the non-missing submatrices from a given matrix. + > ### Aliases: extractSubMatrix + > + > ### ** Examples + > + > # load part of the beatAML data + ... + + row.vars = "inhibitor") + binmatnest.temperature + 13.21221 + Size of Square: 66 rows x 66 columns + Size of Rectangular_row: 6 rows x 105 columns + Size of Rectangular_col: 99 rows x 2 columns + Size of Rectangular_element_max: 59 rows x 79 columns + Error in pm[[2]] : subscript out of bounds + Calls: extractSubMatrix ... plotSubmatrix -> print -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(NIMAA) + Warning message: + In check_dep_version() : ABI version mismatch: + lme4 was built with Matrix ABI version 1 + Current Matrix ABI version is 0 + Please re-install lme4 from source or restore original 'Matrix' package + ... + 1. └─NIMAA::extractSubMatrix(...) at test-extract-nonmissing-submatrix.R:5:3 + 2. └─NIMAA:::plotSubmatrix(...) + 3. ├─base::print(plotly::ggplotly(p)) + 4. ├─plotly::ggplotly(p) + 5. └─plotly:::ggplotly.ggplot(p) + 6. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 4 | SKIP 0 | PASS 7 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘NIMAA-vignette.Rmd’ + ... + + > beatAML_incidence_matrix <- plotIncMatrix(x = beatAML_data, + + index_nominal = c(2, 1), index_numeric = 3, print_skim = FALSE, + + plot_weigh .... [TRUNCATED] + + Na/missing values Proportion: 0.2603 + + When sourcing ‘NIMAA-vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘NIMAA-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘NIMAA-vignette.Rmd’ using rmarkdown + + Quitting from lines 49-57 [plotIncMatrix function] (NIMAA-vignette.Rmd) + Error: processing vignette 'NIMAA-vignette.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘NIMAA-vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘NIMAA-vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + data 2.0Mb + doc 4.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 24 marked UTF-8 strings + ``` + +# nonmem2R + +
+ +* Version: 0.2.5 +* GitHub: NA +* Source code: https://github.com/cran/nonmem2R +* Date/Publication: 2024-03-11 17:30:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "nonmem2R")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nonmem2R-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vpcfig2 + > ### Title: Visual Predictive Check (VPC) based on Perl-speaks-NONMEM (PsN) + > ### generated VPC files (ggplot2-version). + > ### Aliases: vpcfig2 + > + > ### ** Examples + > + ... + VPC based on files: + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpctab004.dat + and + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpc_results.csv + Facetting was set using: + facet_wrap(~strata) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘VPCvignette.Rmd’ + ... + VPC based on files: + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpctab004.dat + and + /tmp/workdir/nonmem2R/new/nonmem2R.Rcheck/nonmem2R/extdata/vpc_results.csv + Facetting was set using: + facet_wrap(~strata) + + When sourcing ‘VPCvignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘GOFvignette.Rmd’ using ‘UTF-8’... OK + ‘VPCvignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘GOFvignette.Rmd’ using rmarkdown + ``` + +# nphRCT + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/nphRCT +* Date/Publication: 2024-06-27 12:30:02 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "nphRCT")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘explanation.Rmd’ + ... + + > km <- survfit(Surv(time, event) ~ arm, data = dat) + + > p_km <- survminer::ggsurvplot(km, data = dat, risk.table = TRUE, + + break.x.by = 6, legend.title = "", xlab = "Time (months)", + + ylab = "Ov ..." ... [TRUNCATED] + + When sourcing ‘explanation.R’: + Error: argument is of length zero + Execution halted + + ‘explanation.Rmd’ using ‘UTF-8’... failed + ‘weighted_log_rank_tests.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘explanation.Rmd’ using rmarkdown + + Quitting from lines 44-73 [unnamed-chunk-1] (explanation.Rmd) + Error: processing vignette 'explanation.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘explanation.Rmd’ + + --- re-building ‘weighted_log_rank_tests.Rmd’ using rmarkdown + ``` + +# nprobust + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/nprobust +* Date/Publication: 2020-08-26 10:40:02 UTC +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "nprobust")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nprobust-Ex.R’ failed + The error most likely occurred in: + + > ### Name: nprobust.plot + > ### Title: Graphical Presentation of Results from 'nprobust' Package. + > ### Aliases: nprobust.plot + > + > ### ** Examples + > + > x <- runif(500) + > y <- sin(4*x) + rnorm(500) + > est <- lprobust(y,x) + > nprobust.plot(est) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +# nzelect + +
+ +* Version: 0.4.0 +* GitHub: NA +* Source code: https://github.com/cran/nzelect +* Date/Publication: 2017-10-02 20:35:23 UTC +* Number of recursive dependencies: 95 + +Run `revdepcheck::cloud_details(, "nzelect")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘nzelect-Ex.R’ failed + The error most likely occurred in: + + > ### Name: polls + > ### Title: New Zealand Opinion Polls + > ### Aliases: polls + > ### Keywords: datasets + > + > ### ** Examples + > + ... + ℹ This can happen when ggplot fails to infer the correct grouping structure in + the data. + ℹ Did you forget to specify a `group` aesthetic or to convert a numerical + variable into a factor? + Warning: Removed 159 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘README.Rmd’ + ... + > proportions <- nzge %>% filter(election_year == 2014) %>% + + group_by(voting_place, voting_type) %>% summarise(`proportion Labour` = sum(votes[p .... [TRUNCATED] + `summarise()` has grouped output by 'voting_place'. You can override using the + `.groups` argument. + + > ggpairs(proportions, aes(colour = voting_type), columns = 3:5) + + When sourcing ‘README.R’: + Error: argument is of length zero + Execution halted + + ‘README.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘README.Rmd’ using rmarkdown + + Quitting from lines 64-82 [unnamed-chunk-3] (README.Rmd) + Error: processing vignette 'README.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘README.Rmd’ + + SUMMARY: processing the following file failed: + ‘README.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + data 5.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 6409 marked UTF-8 strings + ``` + +# OBIC + +
+ +* Version: 3.0.3 +* GitHub: https://github.com/AgroCares/Open-Bodem-Index-Calculator +* Source code: https://github.com/cran/OBIC +* Date/Publication: 2024-09-09 08:30:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "OBIC")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘obic_workability.Rmd’ + ... + > gg2 <- ggplot(data = dt, aes(x = field, fill = field)) + + + geom_col(aes(y = I_P_WO)) + theme_bw() + theme(axis.text = element_text(size = 10, + .... [TRUNCATED] + + > (gg | gg2) + plot_layout(guides = "collect") + plot_annotation(caption = "Baseline workability scores.", + + theme = theme(plot.caption = element .... [TRUNCATED] + + When sourcing ‘obic_workability.R’: + Error: object is not a unit + Execution halted + + ‘description-of-the-columns.Rmd’ using ‘UTF-8’... OK + ‘obic_introduction.Rmd’ using ‘UTF-8’... OK + ‘obic_score_aggregation.Rmd’ using ‘UTF-8’... OK + ‘obic_water_functions.Rmd’ using ‘UTF-8’... OK + ‘obic_workability.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘description-of-the-columns.Rmd’ using rmarkdown + --- finished re-building ‘description-of-the-columns.Rmd’ + + --- re-building ‘obic_introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.0Mb + sub-directories of 1Mb or more: + data 4.0Mb + doc 1.4Mb + ``` + +# oceanic + +
+ +* Version: 0.1.7 +* GitHub: NA +* Source code: https://github.com/cran/oceanic +* Date/Publication: 2024-06-11 03:40:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "oceanic")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘oceanic-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dotplot + > ### Title: dotplot + > ### Aliases: dotplot + > + > ### ** Examples + > + > dotplot(141,23) + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + data 8.0Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1242 marked UTF-8 strings + ``` + +# oddsratio + +
+ +* Version: 2.0.1 +* GitHub: https://github.com/pat-s/oddsratio +* Source code: https://github.com/cran/oddsratio +* Date/Publication: 2020-05-24 22:00:02 UTC +* Number of recursive dependencies: 63 + +Run `revdepcheck::cloud_details(, "oddsratio")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘oddsratio-Ex.R’ failed + The error most likely occurred in: + + > ### Name: insert_or + > ### Title: Insert odds ratios of GAM(M)s into smoothing function + > ### Aliases: insert_or + > + > ### ** Examples + > + > library(oddsratio) + ... + 5. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 6. └─ggplot2:::new_layer_names(object, names(plot$layers)) + 7. └─vctrs::vec_as_names(names, repair = "check_unique") + 8. └─vctrs (local) ``() + 9. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 10. └─vctrs:::stop_names_cannot_be_empty(names, call = call) + 11. └─vctrs:::stop_names(...) + 12. └─vctrs:::stop_vctrs(...) + 13. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘oddsratio.Rmd’ + ... + + pred = "x2", values = c(0.4, 0.6)) + + > insert_or(plot, or_object2, or_yloc = 2.1, values_yloc = 2, + + line_col = "green4", text_col = "black", rect_col = "green4", + + rect_alpha = .... [TRUNCATED] + + When sourcing ‘oddsratio.R’: + Error: Names can't be empty. + ✖ Empty name found at location 1. + Execution halted + + ‘oddsratio.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘oddsratio.Rmd’ using rmarkdown + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘gam’ + ``` + +# ofpetrial + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/DIFM-Brain/ofpetrial +* Source code: https://github.com/cran/ofpetrial +* Date/Publication: 2024-05-15 08:50:03 UTC +* Number of recursive dependencies: 136 + +Run `revdepcheck::cloud_details(, "ofpetrial")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ofpetrial-Ex.R’ failed + The error most likely occurred in: + + > ### Name: check_ortho_with_chars + > ### Title: Check the orthogonality with field/topographic characteristics + > ### Aliases: check_ortho_with_chars + > + > ### ** Examples + > + > data(td_single_input) + ... + 33. │ └─ggplot2:::`+.gg`(init, x[[i]]) + 34. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 35. │ ├─ggplot2::ggplot_add(object, p, objectname) + 36. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 37. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 38. └─base::.handleSimpleError(...) + 39. └─purrr (local) h(simpleError(msg, call)) + 40. └─cli::cli_abort(...) + 41. └─rlang::abort(...) + Execution halted + ``` + +# OmicNavigator + +
+ +* Version: 1.13.13 +* GitHub: https://github.com/abbvie-external/OmicNavigator +* Source code: https://github.com/cran/OmicNavigator +* Date/Publication: 2023-08-25 20:40:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "OmicNavigator")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > # Test files in inst/tinytest/ + > if (requireNamespace("tinytest", quietly = TRUE)) { + + suppressMessages(tinytest::test_package("OmicNavigator")) + + } + + testAdd.R..................... 0 tests + testAdd.R..................... 0 tests + ... + testPlot.R.................... 140 tests OK + testPlot.R.................... 140 tests OK + testPlot.R.................... 141 tests OK + testPlot.R.................... 141 tests OK + testPlot.R.................... 141 tests OK + testPlot.R.................... 142 tests OK + testPlot.R.................... 142 tests OK + testPlot.R.................... 143 tests OK Error in pm[[2]] : subscript out of bounds + Calls: suppressMessages ... plotStudy -> f -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘OmicNavigatorAPI.Rnw’ using Sweave + OmicNavigator R package version: 1.13.13 + The app is not installed. Install it with installApp() + Installing study "ABC" in /tmp/RtmpFyTBK9/file1d2273c45a46 + Exporting study "ABC" as an R package + Note: No maintainer email was specified. Using the placeholder: Unknown + Calculating pairwise overlaps. This may take a while... + Exported study to /tmp/RtmpFyTBK9/ONstudyABC + Success! + ... + l.14 ^^M + + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘OmicNavigatorUsersGuide.Rnw’ + + SUMMARY: processing the following files failed: + ‘OmicNavigatorAPI.Rnw’ ‘OmicNavigatorUsersGuide.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# omu + +
+ +* Version: 1.1.2 +* GitHub: https://github.com/connor-reid-tiffany/Omu +* Source code: https://github.com/cran/omu +* Date/Publication: 2024-03-06 23:40:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "omu")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘omu-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PCA_plot + > ### Title: Create a PCA plot + > ### Aliases: PCA_plot + > + > ### ** Examples + > + > PCA_plot(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata, + + variable = "Treatment", color = "Treatment", response_variable = "Metabolite") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PCA_plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Omu_vignette.Rmd’ using rmarkdown + + Quitting from lines 97-104 [unnamed-chunk-4] (Omu_vignette.Rmd) + Error: processing vignette 'Omu_vignette.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Omu_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘Omu_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Omu_vignette.Rmd’ + ... + + > library(knitr) + + > load("../data/c57_nos2KO_mouse_countDF.rda") + Warning in readChar(con, 5L, useBytes = TRUE) : + cannot open compressed file '../data/c57_nos2KO_mouse_countDF.rda', probable reason 'No such file or directory' + + When sourcing ‘Omu_vignette.R’: + Error: cannot open the connection + Execution halted + + ‘Omu_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +# OncoBayes2 + +
+ +* Version: 0.8-9 +* GitHub: NA +* Source code: https://github.com/cran/OncoBayes2 +* Date/Publication: 2023-07-20 18:40:05 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::cloud_details(, "OncoBayes2")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘OncoBayes2-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_blrm + > ### Title: Plot a fitted model + > ### Aliases: plot_blrm plot_toxicity_curve plot_toxicity_intervals + > ### plot_toxicity_intervals_stacked plot_toxicity_curve.blrmfit + > ### plot_toxicity_curve.blrm_trial plot_toxicity_intervals.blrmfit + > ### plot_toxicity_intervals.blrm_trial + > ### plot_toxicity_intervals_stacked.blrmfit + ... + > # Plot the dose-toxicity curve + > plot_toxicity_curve(blrmfit, + + x = "drug_A", + + group = ~ group_id * drug_B, + + newdata = subset(dose_info_combo2, group_id == "trial_AB"), + + facet_args = list(ncol = 4)) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 76.7Mb + sub-directories of 1Mb or more: + libs 74.7Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# oncomsm + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/Boehringer-Ingelheim/oncomsm +* Source code: https://github.com/cran/oncomsm +* Date/Publication: 2023-04-17 07:00:02 UTC +* Number of recursive dependencies: 126 + +Run `revdepcheck::cloud_details(, "oncomsm")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(dplyr) + + Attaching package: 'dplyr' + + The following objects are masked from 'package:stats': + + filter, lag + ... + 10. └─grid::unit.c(legend.box.margin[4], widths, legend.box.margin[2]) + 11. └─grid:::identicalUnits(x) + + [ FAIL 1 | WARN 0 | SKIP 2 | PASS 59 ] + Deleting unused snapshots: + • plots/plot-mstate-srp-model-2.svg + • plots/plot-mstate-srp-model-3.svg + • plots/plot-srp-model-2.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘avoiding-bias.Rmd’ + ... + + > mdl <- create_srpmodel(A = define_srp_prior(median_t_q05 = c(1, + + 4, 12), median_t_q95 = c(6, 8, 36), shape_q05 = c(0.99, 0.99, + + 0.99), s .... [TRUNCATED] + + > plot(mdl, confidence = 0.9) + + ... + + > plot(mdl, parameter_sample = smpl_prior, confidence = 0.75) + + When sourcing ‘oncomsm.R’: + Error: object is not a unit + Execution halted + + ‘avoiding-bias.Rmd’ using ‘UTF-8’... failed + ‘oncomsm.Rmd’ using ‘UTF-8’... failed + ‘prior-choice.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘avoiding-bias.Rmd’ using rmarkdown + + Quitting from lines 35-46 [unnamed-chunk-2] (avoiding-bias.Rmd) + Error: processing vignette 'avoiding-bias.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘avoiding-bias.Rmd’ + + --- re-building ‘oncomsm.Rmd’ using rmarkdown + + Quitting from lines 211-215 [plotting-the-prior] (oncomsm.Rmd) + Error: processing vignette 'oncomsm.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘oncomsm.Rmd’ + + --- re-building ‘prior-choice.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 59.2Mb + sub-directories of 1Mb or more: + doc 1.1Mb + libs 57.0Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# OneSampleLogRankTest + +
+ +* Version: 0.9.2 +* GitHub: NA +* Source code: https://github.com/cran/OneSampleLogRankTest +* Date/Publication: 2024-02-03 12:30:15 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "OneSampleLogRankTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘OneSampleLogRankTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotKM + > ### Title: Plot Kaplan-Meier Curve against Population + > ### Aliases: plotKM + > + > ### ** Examples + > + > # load data + > data(dataSurv_small) + > data(dataPop_2018_2021) + > + > plotKM(dataSurv_small, dataPop_2018_2021, type = "exact") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plotKM ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘oneSampleLogRankTest.Rmd’ + ... + $estimate + std_mort_ratio_est lwr upr + 1 1.531173 0.8302562 2.823816 + + + > plotKM(dataSurv, dataPop_2018_2021_race_sex_eth, type = "approximate") + + When sourcing ‘oneSampleLogRankTest.R’: + Error: argument is of length zero + Execution halted + + ‘oneSampleLogRankTest.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘oneSampleLogRankTest.Rmd’ using rmarkdown + + Quitting from lines 74-77 [unnamed-chunk-3] (oneSampleLogRankTest.Rmd) + Error: processing vignette 'oneSampleLogRankTest.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘oneSampleLogRankTest.Rmd’ + + SUMMARY: processing the following file failed: + ‘oneSampleLogRankTest.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# onpoint + +
+ +* Version: 1.0.5 +* GitHub: https://github.com/r-spatialecology/onpoint +* Source code: https://github.com/cran/onpoint +* Date/Publication: 2024-01-10 14:03:06 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "onpoint")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘onpoint-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.env_summarized + > ### Title: plot.env_summarized + > ### Aliases: plot.env_summarized + > + > ### ** Examples + > + > set.seed(42) + ... + 39. + + Done. + > + > x <- summarize_envelope(cluster_env) + > plot(x) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# ordbetareg + +
+ +* Version: 0.7.2 +* GitHub: https://github.com/saudiwin/ordbetareg_pack +* Source code: https://github.com/cran/ordbetareg +* Date/Publication: 2023-08-10 07:30:02 UTC +* Number of recursive dependencies: 174 + +Run `revdepcheck::cloud_details(, "ordbetareg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ordbetareg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pp_check_ordbeta + > ### Title: Accurate Posterior Predictive Plots for Ordbetareg Models + > ### Aliases: pp_check_ordbeta + > + > ### ** Examples + > + > + ... + 16. │ └─ggplot2 (local) setup_params(...) + 17. │ └─ggplot2:::make_summary_fun(...) + 18. │ └─rlang::as_function(fun.data) + 19. │ └─base::get(x, envir = env, mode = "function") + 20. └─base::.handleSimpleError(...) + 21. └─rlang (local) h(simpleError(msg, call)) + 22. └─handlers[[1L]](cnd) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + data 7.5Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 36 marked UTF-8 strings + ``` + +# packcircles + +
+ +* Version: 0.3.6 +* GitHub: https://github.com/mbedward/packcircles +* Source code: https://github.com/cran/packcircles +* Date/Publication: 2023-09-08 06:30:02 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "packcircles")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘progressive_packing.Rmd’ + ... + + scale_fill_man .... [TRUNCATED] + + > if (requireNamespace("ggiraph")) { + + gg <- ggplot(data = dat.gg) + ggiraph::geom_polygon_interactive(aes(x, + + y, group = id, fill = fac .... [TRUNCATED] + Loading required namespace: ggiraph + + When sourcing ‘progressive_packing.R’: + Error: argument is of length zero + Execution halted + + ‘graph_packing.Rmd’ using ‘UTF-8’... OK + ‘intro.Rmd’ using ‘UTF-8’... OK + ‘progressive_packing.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘graph_packing.Rmd’ using rmarkdown + --- finished re-building ‘graph_packing.Rmd’ + + --- re-building ‘intro.Rmd’ using rmarkdown + ``` + +# pafr + +
+ +* Version: 0.0.2 +* GitHub: https://github.com/dwinter/pafr +* Source code: https://github.com/cran/pafr +* Date/Publication: 2020-12-08 10:20:12 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::cloud_details(, "pafr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pafr) + Loading required package: ggplot2 + > + > test_check("pafr") + [ FAIL 6 | WARN 2 | SKIP 0 | PASS 70 ] + + ... + ── Failure ('test_plot.r:11:5'): dotplot works produces a plot ───────────────── + unname(labs["xintercept"]) not equal to "xintercept". + target is NULL, current is character + ── Failure ('test_plot.r:12:5'): dotplot works produces a plot ───────────────── + unname(labs["yintercept"]) not equal to "yintercept". + target is NULL, current is character + + [ FAIL 6 | WARN 2 | SKIP 0 | PASS 70 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# patchwork + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/thomasp85/patchwork +* Source code: https://github.com/cran/patchwork +* Date/Publication: 2024-01-08 14:40:02 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "patchwork")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘patchwork-Ex.R’ failed + The error most likely occurred in: + + > ### Name: free + > ### Title: Free a plot from alignment + > ### Aliases: free + > + > ### ** Examples + > + > # Sometimes you have a plot that defies good composition alginment, e.g. due + ... + > p1 / p2 + > + > # We can fix this be using free + > free(p1) / p2 + > + > # We can still collect guides like before + > free(p1) / p2 + plot_layout(guides = "collect") + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# pathviewr + +
+ +* Version: 1.1.7 +* GitHub: https://github.com/ropensci/pathviewr +* Source code: https://github.com/cran/pathviewr +* Date/Publication: 2023-03-08 08:10:05 UTC +* Number of recursive dependencies: 182 + +Run `revdepcheck::cloud_details(, "pathviewr")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pathviewr) + > #library(vdiffr) + > + > test_check("pathviewr") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ] + + ... + ── Error ('test-plot_by_subject.R:168:3'): elev views wrangled correctly via tidyverse ── + Error in `expect_match(elev_all_plots[[3]][[4]][["labels"]][["x"]], "position_height")`: is.character(act$val) is not TRUE + Backtrace: + ▆ + 1. └─testthat::expect_match(...) at test-plot_by_subject.R:168:3 + 2. └─base::stopifnot(is.character(act$val)) + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ] + Error: Test failures + Execution halted + ``` + +# patientProfilesVis + +
+ +* Version: 2.0.9 +* GitHub: https://github.com/openanalytics/patientProfilesVis +* Source code: https://github.com/cran/patientProfilesVis +* Date/Publication: 2024-06-18 09:00:02 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "patientProfilesVis")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘patientProfiles-template-SDTM.Rmd’ + ... + > patientProfilesPlots <- c(patientProfilesPlots, list(MH = mhPlots)) + + > cmPlots <- subjectProfileIntervalPlot(data = dataAll$CM, + + paramVar = c("CMTRT", "CMDOSE", "CMDOSU", "CMROUTE", "CMDOSFRQ"), + + timeStartVa .... [TRUNCATED] + 171 record(s) with missing Study Day of Start of Medication and 208 record(s) with missing Study Day of End of Medication are imputed with minimal imputation. + + ... + + paramVar = "AETERM", timeStartVar = "AESTDY", timeEndVar = "AEENDY", + + colorVar = " ..." ... [TRUNCATED] + 3 record(s) with missing Study Day of Start of Adverse Event and 19 record(s) with missing Study Day of End of Adverse Event are imputed with minimal imputation. + + When sourcing ‘patientProfilesVis-introduction.R’: + Error: argument is of length zero + Execution halted + + ‘patientProfiles-template-SDTM.Rmd’ using ‘UTF-8’... failed + ‘patientProfilesVis-introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘patientProfiles-template-SDTM.Rmd’ using rmarkdown + + Quitting from lines 129-153 [patientProfiles-concomitantMedications] (patientProfiles-template-SDTM.Rmd) + Error: processing vignette 'patientProfiles-template-SDTM.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘patientProfiles-template-SDTM.Rmd’ + + --- re-building ‘patientProfilesVis-introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(patientProfilesVis) + > + > test_check("patientProfilesVis") + [ FAIL 100 | WARN 0 | SKIP 20 | PASS 145 ] + + ══ Skipped tests (20) ══════════════════════════════════════════════════════════ + ... + 11. └─patientProfilesVis (local) .fun(piece, ...) + 12. └─ggplot2:::`+.gg`(...) + 13. └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. ├─ggplot2::ggplot_add(object, p, objectname) + 15. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 100 | WARN 0 | SKIP 20 | PASS 145 ] + Error: Test failures + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.7Mb + sub-directories of 1Mb or more: + doc 5.2Mb + ``` + +# PCADSC + +
+ +* Version: 0.8.0 +* GitHub: https://github.com/annepetersen1/PCADSC +* Source code: https://github.com/cran/PCADSC +* Date/Publication: 2017-04-19 10:07:43 UTC +* Number of recursive dependencies: 35 + +Run `revdepcheck::cloud_details(, "PCADSC")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PCADSC-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CEPlot + > ### Title: Cumulative eigenvalue plot + > ### Aliases: CEPlot + > + > ### ** Examples + > + > #load iris data + ... + > CEPlot(irisPCADSC_fast) + Warning: The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in + ggplot2 3.3.4. + ℹ Please use "none" instead. + ℹ The deprecated feature was likely used in the PCADSC package. + Please report the issue at . + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Matrix’ ‘pander’ + All declared Imports should be used. + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘data.table’ + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# pcutils + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/Asa12138/pcutils +* Source code: https://github.com/cran/pcutils +* Date/Publication: 2024-06-25 21:20:05 UTC +* Number of recursive dependencies: 281 + +Run `revdepcheck::cloud_details(, "pcutils")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘pcutils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: gghist + > ### Title: gg histogram + > ### Aliases: gghist + > + > ### ** Examples + > + > if (requireNamespace("ggpubr")) { + ... + 12. │ └─ggplot2:::`+.gg`(...) + 13. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 14. │ ├─ggplot2::ggplot_add(object, p, objectname) + 15. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 16. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 17. └─base::.handleSimpleError(...) + 18. └─purrr (local) h(simpleError(msg, call)) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +# pdxTrees + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/mcconvil/pdxTrees +* Source code: https://github.com/cran/pdxTrees +* Date/Publication: 2020-08-17 14:00:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "pdxTrees")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘pdxTrees-vignette.Rmd’ + ... + + y = Pollution_Removal_value, color = Mature_Size)) + geom_point(size = 2, + + .... [TRUNCATED] + + > berkeley_graph + transition_states(states = Mature_Size, + + transition_length = 10, state_length = 8) + enter_grow() + + + exit_shrink() + + When sourcing ‘pdxTrees-vignette.R’: + Error: argument "theme" is missing, with no default + Execution halted + + ‘pdxTrees-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# personalized + +
+ +* Version: 0.2.7 +* GitHub: https://github.com/jaredhuling/personalized +* Source code: https://github.com/cran/personalized +* Date/Publication: 2022-06-27 20:20:03 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "personalized")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > Sys.setenv("R_TESTS" = "") + > library(testthat) + > library(personalized) + Loading required package: glmnet + Loading required package: Matrix + Loaded glmnet 4.1-8 + Loading required package: mgcv + ... + 4. └─personalized:::plot.subgroup_validated(subgrp.val, type = "stability") + 5. ├─plotly::subplot(...) + 6. │ └─plotly:::dots2plots(...) + 7. ├─plotly::ggplotly(p.primary, tooltip = paste0("tooltip", 1:4)) + 8. └─plotly:::ggplotly.ggplot(...) + 9. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 215 ] + Error: Test failures + Execution halted + ``` + +# phyloseqGraphTest + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/jfukuyama/phyloseqGraphTest +* Source code: https://github.com/cran/phyloseqGraphTest +* Date/Publication: 2024-02-05 19:00:02 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "phyloseqGraphTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘phyloseqGraphTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_test_network + > ### Title: Plots the graph used for testing + > ### Aliases: plot_test_network + > + > ### ** Examples + > + > library(phyloseq) + ... + > plot_test_network(gt) + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic argument: + • layout = layout + ℹ Did you misspell an argument name? + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘gt_vignette.Rmd’ + ... + > plot_test_network(gt) + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic argument: + • layout = layout + ℹ Did you misspell an argument name? + + When sourcing ‘gt_vignette.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘gt_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘gt_vignette.Rmd’ using rmarkdown + + Quitting from lines 175-176 [unnamed-chunk-5] (gt_vignette.Rmd) + Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘gt_vignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘gt_vignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# PieGlyph + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/rishvish/PieGlyph +* Source code: https://github.com/cran/PieGlyph +* Date/Publication: 2024-06-28 12:00:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "PieGlyph")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PieGlyph-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_pie_interactive + > ### Title: Scatter plots with interactive pie-chart glyphs + > ### Aliases: geom_pie_interactive + > + > ### ** Examples + > + > #' ## Load libraries + ... + > # One of the interactive aesthetics is tooltip. It is set that by default + > # it shows the value and percentage of each slice in the pie-chart. + > # Hover over any pie-chart in the plot to see this + > plot_obj1 <- ggplot(data = plot_data, aes(x = system, y = response)) + + + geom_pie_interactive(slices = c("A", "B", "C", "D"), + + data = plot_data)+ + + theme_classic() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + ... + • geom_pie_interactive/custom-tooltip.svg + • geom_pie_interactive/data-id.svg + • geom_pie_interactive/long-form-data-works.svg + • geom_pie_interactive/multiple-interactive-parameters.svg + • geom_pie_interactive/only-one-attribute.svg + • pie-grob/pie-grob-with-multiple-values-no-fill-works.svg + • pie-grob/pie-grob-with-single-non-zero-value-no-fill-works.svg + • pie-grob/pie-grob-with-single-non-zero-value-works.svg + Error: Test failures + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PieGlyph.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PieGlyph.Rmd’ + ... + + geom_pie_glyph(slices = "Attributes", values = "values") + + + theme_cla .... [TRUNCATED] + + > plot_obj <- ggplot(data = plot_data) + geom_pie_interactive(aes(x = system, + + y = response, data_id = system), slices = c("A", "B", "C", + + .... [TRUNCATED] + + ... + before plotting. + Execution halted + + ‘PieGlyph.Rmd’ using ‘UTF-8’... failed + ‘interactive-pie-glyphs.Rmd’ using ‘UTF-8’... failed + ‘multinomial-classification-example.Rmd’ using ‘UTF-8’... OK + ‘pie-lollipop-example.Rmd’ using ‘UTF-8’... OK + ‘spatial-example.Rmd’ using ‘UTF-8’... OK + ‘time-series-example.Rmd’ using ‘UTF-8’... failed + ‘unusual-situations.Rmd’ using ‘UTF-8’... failed + ``` + +# Plasmidprofiler + +
+ +* Version: 0.1.6 +* GitHub: NA +* Source code: https://github.com/cran/Plasmidprofiler +* Date/Publication: 2017-01-06 01:10:47 +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "Plasmidprofiler")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Plasmidprofiler-Ex.R’ failed + The error most likely occurred in: + + > ### Name: main + > ### Title: Main: Run everything + > ### Aliases: main + > + > ### ** Examples + > + > main(blastdata, + ... + Saving 12 x 7 in image + Warning: Vectorized input to `element_text()` is not officially supported. + ℹ Results may be unexpected or may change in future versions of ggplot2. + Warning in geom_tile(aes(x = Plasmid, y = Sample, label = AMR_gene, fill = Inc_group, : + Ignoring unknown aesthetics: label and text + Warning: Use of `report$Sureness` is discouraged. + ℹ Use `Sureness` instead. + Error in pm[[2]] : subscript out of bounds + Calls: main ... -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# platetools + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/swarchal/platetools +* Source code: https://github.com/cran/platetools +* Date/Publication: 2024-03-07 16:50:02 UTC +* Number of recursive dependencies: 48 + +Run `revdepcheck::cloud_details(, "platetools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(platetools) + > + > test_check("platetools") + [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ] + + ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ + ... + length(out96) not equal to length(ggplot()). + 1/1 mismatches + [1] 11 - 10 == 1 + ── Failure ('test-plot_wrapper.R:34:5'): returns expected ggplot object ──────── + names(out96) not equal to names(ggplot()). + Lengths differ: 11 is not 10 + + [ FAIL 2 | WARN 1 | SKIP 4 | PASS 187 ] + Error: Test failures + Execution halted + ``` + +# PLNmodels + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/pln-team/PLNmodels +* Source code: https://github.com/cran/PLNmodels +* Date/Publication: 2024-03-05 15:50:03 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "PLNmodels")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PLNPCA.Rmd’ + ... + 3 "$contrib" "contributions of the individuals" + + > factoextra::fviz_pca_biplot(myPCA_ICL) + + When sourcing ‘PLNPCA.R’: + Error: ℹ In index: 1. + ℹ With name: y. + ... + ! argument is of length zero + Execution halted + + ‘Import_data.Rmd’ using ‘UTF-8’... OK + ‘PLN.Rmd’ using ‘UTF-8’... OK + ‘PLNLDA.Rmd’ using ‘UTF-8’... OK + ‘PLNPCA.Rmd’ using ‘UTF-8’... failed + ‘PLNmixture.Rmd’ using ‘UTF-8’... failed + ‘PLNnetwork.Rmd’ using ‘UTF-8’... OK + ‘Trichoptera.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Import_data.Rmd’ using rmarkdown + --- finished re-building ‘Import_data.Rmd’ + + --- re-building ‘PLN.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 26.0Mb + sub-directories of 1Mb or more: + R 1.0Mb + data 3.5Mb + doc 2.1Mb + libs 18.6Mb + ``` + +# plotBart + +
+ +* Version: 0.1.7 +* GitHub: https://github.com/priism-center/plotBart +* Source code: https://github.com/cran/plotBart +* Date/Publication: 2022-05-27 07:50:06 UTC +* Number of recursive dependencies: 94 + +Run `revdepcheck::cloud_details(, "plotBart")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(vdiffr) + > library(plotBart) + Loading required package: bartCause + Loading required package: ggplot2 + > + > test_check("plotBart") # run tests + ... + • plots/mod-search.svg + • plots/overlappscoresdensity.svg + • plots/overlapvarsdensity.svg + • plots/pate.svg + • plots/sate.svg + • plots/supportchi.svg + • plots/supportsd.svg + • plots/waterfall2.svg + Error: Test failures + Execution halted + ``` + +# plotDK + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/plotDK +* Date/Publication: 2021-10-01 08:00:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::cloud_details(, "plotDK")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(plotDK) + > + > test_check("plotDK") + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + Error in `expect_setequal(c("x", "y", "group", "subgroup", "text", "fill"), + names(labels))`: `object` and `expected` must both be vectors + Backtrace: + ▆ + 1. └─testthat::expect_setequal(c("x", "y", "group", "subgroup", "text", "fill"), names(labels)) at test-plotDK.R:67:5 + 2. └─rlang::abort("`object` and `expected` must both be vectors") + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 46 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘mapproj’ + All declared Imports should be used. + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 12992 marked UTF-8 strings + ``` + +# plotly + +
+ +* Version: 4.10.4 +* GitHub: https://github.com/plotly/plotly.R +* Source code: https://github.com/cran/plotly +* Date/Publication: 2024-01-13 22:40:02 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "plotly")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘plotly-Ex.R’ failed + The error most likely occurred in: + + > ### Name: style + > ### Title: Modify trace(s) + > ### Aliases: style + > + > ### ** Examples + > + > ## Don't show: + ... + + # this clobbers the previously supplied marker.line.color + + style(p, marker.line = list(width = 2.5), marker.size = 10) + + ## Don't show: + + }) # examplesIf + > (p <- ggplotly(qplot(data = mtcars, wt, mpg, geom = c("point", "smooth")))) + Warning: `qplot()` was deprecated in ggplot2 3.4.0. + `geom_smooth()` using method = 'loess' and formula = 'y ~ x' + Error in pm[[2]] : subscript out of bounds + Calls: ... eval -> eval -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library("testthat") + > library("plotly") + Loading required package: ggplot2 + + Attaching package: 'plotly' + + The following object is masked from 'package:ggplot2': + ... + • plotly-subplot/subplot-bump-axis-annotation.svg + • plotly-subplot/subplot-bump-axis-image.svg + • plotly-subplot/subplot-bump-axis-shape-shared.svg + • plotly-subplot/subplot-bump-axis-shape.svg + • plotly-subplot/subplot-reposition-annotation.svg + • plotly-subplot/subplot-reposition-image.svg + • plotly-subplot/subplot-reposition-shape-fixed.svg + • plotly-subplot/subplot-reposition-shape.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.1Mb + sub-directories of 1Mb or more: + R 1.0Mb + htmlwidgets 4.0Mb + ``` + +# pmartR + +
+ +* Version: 2.4.5 +* GitHub: https://github.com/pmartR/pmartR +* Source code: https://github.com/cran/pmartR +* Date/Publication: 2024-05-21 15:50:02 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "pmartR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pmartR) + > + > test_check("pmartR") + [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2375 ] + + ══ Skipped tests (11) ══════════════════════════════════════════════════════════ + ... + • plots/plot-spansres-color-high-color-low.svg + • plots/plot-spansres.svg + • plots/plot-statres-anova-volcano.svg + • plots/plot-statres-anova.svg + • plots/plot-statres-combined-volcano.svg + • plots/plot-statres-combined.svg + • plots/plot-statres-gtest.svg + • plots/plot-totalcountfilt.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 10.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + help 1.5Mb + libs 6.7Mb + ``` + +# pmxTools + +
+ +* Version: 1.3 +* GitHub: https://github.com/kestrel99/pmxTools +* Source code: https://github.com/cran/pmxTools +* Date/Publication: 2023-02-21 16:00:08 UTC +* Number of recursive dependencies: 85 + +Run `revdepcheck::cloud_details(, "pmxTools")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(pmxTools) + Loading required package: patchwork + > + > test_check("pmxTools") + [ FAIL 1 | WARN 1 | SKIP 12 | PASS 110 ] + + ... + 24. └─handlers[[1L]](cnd) + 25. └─cli::cli_abort(...) + 26. └─rlang::abort(...) + + [ FAIL 1 | WARN 1 | SKIP 12 | PASS 110 ] + Deleting unused snapshots: + • plot/conditioned-distplot.svg + • plot/perc.svg + Error: Test failures + Execution halted + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘DiagrammeR’ + ``` + +# posterior + +
+ +* Version: 1.6.0 +* GitHub: https://github.com/stan-dev/posterior +* Source code: https://github.com/cran/posterior +* Date/Publication: 2024-07-03 23:00:02 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "posterior")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘pareto_diagnostics.Rmd’ using rmarkdown + --- finished re-building ‘pareto_diagnostics.Rmd’ + + --- re-building ‘posterior.Rmd’ using rmarkdown + --- finished re-building ‘posterior.Rmd’ + + --- re-building ‘rvar.Rmd’ using rmarkdown + + Quitting from lines 530-533 [mixture] (rvar.Rmd) + ... + NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list("grey92", NA, NULL, NULL, TRUE), list(), NULL, NULL, NULL, list("white", NULL, NULL, NULL, FALSE, + "white", TRUE), NULL, list(NULL, 0.5, NULL, NULL, FALSE, NULL, TRUE), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, NULL, list("grey85", + NA, NULL, NULL, TRUE), NULL, NULL, "on", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + --- failed re-building ‘rvar.Rmd’ + + SUMMARY: processing the following file failed: + ‘rvar.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘rvar.Rmd’ + ... + > y + rvar<4000>[3] mean ± sd: + [1] 3.00 ± 1.00 2.02 ± 0.99 0.96 ± 0.99 + + > X + y + + When sourcing ‘rvar.R’: + Error: Cannot broadcast array of shape [4000,3,1] to array of shape [4000,4,3]: + All dimensions must be 1 or equal. + Execution halted + + ‘pareto_diagnostics.Rmd’ using ‘UTF-8’... OK + ‘posterior.Rmd’ using ‘UTF-8’... OK + ‘rvar.Rmd’ using ‘UTF-8’... failed + ``` + +# PPQplan + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/allenzhuaz/PPQplan +* Source code: https://github.com/cran/PPQplan +* Date/Publication: 2020-10-08 04:30:06 UTC +* Number of recursive dependencies: 119 + +Run `revdepcheck::cloud_details(, "PPQplan")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PPQnote.Rmd’ using rmarkdown + --- finished re-building ‘PPQnote.Rmd’ + + --- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PPQplan-vignette.Rmd’ + ... + + > devtools::load_all() + + When sourcing ‘PPQplan-vignette.R’: + Error: Could not find a root 'DESCRIPTION' file that starts with '^Package' in + '/tmp/RtmpeoIsxA/file11156538c652/vignettes'. + ℹ Are you in your project directory and does your project have a 'DESCRIPTION' + file? + Execution halted + + ‘PPQnote.Rmd’ using ‘UTF-8’... OK + ‘PPQplan-vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 12.1Mb + sub-directories of 1Mb or more: + doc 12.0Mb + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# ppseq + +
+ +* Version: 0.2.5 +* GitHub: https://github.com/zabore/ppseq +* Source code: https://github.com/cran/ppseq +* Date/Publication: 2024-09-04 22:20:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "ppseq")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘one_sample_expansion.Rmd’ + ... + + + + + > ptest <- plot(one_sample_cal_tbl, type1_range = c(0.05, + + 0.1), minimum_power = 0.7, plotly = TRUE) + + ... + + > ptest <- plot(two_sample_cal_tbl, type1_range = c(0.05, + + 0.1), minimum_power = 0.7, plotly = TRUE) + + When sourcing ‘two_sample_randomized.R’: + Error: subscript out of bounds + Execution halted + + ‘one_sample_expansion.Rmd’ using ‘UTF-8’... failed + ‘two_sample_randomized.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘one_sample_expansion.Rmd’ using rmarkdown + + Quitting from lines 183-188 [unnamed-chunk-13] (one_sample_expansion.Rmd) + Error: processing vignette 'one_sample_expansion.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘one_sample_expansion.Rmd’ + + --- re-building ‘two_sample_randomized.Rmd’ using rmarkdown + ... + Quitting from lines 179-184 [unnamed-chunk-13] (two_sample_randomized.Rmd) + Error: processing vignette 'two_sample_randomized.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘two_sample_randomized.Rmd’ + + SUMMARY: processing the following files failed: + ‘one_sample_expansion.Rmd’ ‘two_sample_randomized.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 11.0Mb + sub-directories of 1Mb or more: + doc 10.5Mb + ``` + +# PPtreeregViz + +
+ +* Version: 2.0.5 +* GitHub: https://github.com/sunsmiling/PPtreeregViz +* Source code: https://github.com/cran/PPtreeregViz +* Date/Publication: 2022-12-23 19:20:05 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "PPtreeregViz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PPtreeregViz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: PPregNodeViz + > ### Title: Node visualization + > ### Aliases: PPregNodeViz + > ### Keywords: tree + > + > ### ** Examples + > + > data(dataXY) + > Model <- PPTreereg(Y~., data = dataXY, DEPTH = 2) + > PPregNodeViz(Model,node.id=1) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: PPregNodeViz ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘PPtreeregViz.Rmd’ + ... + + > plot(Tree.Imp) + + > plot(Tree.Imp, marginal = TRUE, num_var = 5) + + > PPregNodeViz(Model, node.id = 1) + + When sourcing ‘PPtreeregViz.R’: + Error: argument is of length zero + Execution halted + + ‘PPtreeregViz.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘PPtreeregViz.Rmd’ using rmarkdown + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +# precintcon + +
+ +* Version: 2.3.0 +* GitHub: https://github.com/lucasvenez/precintcon +* Source code: https://github.com/cran/precintcon +* Date/Publication: 2016-07-17 13:49:19 +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "precintcon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘precintcon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pplot.deciles + > ### Title: Plot deciles + > ### Aliases: pplot.deciles precintcon.plot.deciles + > ### Keywords: deciles precipitation + > + > ### ** Examples + > + ... + 9. │ └─layout$setup(data, plot$data, plot$plot_env) + 10. │ └─ggplot2 (local) setup(..., self = self) + 11. │ └─base::lapply(...) + 12. │ └─ggplot2 (local) FUN(X[[i]], ...) + 13. │ └─ggplot2::map_data(...) + 14. │ └─vctrs::vec_slice(data, facet_vals$.index) + 15. └─vctrs:::stop_scalar_type(``(``), "x", ``) + 16. └─vctrs:::stop_vctrs(...) + 17. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + Execution halted + ``` + +# precrec + +
+ +* Version: 0.14.4 +* GitHub: https://github.com/evalclass/precrec +* Source code: https://github.com/cran/precrec +* Date/Publication: 2023-10-11 22:10:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "precrec")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + > autoplot(mscurves) + Warning in ggplot2::fortify(object, raw_curves = raw_curves, reduce_points = reduce_points) : + Arguments in `...` must be used. + ✖ Problematic argument: + • raw_curves = raw_curves + ℹ Did you misspell an argument name? + + When sourcing ‘introduction.R’: + Error: object is not a unit + Execution halted + + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + libs 4.3Mb + ``` + +# priorsense + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/priorsense +* Date/Publication: 2024-07-16 10:30:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "priorsense")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘priorsense-Ex.R’ failed + The error most likely occurred in: + + > ### Name: powerscale_plots + > ### Title: Diagnostic plots for power-scaling sensitivity + > ### Aliases: powerscale_plots powerscale_plot_dens powerscale_plot_ecdf + > ### powerscale_plot_ecdf.powerscaled_sequence powerscale_plot_quantities + > ### powerscale_plot_quantities.powerscaled_sequence + > + > ### ** Examples + > + > ex <- example_powerscale_model() + > + > powerscale_plot_dens(ex$draws) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘powerscaling.Rmd’ + ... + + 1 mu 0.435 0.644 prior-data conflict + 2 sigma 0.361 0.677 prior-data conflict + + > powerscale_plot_dens(fit, variable = "mu", facet_rows = "variable") + + When sourcing ‘powerscaling.R’: + Error: unused argument (theme = list(list("black", 0.545454545454545, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.545454545454545, 1, TRUE), list("sans", "plain", "black", 12, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.545454545454545, 0.545454545454545, 1, 1, "sans", 4.21751764217518, 1.63636363636364, 19, TRUE), 6, c(6, 6, 6, 6), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, + NULL, c(3, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 3, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 3), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.4, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NU + Execution halted + + ‘powerscaling.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘powerscaling.Rmd’ using rmarkdown + + Quitting from lines 124-125 [unnamed-chunk-7] (powerscaling.Rmd) + Error: processing vignette 'powerscaling.Rmd' failed with diagnostics: + unused argument (theme = list(list("black", 0.545454545454545, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.545454545454545, 1, TRUE), list("sans", "plain", "black", 12, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.545454545454545, 0.545454545454545, 1, 1, "sans", 4.21751764217518, 1.63636363636364, 19, TRUE), 6, c(6, 6, 6, 6), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, + NULL, c(3, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 3, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 3), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.4, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.4, 0), + NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.4), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, 2.4, 0, 2.4), NULL, TRUE), list("grey20", 0.3, NULL, NULL, FALSE, "grey20", FALSE), NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(NULL, 0.4, NULL, NULL, FALSE, NULL, FALSE), + NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, list(), NULL, 2, NULL, NULL, list(), 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 13, 0, NULL, NULL, NULL, NULL, NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list(), list(), 1.5, NULL, NULL, list(), NULL, list(NULL, 0.5, NULL, NULL, FALSE, NULL, TRUE), NULL, NULL, + NULL, NULL, FALSE, list(), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 6, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 6, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(6, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", NULL, NULL, list(), NULL, NULL, "on", "outside", list(NULL, NULL, "grey10", 0.9, NULL, NULL, NULL, NULL, c(4.8, 4.8, 4.8, 4.8), NULL, FALSE), NULL, NULL, + NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 3, 3, list(), list(NULL, NULL, NULL, NULL, FALSE, NULL, TRUE), list(NULL, NULL, NULL, NULL, FALSE, NULL, TRUE), list(NULL, NULL, NULL, NULL, FALSE, NULL, TRUE), list(NULL, NULL, NULL, NULL, 0.5, 0.5, 0, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), 0.666666666666667, 0.333333333333333)) + --- failed re-building ‘powerscaling.Rmd’ + + SUMMARY: processing the following file failed: + ‘powerscaling.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# probably + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/tidymodels/probably +* Source code: https://github.com/cran/probably +* Date/Publication: 2024-02-23 03:20:02 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "probably")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + `actual$ymin` is absent + `expected$ymin` is a character vector ('lower') + + `actual$ymax` is absent + `expected$ymax` is a character vector ('upper') + + [ FAIL 2 | WARN 0 | SKIP 46 | PASS 466 ] + Error: Test failures + Execution halted + ``` + +# processmapR + +
+ +* Version: 0.5.5 +* GitHub: https://github.com/bupaverse/processmapr +* Source code: https://github.com/cran/processmapR +* Date/Publication: 2024-08-30 13:10:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "processmapR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(processmapR) + + Attaching package: 'processmapR' + + The following object is masked from 'package:stats': + + ... + 10. └─processmapR:::return_plotly(p, plotly) + 11. ├─plotly::ggplotly(p) + 12. └─plotly:::ggplotly.ggplot(p) + 13. └─plotly::gg2list(...) + ── Failure ('test_trace_explorer.R:240:3'): test trace_explorer on eventlog with param `plotly` ── + `chart` inherits from 'gg'/'ggplot' not 'plotly'. + + [ FAIL 6 | WARN 0 | SKIP 10 | PASS 107 ] + Error: Test failures + Execution halted + ``` + +# projpred + +
+ +* Version: 2.8.0 +* GitHub: https://github.com/stan-dev/projpred +* Source code: https://github.com/cran/projpred +* Date/Publication: 2023-12-15 00:00:02 UTC +* Number of recursive dependencies: 157 + +Run `revdepcheck::cloud_details(, "projpred")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘projpred-Ex.R’ failed + The error most likely occurred in: + + > ### Name: as.matrix.projection + > ### Title: Extract projected parameter draws and coerce to matrix + > ### Aliases: as.matrix.projection + > + > ### ** Examples + > + > ## Don't show: + ... + 2 X1 1.70 0.155 1.40 1.97 + 3 X3 0.924 0.266 0.560 1.45 + 4 X5 -1.21 0.111 -1.53 -0.602 + 5 sigma 2.01 0.183 1.83 2.35 + > if (requireNamespace("bayesplot", quietly = TRUE)) { + + print(bayesplot::mcmc_intervals(prj_mat)) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘projpred.Rmd’ + ... + + + > bayesplot_theme_set(ggplot2::theme_bw()) + + > mcmc_intervals(prj_mat) + ggplot2::coord_cartesian(xlim = c(-1.5, + + 1.6)) + + When sourcing ‘projpred.R’: + Error: argument is of length zero + Execution halted + + ‘latent.Rmd’ using ‘UTF-8’... OK + ‘projpred.Rmd’ using ‘UTF-8’... failed + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(projpred) + This is projpred version 2.8.0. NOTE: In projpred 2.7.0, the default search method was set to "forward" (for all kinds of models). + > + > test_check("projpred") + Warning in check_dep_version() : + ABI version mismatch: + ... + 41. │ └─methods (local) ``(...) + 42. │ └─methods::new(def, ...) + 43. │ ├─methods::initialize(value, ...) + 44. │ └─methods::initialize(value, ...) + 45. │ └─.Object$initialize(...) + 46. │ └─lme4 (local) initializePtr() + 47. └─base::.handleSimpleError(...) + 48. └─testthat (local) h(simpleError(msg, call)) + 49. └─rlang::abort(...) + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.5Mb + sub-directories of 1Mb or more: + doc 1.4Mb + libs 3.1Mb + ``` + +# psborrow + +
+ +* Version: 0.2.1 +* GitHub: NA +* Source code: https://github.com/cran/psborrow +* Date/Publication: 2023-03-03 10:30:07 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "psborrow")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(psborrow) + > + > test_check("psborrow") + [ FAIL 10 | WARN 0 | SKIP 1 | PASS 142 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + ... + `expected` is a character vector ('ref') + ── Failure ('test-plots.R:126:5'): Ensure output is producing a ggplot2 object with appropriate parameters ── + p1$labels$yintercept (`actual`) not equal to "ref" (`expected`). + + `actual` is NULL + `expected` is a character vector ('ref') + + [ FAIL 10 | WARN 0 | SKIP 1 | PASS 142 ] + Error: Test failures + Execution halted + ``` + +# pubh + +
+ +* Version: 1.3.7 +* GitHub: https://github.com/josie-athens/pubh +* Source code: https://github.com/cran/pubh +* Date/Publication: 2024-08-17 02:20:02 UTC +* Number of recursive dependencies: 187 + +Run `revdepcheck::cloud_details(, "pubh")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + ─────────────────────────────────────────────────────────────── + R2 = 0.123 + + Column names: Parameter, Coefficient, Pr(>|t|) + + > multiple(model_bwt, ~race)$df + + ... + > gf_labs(gf_facet_wrap(gf_errorbar(gf_point(estimate_means(model_norm, + + c("race", "smoke")), Mean ~ race), CI_low + CI_high ~ race, + + widt .... [TRUNCATED] + + When sourcing ‘regression.R’: + Error: argument is of length zero + Execution halted + + ‘introduction.Rmd’ using ‘UTF-8’... failed + ‘regression.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘introduction.Rmd’ using rmarkdown + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘pubh-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Kirkwood + > ### Title: Body weight and plasma volume. + > ### Aliases: Kirkwood + > ### Keywords: datasets + > + > ### ** Examples + > + > data(Kirkwood) + > + > Kirkwood |> + + gf_point(volume ~ weight) |> + + gf_lm(col = "indianred3", interval = "confidence", fill = "indianred3") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gf_lm ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# PUPMSI + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/PUPMSI +* Date/Publication: 2022-05-31 10:50:04 UTC +* Number of recursive dependencies: 32 + +Run `revdepcheck::cloud_details(, "PUPMSI")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘PUPMSI-Ex.R’ failed + The error most likely occurred in: + + > ### Name: BradleyMSI + > ### Title: Bradley Moisture Sorption Isotherm + > ### Aliases: BradleyMSI + > + > ### ** Examples + > + > WaterAct <- c(0.1145,0.2274,0.3265,0.4291,0.6342,0.7385,0.8274,0.9573) + ... + Adsorption 0.002148893 0.001891231 4.617743e-06 0.04298251 7.517135e-18 + Desorption 0.004371350 0.003905913 1.910870e-05 0.10015162 3.122502e-17 + Constants of Bradley Sorption Model + Isotherm k1 k2 + Adsorption 1.752876e-10 3.525154 + Desorption 3.920525e-12 8.480898 + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: BradleyMSI -> BradleyMSIPlot + Execution halted + ``` + +# qacBase + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/rkabacoff/qacBase +* Source code: https://github.com/cran/qacBase +* Date/Publication: 2022-02-09 22:20:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "qacBase")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘qacBase-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatter + > ### Title: Scatterplot + > ### Aliases: scatter + > + > ### ** Examples + > + > scatter(cars74, hp, mpg) + > scatter(cars74, wt, hp) + > p <- scatter(ggplot2::mpg, displ, hwy, + + margin="histogram", + + title="Engine Displacement vs. Highway Mileage") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: scatter ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# qPCRhelper + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/qPCRhelper +* Date/Publication: 2023-02-23 14:00:08 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "qPCRhelper")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘qPCRhelper-Ex.R’ failed + The error most likely occurred in: + + > ### Name: qPCRhelper + > ### Title: qPCRhelper + > ### Aliases: qPCRhelper + > + > ### ** Examples + > + > ## Create sample table with expected 'Sample', 'Group', and gene Ct columns + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘qPCRhelper.Rmd’ + ... + + ref.gene = "GAPDH", ref.group = "Control") + Warning in (function (mapping = NULL, data = NULL, geom = "boxplot", position = "dodge2", : + Ignoring unknown aesthetics: fill + + When sourcing ‘qPCRhelper.R’: + Error: ℹ In index: 1. + ℹ With name: log2RelExp. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘qPCRhelper.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘qPCRhelper.Rmd’ using rmarkdown + + Quitting from lines 18-29 [setup] (qPCRhelper.Rmd) + Error: processing vignette 'qPCRhelper.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: log2RelExp. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘qPCRhelper.Rmd’ + + SUMMARY: processing the following file failed: + ‘qPCRhelper.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# r2dii.plot + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/RMI-PACTA/r2dii.plot +* Source code: https://github.com/cran/r2dii.plot +* Date/Publication: 2024-02-29 16:40:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "r2dii.plot")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(r2dii.plot) + > + > test_check("r2dii.plot") + Scale for colour is already present. + Adding another scale for colour, which will replace the existing scale. + ... + `expected` is a character vector ('year') + ── Failure ('test-plot_trajectory.R:41:3'): outputs default axis labels ──────── + p$labels$y (`actual`) not equal to "value" (`expected`). + + `actual` is NULL + `expected` is a character vector ('value') + + [ FAIL 2 | WARN 2 | SKIP 40 | PASS 122 ] + Error: Test failures + Execution halted + ``` + +# r2spss + +
+ +* Version: 0.3.2 +* GitHub: https://github.com/aalfons/r2spss +* Source code: https://github.com/cran/r2spss +* Date/Publication: 2022-05-25 11:00:08 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "r2spss")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘r2spss-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ANOVA + > ### Title: One-way and Two-way ANOVA + > ### Aliases: ANOVA to_SPSS.ANOVA_SPSS print.ANOVA_SPSS plot.ANOVA_SPSS + > ### Keywords: htest + > + > ### ** Examples + > + ... + \arrayrulecolor{darkgraySPSS}\hline + Total & 495.474 & 416 & & & \\ + \arrayrulecolor{black}\hline + \noalign{\smallskip} + \end{NiceTabular} + + > plot(oneway) # create profile plot + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘r2spss-intro.Rnw’ + ... + Valid N (listwise) & 417 & & & & \\ + \hline + \noalign{\smallskip} + \end{tabular} + + > histogram(Eredivisie, "logMarketValue") + + When sourcing 'r2spss-intro.R': + Error: argument is of length zero + Execution halted + + ‘r2spss-intro.Rnw’ using ‘UTF-8’... failed + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘r2spss-intro.Rnw’ using knitr + + Quitting from lines 327-328 [unnamed-chunk-8] (r2spss-intro.Rnw) + Error: processing vignette 'r2spss-intro.Rnw' failed with diagnostics: + argument is of length zero + --- failed re-building ‘r2spss-intro.Rnw’ + + SUMMARY: processing the following file failed: + ‘r2spss-intro.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# radiant.basics + +
+ +* Version: 1.6.6 +* GitHub: https://github.com/radiant-rstats/radiant.basics +* Source code: https://github.com/cran/radiant.basics +* Date/Publication: 2024-05-15 04:30:07 UTC +* Number of recursive dependencies: 152 + +Run `revdepcheck::cloud_details(, "radiant.basics")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘radiant.basics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.clt + > ### Title: Plot method for the Central Limit Theorem simulation + > ### Aliases: plot.clt + > + > ### ** Examples + > + > clt("Uniform", 100, 100, unif_min = 10, unif_max = 20) %>% plot() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# radiant.data + +
+ +* Version: 1.6.6 +* GitHub: https://github.com/radiant-rstats/radiant.data +* Source code: https://github.com/cran/radiant.data +* Date/Publication: 2024-05-14 23:30:02 UTC +* Number of recursive dependencies: 155 + +Run `revdepcheck::cloud_details(, "radiant.data")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘radiant.data-Ex.R’ failed + The error most likely occurred in: + + > ### Name: visualize + > ### Title: Visualize data using ggplot2 + > ### Aliases: visualize + > + > ### ** Examples + > + > visualize(diamonds, "price:cut", type = "dist", fillcol = "red") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: visualize ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# radiant.model + +
+ +* Version: 1.6.6 +* GitHub: https://github.com/radiant-rstats/radiant.model +* Source code: https://github.com/cran/radiant.model +* Date/Publication: 2024-05-15 09:10:08 UTC +* Number of recursive dependencies: 176 + +Run `revdepcheck::cloud_details(, "radiant.model")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘radiant.model-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.simulater + > ### Title: Plot method for the simulater function + > ### Aliases: plot.simulater + > + > ### ** Examples + > + > simdat <- simulater( + ... + + const = "cost 3", + + norm = "demand 2000 1000", + + discrete = "price 5 8 .3 .7", + + form = "profit = demand * (price - cost)", + + seed = 1234 + + ) + > plot(simdat, bins = 25) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# Radviz + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/yannabraham/Radviz +* Source code: https://github.com/cran/Radviz +* Date/Publication: 2022-03-25 18:10:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "Radviz")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Radviz-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Radviz + > ### Title: Radviz Projection of Multidimensional Data + > ### Aliases: Radviz + > + > ### ** Examples + > + > data(iris) + > das <- c('Sepal.Length','Sepal.Width','Petal.Length','Petal.Width') + > S <- make.S(das) + > rv <- do.radviz(iris,S) + > plot(rv,anchors.only=FALSE) + Error in plot.radviz(rv, anchors.only = FALSE) : + 'language' object cannot be coerced to type 'double' + Calls: plot -> plot.radviz + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘multivariate_analysis.Rmd’ + ... + + > classic.S <- make.S(get.optim(classic.optim)) + + > btcells.rv <- do.radviz(btcells.df, classic.S) + + > plot(btcells.rv) + geom_point(aes(color = Treatment)) + + ... + [1] 15792 18 + + > ct.rv + + When sourcing ‘single_cell_projections.R’: + Error: 'language' object cannot be coerced to type 'double' + Execution halted + + ‘multivariate_analysis.Rmd’ using ‘UTF-8’... failed + ‘single_cell_projections.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘multivariate_analysis.Rmd’ using rmarkdown + ``` + +# randomForestExplainer + +
+ +* Version: 0.10.1 +* GitHub: https://github.com/ModelOriented/randomForestExplainer +* Source code: https://github.com/cran/randomForestExplainer +* Date/Publication: 2020-07-11 20:30:02 UTC +* Number of recursive dependencies: 105 + +Run `revdepcheck::cloud_details(, "randomForestExplainer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘randomForestExplainer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_min_depth_interactions + > ### Title: Plot the top mean conditional minimal depth + > ### Aliases: plot_min_depth_interactions + > + > ### ** Examples + > + > forest <- randomForest::randomForest(Species ~ ., data = iris, ntree = 100) + ... + The first warning was: + ℹ In argument: `Petal.Width = min(Petal.Width, na.rm = TRUE)`. + ℹ In group 1: `tree = 1` and `split var = "Petal.Length"`. + Caused by warning in `min()`: + ! no non-missing arguments to min; returning Inf + ℹ Run `dplyr::last_dplyr_warnings()` to see the 203 remaining warnings. + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(randomForestExplainer) + > + > test_check("randomForestExplainer") + [ FAIL 6 | WARN 70 | SKIP 0 | PASS 55 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 24. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 25. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 26. └─grid:::drawGrob(x) + 27. ├─grid::drawDetails(x, recording = FALSE) + 28. └─grid:::drawDetails.segments(x, recording = FALSE) + 29. └─grid:::grid.Call.graphics(...) + + [ FAIL 6 | WARN 70 | SKIP 0 | PASS 55 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘randomForestExplainer.Rmd’ + ... + 3 3.308 + 23 2.600 + 33 1.288 + 8 3.512 + + > plot_min_depth_interactions(interactions_frame) + + When sourcing ‘randomForestExplainer.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘randomForestExplainer.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘randomForestExplainer.Rmd’ using rmarkdown + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# rassta + +
+ +* Version: 1.0.6 +* GitHub: https://github.com/bafuentes/rassta +* Source code: https://github.com/cran/rassta +* Date/Publication: 2024-08-19 06:20:13 UTC +* Number of recursive dependencies: 121 + +Run `revdepcheck::cloud_details(, "rassta")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rassta-Ex.R’ failed + The error most likely occurred in: + + > ### Name: select_functions + > ### Title: Select Constrained Univariate Distribution Functions + > ### Aliases: select_functions + > + > ### ** Examples + > + > require(terra) + ... + > tvars <- terra::rast(tf) + > # Single-layer SpatRaster of topographic classification units + > ## 5 classification units + > tcf <- list.files(path = p, pattern = "topography.tif", full.names = TRUE) + > tcu <- terra::rast(tcf) + > # Automatic selection of distribution functions + > tdif <- select_functions(cu.rast = tcu, var.rast = tvars, fun = mean) + Error in pm[[2]] : subscript out of bounds + Calls: select_functions -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("rassta") + + } + + Attaching package: 'rassta' + + ... + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests + test_select_functions.R....... 0 tests Error in pm[[2]] : subscript out of bounds + Calls: ... select_functions -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘signature.Rmd’ + ... + > clim.var <- rast(vardir) + + > clim.cu <- rast(paste(d, "/climate.tif", sep = "")) + + > clim.difun <- select_functions(cu.rast = clim.cu, + + var.rast = clim.var, mode = "auto") + + ... + When sourcing ‘signature.R’: + Error: subscript out of bounds + Execution halted + + ‘classunits.Rmd’ using ‘UTF-8’... OK + ‘modeling.Rmd’ using ‘UTF-8’... OK + ‘sampling.Rmd’ using ‘UTF-8’... OK + ‘signature.Rmd’ using ‘UTF-8’... failed + ‘similarity.Rmd’ using ‘UTF-8’... OK + ‘stratunits.Rmd’ using ‘UTF-8’... OK + ``` + +# rater + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/jeffreypullin/rater +* Source code: https://github.com/cran/rater +* Date/Publication: 2023-09-11 17:40:02 UTC +* Number of recursive dependencies: 92 + +Run `revdepcheck::cloud_details(, "rater")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(rater) + * The rater package uses `Stan` to fit bayesian models. + * If you are working on a local, multicore CPU with excess RAM please call: + * options(mc.cores = parallel::detectCores()) + * This will allow Stan to run inference on multiple cores in parallel. + > + ... + ── Failure ('test_plotting.R:65:3'): plot_theta_points output has correct type ── + get_geoms(ds_plot) (`actual`) not equal to c("GeomPoint", "GeomErrorbar") (`expected`). + + `names(actual)` is a character vector ('geom_point', 'geom_errorbar') + `names(expected)` is absent + + [ FAIL 4 | WARN 0 | SKIP 6 | PASS 375 ] + Error: Test failures + In addition: There were 14 warnings (use warnings() to see them) + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 128.0Mb + sub-directories of 1Mb or more: + libs 127.3Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# RBesT + +
+ +* Version: 1.7-3 +* GitHub: https://github.com/Novartis/RBesT +* Source code: https://github.com/cran/RBesT +* Date/Publication: 2024-01-08 15:20:02 UTC +* Number of recursive dependencies: 143 + +Run `revdepcheck::cloud_details(, "RBesT")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RBesT-Ex.R’ failed + The error most likely occurred in: + + > ### Name: forest_plot + > ### Title: Forest Plot + > ### Aliases: forest_plot + > + > ### ** Examples + > + > # we consider the example AS MAP analysis + ... + Please consider increasing the MCMC simulation size. + + AS> ## Recover user set sampling defaults + AS> options(.user_mc_options) + > + > # default forest plot for a gMAP analysis + > forest_plot(map_AS) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: forest_plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + + MAP Prior MCMC sample + mean sd 2.5% 50% 97.5% + 0.2580 0.0842 0.1120 0.2510 0.4590 + + > pl <- plot(map_mcmc) + + When sourcing ‘introduction.R’: + Error: argument is of length zero + Execution halted + + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘introduction.Rmd’ using rmarkdown + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + Warning in hook_png(..., cmd = "pngquant", post_process = function(x) { : + cannot find pngquant; please install and put it in PATH + + Quitting from lines 104-126 [unnamed-chunk-4] (introduction.Rmd) + Error: processing vignette 'introduction.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘introduction.Rmd’ + + SUMMARY: processing the following file failed: + ‘introduction.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 97.6Mb + sub-directories of 1Mb or more: + libs 95.7Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# rddensity + +
+ +* Version: 2.5 +* GitHub: NA +* Source code: https://github.com/cran/rddensity +* Date/Publication: 2024-01-22 21:10:07 UTC +* Number of recursive dependencies: 29 + +Run `revdepcheck::cloud_details(, "rddensity")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rddensity-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rddensity + > ### Title: Manipulation Testing Using Local Polynomial Density Estimation + > ### Aliases: rddensity + > + > ### ** Examples + > + > ### Continuous Density + ... + sum densities 0.6532 3.9572 0.0042 + + > + > ### Plotting using rdplotdensity() + > # 1. From -2 to 2 with 25 evaluation points at each side + > plot1 <- rdplotdensity(rdd, x, plotRange = c(-2, 2), plotN = 25) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: rdplotdensity ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# RecordTest + +
+ +* Version: 2.2.0 +* GitHub: https://github.com/JorgeCastilloMateo/RecordTest +* Source code: https://github.com/cran/RecordTest +* Date/Publication: 2023-08-07 20:20:08 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "RecordTest")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RecordTest-Ex.R’ failed + The error most likely occurred in: + + > ### Name: N.plot + > ### Title: Number of Records Plot + > ### Aliases: N.plot + > + > ### ** Examples + > + > # Plot at Zaragoza, with linear weights and error bar as RIs aesthetic + > N.plot(ZaragozaSeries, weights = function(t) t-1, conf.aes = "errorbar") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘RecordTest.Rmd’ + ... + + R_lower = Olympic_records_200m$value, Trows = 27) + + > records(or200m, type = "points", alpha = c(1, 0, 1, + + 0)) + ggplot2::ylab("seconds") + + > N.plot(or200m, record = c(0, 1, 0, 0)) + + When sourcing ‘RecordTest.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘RecordTest.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘RecordTest.Rmd’ using rmarkdown + ``` + +# reda + +
+ +* Version: 0.5.4 +* GitHub: https://github.com/wenjie2wang/reda +* Source code: https://github.com/cran/reda +* Date/Publication: 2022-07-08 21:50:02 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "reda")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reda-Ex.R’ failed + The error most likely occurred in: + + > ### Name: mcf + > ### Title: Mean Cumulative Function (MCF) + > ### Aliases: mcf mcf,formula-method mcf,rateReg-method + > + > ### ** Examples + > + > library(reda) + ... + > + > ## Example 2. the simulated data + > simuMcf <- mcf(Recur(time, ID, event) ~ group + gender, + + data = simuDat, ID %in% 1 : 50) + > plot(simuMcf, conf.int = TRUE, lty = 1 : 4, + + legendName = "Treatment & Gender") + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘reda-intro.Rmd’ + ... + + data = simuDat, subset = ID %in% seq_len(50)) + + > plot(valveMcf0, conf.int = TRUE, mark.time = TRUE, + + addOrigin = TRUE, col = 2) + ggplot2::xlab("Days") + ggplot2::theme_bw() + + > plot(simuMcf, conf.int = TRUE, lty = 1:4, legendName = "Treatment & Gender") + + When sourcing ‘reda-intro.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘reda-Recur.Rmd’ using ‘UTF-8’... OK + ‘reda-intro.Rmd’ using ‘UTF-8’... failed + ‘reda-simulate.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘reda-Recur.Rmd’ using rmarkdown + --- finished re-building ‘reda-Recur.Rmd’ + + --- re-building ‘reda-intro.Rmd’ using rmarkdown + + Quitting from lines 123-129 [plot-sampleMcf] (reda-intro.Rmd) + Error: processing vignette 'reda-intro.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + ... + --- failed re-building ‘reda-intro.Rmd’ + + --- re-building ‘reda-simulate.Rmd’ using rmarkdown + --- finished re-building ‘reda-simulate.Rmd’ + + SUMMARY: processing the following file failed: + ‘reda-intro.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.1Mb + sub-directories of 1Mb or more: + doc 3.3Mb + libs 4.1Mb + ``` + +# redist + +
+ +* Version: 4.2.0 +* GitHub: https://github.com/alarm-redist/redist +* Source code: https://github.com/cran/redist +* Date/Publication: 2024-01-13 13:20:02 UTC +* Number of recursive dependencies: 132 + +Run `revdepcheck::cloud_details(, "redist")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘redist.Rmd’ + ... + # ℹ 991 more rows + + > library(patchwork) + + > hist(plan_sum, max_dev) + hist(iowa_plans, comp) + + + plot_layout(guides = "collect") + + When sourcing ‘redist.R’: + Error: object is not a unit + Execution halted + + ‘common_args.Rmd’ using ‘UTF-8’... OK + ‘flip.Rmd’ using ‘UTF-8’... OK + ‘map-preproc.Rmd’ using ‘UTF-8’... OK + ‘redist.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘common_args.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 29.5Mb + sub-directories of 1Mb or more: + data 1.2Mb + libs 25.5Mb + ``` + +# registr + +
+ +* Version: 2.1.0 +* GitHub: NA +* Source code: https://github.com/cran/registr +* Date/Publication: 2022-10-02 21:40:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "registr")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘incomplete_curves.Rmd’ + ... + + ggplot(reg4_joint$Y, aes(x = t_hat, y = value, group = id)) + + + geom_line(alpha = 0.3) + xlab("t [registered]") + .... [TRUNCATED] + + > if (have_ggplot2) { + + plot(reg4_joint$fpca_obj) + + } + + ... + > if (have_ggplot2 && requireNamespace("cowplot", quietly = TRUE)) { + + registr:::plot.fpca(bfpca_object) + + } + + When sourcing ‘registr.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘incomplete_curves.Rmd’ using ‘UTF-8’... failed + ‘registr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘incomplete_curves.Rmd’ using rmarkdown + ``` + +## In both + +* checking examples ... ERROR + ``` + Running examples in ‘registr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fpca_gauss + > ### Title: Functional principal components analysis via variational EM + > ### Aliases: fpca_gauss + > + > ### ** Examples + > + > data(growth_incomplete) + ... + > + > # estimate 2 FPCs + > fpca_obj = fpca_gauss(Y = growth_incomplete, npc = 2) + Warning in (function (npc, npc_varExplained = NULL, Kt, maxiter, print.iter, : + fpca_gauss convergence not reached. Try increasing maxiter. + > plot(fpca_obj) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(registr) + Warning message: + In check_dep_version() : ABI version mismatch: + lme4 was built with Matrix ABI version 1 + Current Matrix ABI version is 0 + Please re-install lme4 from source or restore original 'Matrix' package + ... + 12. └─methods (local) ``(...) + 13. └─methods::new(def, ...) + 14. ├─methods::initialize(value, ...) + 15. └─methods::initialize(value, ...) + 16. └─.Object$initialize(...) + 17. └─lme4 (local) initializePtr() + + [ FAIL 13 | WARN 6 | SKIP 6 | PASS 166 ] + Error: Test failures + Execution halted + ``` + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + doc 1.8Mb + libs 3.1Mb + ``` + +# reliabilitydiag + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/aijordan/reliabilitydiag +* Source code: https://github.com/cran/reliabilitydiag +* Date/Publication: 2022-06-29 00:20:06 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "reliabilitydiag")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reliabilitydiag-Ex.R’ failed + The error most likely occurred in: + + > ### Name: c.reliabilitydiag + > ### Title: Combining reliability diagram objects + > ### Aliases: c.reliabilitydiag + > + > ### ** Examples + > + > data("precip_Niamey_2016", package = "reliabilitydiag") + > + > X <- precip_Niamey_2016[c("EMOS", "ENS")] + > Y <- precip_Niamey_2016$obs + > r0 <- reliabilitydiag0(Y) + > r1 <- c(r0, X, EPC = precip_Niamey_2016$EPC, region.level = NA) + > r1 + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# relliptical + +
+ +* Version: 1.3.0 +* GitHub: NA +* Source code: https://github.com/cran/relliptical +* Date/Publication: 2024-02-07 12:50:02 UTC +* Number of recursive dependencies: 73 + +Run `revdepcheck::cloud_details(, "relliptical")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘relliptical-Ex.R’ failed + The error most likely occurred in: + + > ### Name: rtelliptical + > ### Title: Sampling Random Numbers from Truncated Multivariate Elliptical + > ### Distributions + > ### Aliases: rtelliptical + > + > ### ** Examples + > + ... + > Sigma = matrix(c(1,-0.5,-0.5,1), 2, 2) + > lower = c(-2, -2) + > upper = c(3, 2) + > sample4 = rtelliptical(2000, mu, Sigma, lower, upper, gFun=function(t){t^(-1/2)*exp(-2*t^(1/4))}) + > f1 = ggplot(data.frame(sample4), aes(x=X1,y=X2)) + geom_point(size=0.50) + + + labs(x=expression(X[1]), y=expression(X[2]), subtitle="Kotz(2,1/4,1/2)") + theme_bw() + > ggMarginal(f1, type="histogram", fill="grey") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggMarginal ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.6Mb + sub-directories of 1Mb or more: + libs 6.5Mb + ``` + +# reportRmd + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/reportRmd +* Date/Publication: 2023-11-16 17:00:03 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "reportRmd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reportRmd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotuv + > ### Title: Plot multiple bivariate relationships in a single plot + > ### Aliases: plotuv + > ### Keywords: plot + > + > ### ** Examples + > + ... + > plotuv(data=pembrolizumab, response='cbr', + + covs=c('age','sex','l_size','baseline_ctdna'),showN=TRUE) + Warning: `stat(count)` was deprecated in ggplot2 3.4.0. + ℹ Please use `after_stat(count)` instead. + ℹ The deprecated feature was likely used in the reportRmd package. + Please report the issue to the authors. + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘reportRmd.Rmd’ + ... + > ctDNA <- clear_labels(ctDNA) + + > plotuv(data = pembrolizumab, response = "orr", covs = c("age", + + "cohort", "pdl1", "change_ctdna_group")) + Boxplots not shown for categories with fewer than 20 observations. + Boxplots not shown for categories with fewer than 20 observations. + + When sourcing ‘reportRmd.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘reportRmd.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘reportRmd.Rmd’ using rmarkdown + + Quitting from lines 380-383 [unnamed-chunk-30] (reportRmd.Rmd) + Error: processing vignette 'reportRmd.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘reportRmd.Rmd’ + + SUMMARY: processing the following file failed: + ‘reportRmd.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# reservr + +
+ +* Version: 0.0.3 +* GitHub: https://github.com/AshesITR/reservr +* Source code: https://github.com/cran/reservr +* Date/Publication: 2024-06-24 16:40:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "reservr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘reservr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: blended_transition + > ### Title: Transition functions for blended distributions + > ### Aliases: blended_transition blended_transition_inv + > + > ### ** Examples + > + > library(ggplot2) + ... + + theme_bw() %+% + + theme( + + legend.position = "bottom", legend.box = "horizontal" + + ) %+% + + guides(color = guide_legend(direction = "horizontal", title = ""), linetype = guide_none()) %+% + + scale_linetype_manual(values = c("TRUE" = 1, "FALSE" = 3)) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘distributions.Rmd’ using rmarkdown + + Quitting from lines 170-227 [unnamed-chunk-10] (distributions.Rmd) + Error: processing vignette 'distributions.Rmd' failed with diagnostics: + object is not a unit + --- failed re-building ‘distributions.Rmd’ + + --- re-building ‘jss_paper.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘distributions.Rmd’ + ... + + > attr(trunc_fit$logLik, "nobs") + [1] 62 + + > plot_distributions(true = norm, fit1 = norm, fit2 = norm2, + + fit3 = dist_normal(3), .x = seq(-2, 7, 0.01), with_params = list(true = list(mean .... [TRUNCATED] + + ... + + > dist$sample(1) + + When sourcing ‘jss_paper.R’: + Error: invalid arguments + Execution halted + + ‘distributions.Rmd’ using ‘UTF-8’... failed + ‘jss_paper.Rmd’ using ‘UTF-8’... failed + ‘tensorflow.Rmd’ using ‘UTF-8’... OK + ``` + +* checking installed package size ... NOTE + ``` + installed size is 15.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 1.2Mb + libs 12.8Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# RestoreNet + +
+ +* Version: 1.0.1 +* GitHub: NA +* Source code: https://github.com/cran/RestoreNet +* Date/Publication: 2024-02-15 11:00:02 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "RestoreNet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘RestoreNet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: get.scatterpie + > ### Title: Clonal pie-chart + > ### Aliases: get.scatterpie + > + > ### ** Examples + > + > rcts <- c("A->1", "B->1", "C->1", "D->1", + ... + computing A^-1... + computing rho... + computing Chi2... + computing KLdiv... + computing BhattDist... + > + > get.scatterpie(re.res, txt = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: get.scatterpie ... ggplot_add.layer_scatterpie -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... WARNING + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘RestoreNet.ltx’ using tex + Error: processing vignette 'RestoreNet.ltx' failed with diagnostics: + Running 'texi2dvi' on 'RestoreNet.ltx' failed. + LaTeX errors: + ! LaTeX Error: File `realboxes.sty' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: sty) + ... + l.12 \usepackage + {amssymb}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘RestoreNet.ltx’ + + SUMMARY: processing the following file failed: + ‘RestoreNet.ltx’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# rfPermute + +
+ +* Version: 2.5.2 +* GitHub: https://github.com/EricArcher/rfPermute +* Source code: https://github.com/cran/rfPermute +* Date/Publication: 2023-08-23 17:40:02 UTC +* Number of recursive dependencies: 76 + +Run `revdepcheck::cloud_details(, "rfPermute")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘rfPermute-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotTrace + > ### Title: Plot Trace + > ### Aliases: plotTrace + > + > ### ** Examples + > + > library(randomForest) + ... + randomForest 4.7-1.1 + Type rfNews() to see new features/changes/bug fixes. + > data(mtcars) + > + > rf <- randomForest(factor(am) ~ ., mtcars) + > plotTrace(rf) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plotTrace ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# RKorAPClient + +
+ +* Version: 0.8.1 +* GitHub: https://github.com/KorAP/RKorAPClient +* Source code: https://github.com/cran/RKorAPClient +* Date/Publication: 2024-05-02 11:42:54 UTC +* Number of recursive dependencies: 124 + +Run `revdepcheck::cloud_details(, "RKorAPClient")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library("testthat") + > library("RKorAPClient") + > + > test_check("RKorAPClient") + + apiUrl: https://korap.ids-mannheim.de/api/v1.0/ + [ FAIL 1 | WARN 0 | SKIP 30 | PASS 25 ] + ... + 'test-demos.R:129:3', 'test-textMetadata.R:2:3', 'test-textMetadata.R:9:3' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-misc.R:224:5'): geom_freq_by_year_ci works correctly ───────── + gpt[["labels"]][["url"]] not equal to "webUIRequestUrl". + target is NULL, current is character + + [ FAIL 1 | WARN 0 | SKIP 30 | PASS 25 ] + Error: Test failures + Execution halted + ``` + +# roahd + +
+ +* Version: 1.4.3 +* GitHub: https://github.com/astamm/roahd +* Source code: https://github.com/cran/roahd +* Date/Publication: 2021-11-04 00:10:02 UTC +* Number of recursive dependencies: 88 + +Run `revdepcheck::cloud_details(, "roahd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘roahd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.depthgram + > ### Title: Specialized method to plot 'depthgram' objects + > ### Aliases: plot.depthgram + > + > ### ** Examples + > + > N <- 50 + ... + + N, + + centerline = sin(2 * pi * grid), + + Cov = Cov + + ) + > names <- paste0("id_", 1:nrow(Data[[1]])) + > DG <- depthgram(Data, marginal_outliers = TRUE, ids = names) + > plot(DG) + Error in pm[[2]] : subscript out of bounds + Calls: plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.4Mb + sub-directories of 1Mb or more: + data 5.0Mb + doc 1.7Mb + ``` + +# robCompositions + +
+ +* Version: 2.4.1 +* GitHub: NA +* Source code: https://github.com/cran/robCompositions +* Date/Publication: 2023-08-25 15:30:06 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::cloud_details(, "robCompositions")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘robCompositions-Ex.R’ failed + The error most likely occurred in: + + > ### Name: biplot.pcaCoDa + > ### Title: Biplot method + > ### Aliases: biplot.pcaCoDa + > ### Keywords: aplot + > + > ### ** Examples + > + ... + > ## with labels for the scores: + > data(arcticLake) + > rownames(arcticLake) <- paste(sample(letters[1:26], nrow(arcticLake), replace=TRUE), + + 1:nrow(arcticLake), sep="") + > pc <- pcaCoDa(arcticLake, method="classical") + > plot(pc, xlabs=rownames(arcticLake), which = 2) + > plot(pc, xlabs=rownames(arcticLake), which = 3) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 24.6Mb + sub-directories of 1Mb or more: + data 2.0Mb + libs 21.3Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1 marked UTF-8 string + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘imputation.Rnw’ using knitr + Error: processing vignette 'imputation.Rnw' failed with diagnostics: + Running 'texi2dvi' on 'imputation.tex' failed. + LaTeX errors: + ! LaTeX Error: File `scrartcl.cls' not found. + + Type X to quit or to proceed, + or enter new name. (Default extension: cls) + + ... + l.3 \usepackage + [pdftex]{hyperref}^^M + ! ==> Fatal error occurred, no output PDF file produced! + --- failed re-building ‘robCompositions-overview.Rnw’ + + SUMMARY: processing the following files failed: + ‘imputation.Rnw’ ‘robCompositions-overview.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# romic + +
+ +* Version: 1.1.3 +* GitHub: NA +* Source code: https://github.com/cran/romic +* Date/Publication: 2023-09-21 05:40:02 UTC +* Number of recursive dependencies: 113 + +Run `revdepcheck::cloud_details(, "romic")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘romic-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_bivariate + > ### Title: Bivariate Plot + > ### Aliases: plot_bivariate + > + > ### ** Examples + > + > library(dplyr) + ... + > brauer_augmented <- brauer_2008_tidy %>% + + add_pcs(npcs = 5) %>% + + tomic_to("triple_omic") + 40 features dropped due to missing values + > + > tomic_table <- brauer_augmented$samples + > plot_bivariate(tomic_table, "PC1", "PC2", "nutrient", "nutrient", 0.5, 10) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_bivariate ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 1. └─romic::plot_bivariate(...) at test-module_ggbiv.R:8:3 + 2. └─ggplot2:::`+.gg`(ggplot(tomic_table, running_aes), plot_call) + 3. └─ggplot2:::add_ggplot(e1, e2, e2name) + 4. ├─ggplot2::ggplot_add(object, p, objectname) + 5. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 6. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 0 | SKIP 7 | PASS 64 ] + Error: Test failures + Execution halted + ``` + +# roptions + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/roptions +* Date/Publication: 2020-05-11 11:10:06 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "roptions")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘roptions-Ex.R’ failed + The error most likely occurred in: + + > ### Name: box.spread + > ### Title: Box Spread Strategy Function + > ### Aliases: box.spread + > + > ### ** Examples + > + > box.spread(100, 105, 95, 110, 3.2, 2.6, 1.1, 2.4) + ... + 35 5.7 + 36 5.7 + 37 5.7 + 38 5.7 + 39 5.7 + 40 5.7 + 41 5.7 + Error in pm[[2]] : subscript out of bounds + Calls: box.spread -> print -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# rSAFE + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/ModelOriented/rSAFE +* Source code: https://github.com/cran/rSAFE +* Date/Publication: 2022-08-13 13:20:02 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "rSAFE")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(rSAFE) + Welcome to rSAFE (version: 0.1.4). + > + > test_check("rSAFE") + Single variables processing... + ... + 8. └─ggplot2:::add_ggplot(e1, e2, e2name) + 9. ├─ggplot2::ggplot_add(object, p, objectname) + 10. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 11. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 10 | SKIP 0 | PASS 56 ] + Deleting unused snapshots: + • extraction/plot-continuous-variable.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘example_apartments.Rmd’ + ... + + > plot(safe_extractor, variable = "district") + Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the rSAFE package. + Please report the issue at . + + ... + of ggplot2 3.3.4. + ℹ The deprecated feature was likely used in the rSAFE package. + Please report the issue at . + + When sourcing ‘example_hr.R’: + Error: argument is of length zero + Execution halted + + ‘example_apartments.Rmd’ using ‘UTF-8’... failed + ‘example_hr.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘example_apartments.Rmd’ using rmarkdown + ``` + +# santaR + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/adwolfer/santaR +* Source code: https://github.com/cran/santaR +* Date/Publication: 2024-03-07 00:30:02 UTC +* Number of recursive dependencies: 93 + +Run `revdepcheck::cloud_details(, "santaR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(santaR) + + This is santaR version 1.2.4 + + > + > test_check("santaR") + ... + 1/1 mismatches + [1] 11 - 10 == 1 + ── Failure ('test_dfSearch-plot_nbTP_histogram.R:69:3'): change dfCuttOff ────── + length(result_nbTPHisto) not equal to length(ggplot2::ggplot()). + 1/1 mismatches + [1] 11 - 10 == 1 + + [ FAIL 8 | WARN 4 | SKIP 0 | PASS 681 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘getting-started.Rmd’ + ... + + > knitr::include_graphics("../man/figures/santaR-approach.jpg") + + When sourcing ‘getting-started.R’: + Error: Cannot find the file(s): "../man/figures/santaR-approach.jpg" + Execution halted + when running code in ‘selecting-optimal-df.Rmd’ + ... + Execution halted + + ‘advanced-command-line-functions.Rmd’ using ‘UTF-8’... OK + ‘automated-command-line.Rmd’ using ‘UTF-8’... OK + ‘getting-started.Rmd’ using ‘UTF-8’... failed + ‘plotting-options.Rmd’ using ‘UTF-8’... OK + ‘prepare-input-data.Rmd’ using ‘UTF-8’... OK + ‘selecting-optimal-df.Rmd’ using ‘UTF-8’... failed + ‘theoretical-background.Rmd’ using ‘UTF-8’... OK + ‘santaR-GUI.pdf.asis’ using ‘UTF-8’... OK + ``` + +# saros + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/NIFU-NO/saros +* Source code: https://github.com/cran/saros +* Date/Publication: 2024-09-03 07:40:02 UTC +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "saros")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘saros-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fig_height_h_barchart2 + > ### Title: Estimate figure height for a horizontal bar chart + > ### Aliases: fig_height_h_barchart2 + > + > ### ** Examples + > + > fig_height_h_barchart2(makeme(data=ex_survey, dep=b_1:b_3, indep=x1_sex)) + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic argument: + • cumulative = TRUE + ℹ Did you misspell an argument name? + Error in if (new_name %in% existing) { : argument is of length zero + Calls: fig_height_h_barchart2 ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(saros) + > + > testthat::test_check("saros") + Starting 2 test processes + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 194 ] + ... + 9. └─saros:::make_content.cat_plot_html(...) + 10. └─ggplot2:::`+.gg`(...) + 11. └─ggplot2:::add_ggplot(e1, e2, e2name) + 12. ├─ggplot2::ggplot_add(object, p, objectname) + 13. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 14. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 194 ] + Error: Test failures + Execution halted + ``` + +# scatterpie + +
+ +* Version: 0.2.4 +* GitHub: NA +* Source code: https://github.com/cran/scatterpie +* Date/Publication: 2024-08-28 17:20:02 UTC +* Number of recursive dependencies: 67 + +Run `revdepcheck::cloud_details(, "scatterpie")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘scatterpie-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_scatterpie + > ### Title: geom_scatterpie + > ### Aliases: geom_scatterpie geom_scatterpie2 + > + > ### ** Examples + > + > library(ggplot2) + ... + > d$C <- abs(rnorm(5, sd=3)) + > + > ggplot() + + + geom_scatterpie( + + aes(x=x, y=y), data=d, cols=c("A", "B", "C") + + ) + + + coord_fixed() + Error in if (new_name %in% existing) { : argument is of length zero + Calls: +.gg ... ggplot_add.layer_scatterpie -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘scatterpie.Rmd’ + ... + 5 12.928774 -11.288549 4 0.34754260 3.144288 3.789556 2.295894 + 8 -126.506123 29.230687 5 0.95161857 3.029335 1.048951 2.471943 + 9 -68.685285 6.192712 6 0.04502772 3.203072 2.596539 4.439393 + + > ggplot() + geom_scatterpie(aes(x = long, y = lat, + + group = region), data = d, cols = LETTERS[1:4]) + coord_equal() + + When sourcing ‘scatterpie.R’: + Error: argument is of length zero + Execution halted + + ‘scatterpie.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘scatterpie.Rmd’ using rmarkdown + + Quitting from lines 52-54 [unnamed-chunk-3] (scatterpie.Rmd) + Error: processing vignette 'scatterpie.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘scatterpie.Rmd’ + + SUMMARY: processing the following file failed: + ‘scatterpie.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# scdtb + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/mightymetrika/scdtb +* Source code: https://github.com/cran/scdtb +* Date/Publication: 2024-04-30 08:50:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "scdtb")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + ── Failure ('test-mixed_model_analysis.R:119:3'): mixed_model_analysis uses the .participant variable to label data points + when .participant is not NULL ── + res$plot$labels$shape (`actual`) not equal to "factor(part)" (`expected`). + + `actual` is NULL + `expected` is a character vector ('factor(part)') + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ] + Error: Test failures + Execution halted + ``` + +# scoringutils + +
+ +* Version: 1.2.2 +* GitHub: https://github.com/epiforecasts/scoringutils +* Source code: https://github.com/cran/scoringutils +* Date/Publication: 2023-11-29 15:50:10 UTC +* Number of recursive dependencies: 81 + +Run `revdepcheck::cloud_details(, "scoringutils")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘scoringutils-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_predictions + > ### Title: Plot Predictions vs True Values + > ### Aliases: plot_predictions + > + > ### ** Examples + > + > library(ggplot2) + ... + + by = c("target_type", "location"), + + range = c(0, 50, 90, 95) + + ) + + + facet_wrap(~ location + target_type, scales = "free_y") + + + aes(fill = model, color = model) + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NU + Calls: ... -> -> compute_geom_2 -> + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘metric-details.Rmd’ using rmarkdown + --- finished re-building ‘metric-details.Rmd’ + + --- re-building ‘scoring-forecasts-directly.Rmd’ using rmarkdown + --- finished re-building ‘scoring-forecasts-directly.Rmd’ + + --- re-building ‘scoringutils.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘scoringutils.Rmd’ + ... + The following messages were produced when checking inputs: + 1. 144 values for `prediction` are NA in the data provided and the corresponding rows were removed. This may indicate a problem if unexpected. + + > example_quantile %>% make_NA(what = "truth", target_end_date >= + + "2021-07-15", target_end_date < "2021-05-22") %>% make_NA(what = "forecast", .... [TRUNCATED] + + When sourcing ‘scoringutils.R’: + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL + Execution halted + + ‘metric-details.Rmd’ using ‘UTF-8’... OK + ‘scoring-forecasts-directly.Rmd’ using ‘UTF-8’... OK + ‘scoringutils.Rmd’ using ‘UTF-8’... failed + ``` + +# scUtils + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/scUtils +* Date/Publication: 2020-06-25 16:20:02 UTC +* Number of recursive dependencies: 52 + +Run `revdepcheck::cloud_details(, "scUtils")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(scUtils) + > + > test_check("scUtils") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-plots.R:59:3'): all kinds of colnames are allowed ──────────── + p$labels not equal to list(y = "Dim2", x = "Dim1", colour = "expression"). + Length mismatch: comparison on first 2 components + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# SCVA + +
+ +* Version: 1.3.1 +* GitHub: NA +* Source code: https://github.com/cran/SCVA +* Date/Publication: 2020-01-09 22:50:10 UTC +* Number of recursive dependencies: 80 + +Run `revdepcheck::cloud_details(, "SCVA")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SCVA-Ex.R’ failed + The error most likely occurred in: + + > ### Name: graphly + > ### Title: Interactive plot of single-case data + > ### Aliases: graphly + > ### Keywords: Single-case design Graph + > + > ### ** Examples + > + > data(AB) + > graphly(design = "AB", data = AB) + Error in pm[[2]] : subscript out of bounds + Calls: graphly -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# sdmTMB + +
+ +* Version: 0.6.0 +* GitHub: https://github.com/pbs-assess/sdmTMB +* Source code: https://github.com/cran/sdmTMB +* Date/Publication: 2024-05-30 00:00:02 UTC +* Number of recursive dependencies: 149 + +Run `revdepcheck::cloud_details(, "sdmTMB")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sdmTMB-Ex.R’ failed + The error most likely occurred in: + + > ### Name: emmeans.sdmTMB + > ### Title: Estimated marginal means with the 'emmeans' package with + > ### 'sdmTMB' + > ### Aliases: emmeans.sdmTMB + > + > ### ** Examples + > + ... + year2013 - year2017 -0.15358 0.259 959 -0.593 0.9342 + year2015 - year2017 0.03703 0.263 959 0.141 0.9990 + + P value adjustment: tukey method for comparing a family of 4 estimates + + > emmeans::emmip(fit2, year ~ depth_scaled, at = list(depth_scaled = seq(-2.5, + + 2.5, length.out = 50)), CIs = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 88.5Mb + sub-directories of 1Mb or more: + libs 86.4Mb + ``` + +# SDMtune + +
+ +* Version: 1.3.1 +* GitHub: https://github.com/ConsBiol-unibern/SDMtune +* Source code: https://github.com/cran/SDMtune +* Date/Publication: 2023-07-03 12:20:02 UTC +* Number of recursive dependencies: 125 + +Run `revdepcheck::cloud_details(, "SDMtune")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(SDMtune) + + _____ ____ __ ___ __ + / ___/ / __ \ / |/ // /_ __ __ ____ ___ + \__ \ / / / // /|_/ // __// / / // __ \ / _ \ + ___/ // /_/ // / / // /_ / /_/ // / / // __/ + ... + `expected` is a character vector ('Var2') + ── Failure ('test-plotCor.R:6:3'): The plot has the correct labels and text size ── + p$labels$y (`actual`) not equal to "Var1" (`expected`). + + `actual` is NULL + `expected` is a character vector ('Var1') + + [ FAIL 2 | WARN 0 | SKIP 55 | PASS 315 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘basic-use.Rmd’ + ... + [1] 0.8336850 0.8672387 + + > folds <- randomFolds(data, k = 4, only_presence = TRUE, + + seed = 25) + + > auc(cv_model) + + When sourcing ‘basic-use.R’: + Error: object 'cv_model' not found + Execution halted + + ‘basic-use.Rmd’ using ‘UTF-8’... failed + ‘hyper-tuning.Rmd’ using ‘UTF-8’... OK + ‘presence-absence.Rmd’ using ‘UTF-8’... OK + ‘var-selection.Rmd’ using ‘UTF-8’... OK + ``` + +# sedproxy + +
+ +* Version: 0.7.5 +* GitHub: https://github.com/EarthSystemDiagnostics/sedproxy +* Source code: https://github.com/cran/sedproxy +* Date/Publication: 2023-02-26 10:50:02 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "sedproxy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sedproxy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ClimToProxyClim + > ### Title: Simulate sediment archived proxy records from an input climate + > ### signal. + > ### Aliases: ClimToProxyClim + > + > ### ** Examples + > + ... + > + > PlotPFMs(PFM$everything, max.replicates = 1, stage.order = "seq") + + + facet_wrap(~stage) + Joining with `by = join_by(stage, scale)` + Scale for alpha is already present. + Adding another scale for alpha, which will replace the existing scale. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction-to-sedproxy.Rmd’ + ... + Timepoint(s) 1, 101 are in the mixed layer + + > PlotPFMs(PFM) + Joining with `by = join_by(stage, scale)` + Scale for alpha is already present. + Adding another scale for alpha, which will replace the existing scale. + + When sourcing ‘introduction-to-sedproxy.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘effect-of-climate-dependent-flux.Rmd’ using ‘UTF-8’... OK + ‘introduction-to-sedproxy.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘effect-of-climate-dependent-flux.Rmd’ using rmarkdown + ``` + +# see + +
+ +* Version: 0.9.0 +* GitHub: https://github.com/easystats/see +* Source code: https://github.com/cran/see +* Date/Publication: 2024-09-06 04:30:02 UTC +* Number of recursive dependencies: 243 + +Run `revdepcheck::cloud_details(, "see")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘see-Ex.R’ failed + The error most likely occurred in: + + > ### Name: geom_binomdensity + > ### Title: Add dot-densities for binary 'y' variables + > ### Aliases: geom_binomdensity + > + > ### ** Examples + > + > ## Don't show: + ... + 14. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 15. │ └─l$compute_geom_2(d, theme = plot$theme) + 16. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 17. │ └─self$geom$use_defaults(...) + 18. └─base::.handleSimpleError(...) + 19. └─rlang (local) h(simpleError(msg, call)) + 20. └─handlers[[1L]](cnd) + 21. └─cli::cli_abort(...) + 22. └─rlang::abort(...) + Execution halted + ``` + +# seedreg + +
+ +* Version: 1.0.3 +* GitHub: NA +* Source code: https://github.com/cran/seedreg +* Date/Publication: 2022-07-07 21:20:02 UTC +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "seedreg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘seedreg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: lineplot + > ### Title: Graph: line chart + > ### Aliases: lineplot + > + > ### ** Examples + > + > data("substrate") + ... + 16. │ └─ggplot2 (local) setup_params(...) + 17. │ └─ggplot2:::make_summary_fun(...) + 18. │ └─rlang::as_function(fun.data) + 19. │ └─base::get(x, envir = env, mode = "function") + 20. └─base::.handleSimpleError(...) + 21. └─rlang (local) h(simpleError(msg, call)) + 22. └─handlers[[1L]](cnd) + 23. └─cli::cli_abort(...) + 24. └─rlang::abort(...) + Execution halted + ``` + +# semfindr + +
+ +* Version: 0.1.8 +* GitHub: https://github.com/sfcheung/semfindr +* Source code: https://github.com/cran/semfindr +* Date/Publication: 2024-04-08 13:30:03 UTC +* Number of recursive dependencies: 72 + +Run `revdepcheck::cloud_details(, "semfindr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘semfindr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: cfa_dat2 + > ### Title: Sample Data: A CFA Model with an Influential Case + > ### Aliases: cfa_dat2 + > ### Keywords: datasets + > + > ### ** Examples + > + ... + .x5 0.227 0.136 1.675 0.094 + .x6 0.472 0.108 4.378 0.000 + f1 0.073 0.063 1.161 0.245 + f2 0.149 0.078 1.926 0.054 + + > inf_out <- influence_stat(fit) + > gcd_plot(inf_out) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: gcd_plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(semfindr) + > + > test_check("semfindr") + Starting 2 test processes + [ FAIL 2 | WARN 0 | SKIP 13 | PASS 387 ] + + ... + 1. └─semfindr::index_plot(fit_est_change, "gcd") at test-index_plot.R:22:1 + 2. └─ggplot2:::`+.gg`(p, do.call(ggplot2::geom_point, point_aes)) + 3. └─ggplot2:::add_ggplot(e1, e2, e2name) + 4. ├─ggplot2::ggplot_add(object, p, objectname) + 5. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 6. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 0 | SKIP 13 | PASS 387 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘semfindr.Rmd’ + ... + + Note: + - Only the first 10 case(s) is/are displayed. Set ‘first’ to NULL to display all cases. + - Cases sorted by Mahalanobis distance in decreasing order. + + > gcd_plot(fit_influence, largest_gcd = 3) + + ... + > gcd_plot(fit_influence, largest_gcd = 3) + + When sourcing ‘user_id.R’: + Error: argument is of length zero + Execution halted + + ‘casewise_scores.Rmd’ using ‘UTF-8’... OK + ‘selecting_cases.Rmd’ using ‘UTF-8’... OK + ‘semfindr.Rmd’ using ‘UTF-8’... failed + ‘user_id.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘casewise_scores.Rmd’ using rmarkdown + ``` + +# sensiPhy + +
+ +* Version: 0.8.5 +* GitHub: https://github.com/paternogbc/sensiPhy +* Source code: https://github.com/cran/sensiPhy +* Date/Publication: 2020-04-02 14:50:02 UTC +* Number of recursive dependencies: 84 + +Run `revdepcheck::cloud_details(, "sensiPhy")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sensiPhy-Ex.R’ failed + The error most likely occurred in: + + > ### Name: clade_physig + > ### Title: Influential clade detection - Phylogenetic signal + > ### Aliases: clade_physig + > + > ### ** Examples + > + > data(alien) + ... + 4 0.8975481 0.25 + 5 0.8827772 0.40 + + > sensi_plot(clade, "Bovidae") + Warning: Use of `nd$estimate` is discouraged. + ℹ Use `estimate` instead. + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: sensi_plot ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘sensiPhy_vignette.Rmd’ + ... + + When sourcing ‘sensiPhy_vignette.R’: + Error: attempt to use zero-length variable name + Execution halted + + ‘sensiPhy_vignette.Rmd’ using ‘UTF-8’... failed + ``` + +# sglg + +
+ +* Version: 0.2.2 +* GitHub: NA +* Source code: https://github.com/cran/sglg +* Date/Publication: 2022-09-04 03:50:01 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "sglg")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sglg-Ex.R’ failed + The error most likely occurred in: + + > ### Name: deviance_residuals + > ### Title: Deviance Residuals for a Generalized Log-gamma Regression Model + > ### Aliases: deviance_residuals + > + > ### ** Examples + > + > # Example 1 + > n <- 300 + > error <- rglg(n,0,1,1) + > y <- 0.5 + error + > fit <- glg(y~1,data=as.data.frame(y)) + > deviance_residuals(fit) + Error in pm[[2]] : subscript out of bounds + Calls: deviance_residuals ... dots2plots -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# sgsR + +
+ +* Version: 1.4.5 +* GitHub: https://github.com/tgoodbody/sgsR +* Source code: https://github.com/cran/sgsR +* Date/Publication: 2024-03-03 15:10:02 UTC +* Number of recursive dependencies: 124 + +Run `revdepcheck::cloud_details(, "sgsR")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + ... + `expected` is a character vector ('zq90') + ── Failure ('test-utils-plot.R:19:3'): scatter messages ──────────────────────── + o1$labels$x (`actual`) not equal to "pzabove2" (`expected`). + + `actual` is NULL + `expected` is a character vector ('pzabove2') + + [ FAIL 2 | WARN 115 | SKIP 19 | PASS 508 ] + Error: Test failures + Execution halted + ``` + +# SHAPforxgboost + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/liuyanguu/SHAPforxgboost +* Source code: https://github.com/cran/SHAPforxgboost +* Date/Publication: 2023-05-29 17:20:07 UTC +* Number of recursive dependencies: 112 + +Run `revdepcheck::cloud_details(, "SHAPforxgboost")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SHAPforxgboost-Ex.R’ failed + The error most likely occurred in: + + > ### Name: scatter.plot.diagonal + > ### Title: Make customized scatter plot with diagonal line and R2 printed. + > ### Aliases: scatter.plot.diagonal + > + > ### ** Examples + > + > scatter.plot.diagonal(data = iris, x = "Sepal.Length", y = "Petal.Length") + [1] "R2 is 0.76 ." + `geom_smooth()` using formula = 'y ~ x' + Error in if (new_name %in% existing) { : argument is of length zero + Calls: scatter.plot.diagonal ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# ShapleyOutlier + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/ShapleyOutlier +* Date/Publication: 2023-02-20 10:30:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "ShapleyOutlier")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘ShapleyOutlier-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MOE + > ### Title: Detecting cellwise outliers using Shapley values based on local + > ### outlyingness. + > ### Aliases: MOE + > + > ### ** Examples + > + ... + > mu <- rep(0,p) + > Sigma <- matrix(0.9, p, p); diag(Sigma) = 1 + > Sigma_inv <- solve(Sigma) + > x <- c(0,1,2,2.3,2.5) + > MOE_x <- MOE(x = x, mu = mu, Sigma = Sigma) + > plot(MOE_x) + Error in grid.Call.graphics(C_segments, x$x0, x$y0, x$x1, x$y1, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plot ... drawDetails -> drawDetails.segments -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘ShapleyOutlier_examples.Rmd’ + ... + + > rownames(phi_SCD) <- paste("Step", 0:(nrow(phi_SCD) - + + 1)) + + > plot(new_shapley(phi = phi_SCD), abbrev.var = FALSE, + + abbrev.obs = FALSE, sort.obs = FALSE, sort.var = FALSE) + + When sourcing ‘ShapleyOutlier_examples.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘ShapleyOutlier_examples.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘ShapleyOutlier_examples.Rmd’ using rmarkdown + ``` + +# shinipsum + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/Thinkr-open/shinipsum +* Source code: https://github.com/cran/shinipsum +* Date/Publication: 2024-02-09 15:50:05 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "shinipsum")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(shinipsum) + > + > test_check("shinipsum") + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 3150 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + `a` has length 11, not length 10. + Backtrace: + ▆ + 1. └─base::lapply(...) at test-ggplot.R:3:3 + 2. └─shinipsum (local) FUN(X[[i]], ...) + 3. └─testthat::expect_length(a, expected_length) at test-ggplot.R:8:7 + + [ FAIL 2 | WARN 1 | SKIP 0 | PASS 3150 ] + Error: Test failures + Execution halted + ``` + +# signatureSurvival + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/signatureSurvival +* Date/Publication: 2023-07-19 11:10:02 UTC +* Number of recursive dependencies: 99 + +Run `revdepcheck::cloud_details(, "signatureSurvival")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘signatureSurvival-Ex.R’ failed + The error most likely occurred in: + + > ### Name: MKMplot + > ### Title: Multivariate Kaplan-Meier survival curve plot + > ### Aliases: MKMplot + > ### Keywords: multivariate survival analysis + > + > ### ** Examples + > + ... + Loading required package: survival + > require(ggplot2) + Loading required package: ggplot2 + > data(GSE50081) + > MKMplot(data=GSE50081,mol=56,X=c("t.stage","n.stage", "m.stage"),time="month", + + status="status1",sml="none",quant=c("No",-0.2,0.2),plotmethod="ggsurvplot", + + adjx = 5) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: MKMplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.2Mb + sub-directories of 1Mb or more: + data 7.5Mb + ``` + +# SimCorrMix + +
+ +* Version: 0.1.1 +* GitHub: https://github.com/AFialkowski/SimCorrMix +* Source code: https://github.com/cran/SimCorrMix +* Date/Publication: 2018-07-01 13:31:03 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "SimCorrMix")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SimCorrMix-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_simpdf_theory + > ### Title: Plot Simulated Probability Density Function and Target PDF by + > ### Distribution Name or Function for Continuous or Count Variables + > ### Aliases: plot_simpdf_theory + > ### Keywords: plot + > + > ### ** Examples + ... + + mix_sixths = c(0, 0)) + Total Simulation time: 0 minutes + > plot_simpdf_theory(Nmix$Y_mix[, 1], + + title = "Mixture of Normal Distributions", + + fx = function(x) 0.4 * dnorm(x, -2, 1) + 0.6 * dnorm(x, 2, 1), + + lower = -5, upper = 5) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘cont_mixture.Rmd’ + ... + > sim_cdf_prob(sim_y = Nmix2$Y_mix[, 1], delta = y_star)$cumulative_prob + [1] 0.9504 + + > plot_simpdf_theory(sim_y = Nmix2$Y_mix[, 1], ylower = -10, + + yupper = 10, title = "PDF of Mixture of Normal Distributions", + + fx = fx, low .... [TRUNCATED] + + ... + + When sourcing ‘workflow.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘cont_mixture.Rmd’ using ‘UTF-8’... failed + ‘corr_mixture.Rmd’ using ‘UTF-8’... OK + ‘method_comp.Rmd’ using ‘UTF-8’... OK + ‘variable_types.Rmd’ using ‘UTF-8’... OK + ‘workflow.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘cont_mixture.Rmd’ using rmarkdown + + Quitting from lines 129-132 [unnamed-chunk-8] (cont_mixture.Rmd) + Error: processing vignette 'cont_mixture.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘cont_mixture.Rmd’ + + --- re-building ‘corr_mixture.Rmd’ using rmarkdown + --- finished re-building ‘corr_mixture.Rmd’ + ... + Quitting from lines 294-308 [unnamed-chunk-17] (workflow.Rmd) + Error: processing vignette 'workflow.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘workflow.Rmd’ + + SUMMARY: processing the following files failed: + ‘cont_mixture.Rmd’ ‘workflow.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘MASS’ ‘grid’ + All declared Imports should be used. + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘PoisNor’ + ``` + +* checking LazyData ... NOTE + ``` + 'LazyData' is specified without a 'data' directory + ``` + +# SimMultiCorrData + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/AFialkowski/SimMultiCorrData +* Source code: https://github.com/cran/SimMultiCorrData +* Date/Publication: 2018-06-28 17:37:55 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "SimMultiCorrData")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘dist_comp.Rmd’ + ... + + > 1 - pnorm(z_prime) + [1] 0.04999249 + + > plot_sim_pdf_theory(sim_y = H_exp$continuous_variable[, + + 1], Dist = "Exponential", params = 0.5) + + ... + Execution halted + + ‘benefits.Rmd’ using ‘UTF-8’... OK + ‘dist_comp.Rmd’ using ‘UTF-8’... failed + ‘errorloop.Rmd’ using ‘UTF-8’... OK + ‘functions.Rmd’ using ‘UTF-8’... OK + ‘method_comp.Rmd’ using ‘UTF-8’... OK + ‘sixth_validpdf.Rmd’ using ‘UTF-8’... failed + ‘variable_types.Rmd’ using ‘UTF-8’... OK + ‘workflow.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘benefits.Rmd’ using rmarkdown + --- finished re-building ‘benefits.Rmd’ + + --- re-building ‘dist_comp.Rmd’ using rmarkdown + + Quitting from lines 107-109 [unnamed-chunk-11] (dist_comp.Rmd) + Error: processing vignette 'dist_comp.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘dist_comp.Rmd’ + ... + + Quitting from lines 208-214 [unnamed-chunk-15] (sixth_validpdf.Rmd) + Error: processing vignette 'sixth_validpdf.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘sixth_validpdf.Rmd’ + + --- re-building ‘variable_types.Rmd’ using rmarkdown + --- finished re-building ‘variable_types.Rmd’ + + --- re-building ‘workflow.Rmd’ using rmarkdown + ``` + +## In both + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’ + ``` + +# SimNPH + +
+ +* Version: 0.5.5 +* GitHub: https://github.com/SimNPH/SimNPH +* Source code: https://github.com/cran/SimNPH +* Date/Publication: 2024-03-04 10:10:02 UTC +* Number of recursive dependencies: 134 + +Run `revdepcheck::cloud_details(, "SimNPH")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(SimNPH) + Loading required package: SimDesign + Loading required package: survival + > + > test_check("SimNPH") + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 343 ] + ... + + `names(actual)`: "x" + `names(expected)`: "x" "y" + + `actual$y` is absent + `expected$y` is a character vector ('mpg') + + [ FAIL 2 | WARN 0 | SKIP 0 | PASS 343 ] + Error: Test failures + Execution halted + ``` + +# slendr + +
+ +* Version: 0.9.1 +* GitHub: https://github.com/bodkan/slendr +* Source code: https://github.com/cran/slendr +* Date/Publication: 2024-02-21 23:20:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "slendr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘slendr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: area + > ### Title: Calculate the area covered by the given slendr object + > ### Aliases: area + > + > ### ** Examples + > + > region_a <- region("A", center = c(20, 50), radius = 20) + ... + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggproto_parent(Coord, self)$setup_params(data) + 10. └─ggplot2 (local) setup_params(..., self = self) + 11. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 12. └─ggplot2:::check_logical(expand) + 13. └─ggplot2:::stop_input_type(...) + 14. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette-01-tutorial.Rmd’ + ... + dependencies automatically by running the function `setup_env()`. + + > init_env() + + When sourcing ‘vignette-01-tutorial.R’: + Error: Could not activate slendr's Python environment because it is not + present on your system ('Python-3.12_msprime-1.3.1_tskit-0.5.6_pyslim-1.0.4_tspop-0.0.2'). + ... + ‘vignette-01-tutorial.Rmd’ using ‘UTF-8’... failed + ‘vignette-02-grid-model.Rmd’ using ‘UTF-8’... failed + ‘vignette-03-interactions.Rmd’ using ‘UTF-8’... failed + ‘vignette-04-nonspatial-models.Rmd’ using ‘UTF-8’... failed + ‘vignette-05-tree-sequences.Rmd’ using ‘UTF-8’... failed + ‘vignette-06-locations.Rmd’ using ‘UTF-8’... failed + ‘vignette-07-backends.Rmd’ using ‘UTF-8’... failed + ‘vignette-08-nonslendr-tskit.Rmd’ using ‘UTF-8’... failed + ‘vignette-09-paper.Rmd’ using ‘UTF-8’... failed + ‘vignette-10-tracts.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 5.0Mb + sub-directories of 1Mb or more: + doc 3.7Mb + ``` + +# smallsets + +
+ +* Version: 2.0.0 +* GitHub: https://github.com/lydialucchesi/smallsets +* Source code: https://github.com/cran/smallsets +* Date/Publication: 2023-12-05 00:00:02 UTC +* Number of recursive dependencies: 96 + +Run `revdepcheck::cloud_details(, "smallsets")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘smallsets-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Smallset_Timeline + > ### Title: Smallset Timeline + > ### Aliases: Smallset_Timeline + > + > ### ** Examples + > + > set.seed(145) + > + > Smallset_Timeline( + + data = s_data, + + code = system.file("s_data_preprocess.R", package = "smallsets") + + ) + Error in as.unit(value) : object is not coercible to a unit + Calls: ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘smallsets.Rmd’ + ... + > library(smallsets) + + > set.seed(145) + + > Smallset_Timeline(data = s_data, code = system.file("s_data_preprocess.R", + + package = "smallsets")) + + When sourcing ‘smallsets.R’: + Error: object is not coercible to a unit + Execution halted + + ‘smallsets.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘smallsets.Rmd’ using rmarkdown + + Quitting from lines 36-42 [timeline1] (smallsets.Rmd) + Error: processing vignette 'smallsets.Rmd' failed with diagnostics: + object is not coercible to a unit + --- failed re-building ‘smallsets.Rmd’ + + SUMMARY: processing the following file failed: + ‘smallsets.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘gurobi’ + ``` + +# spinifex + +
+ +* Version: 0.3.7.0 +* GitHub: https://github.com/nspyrison/spinifex +* Source code: https://github.com/cran/spinifex +* Date/Publication: 2024-01-29 14:40:02 UTC +* Number of recursive dependencies: 165 + +Run `revdepcheck::cloud_details(, "spinifex")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(spinifex) + Loading required package: tourr + -------------------------------------------------------- + spinifex --- version 0.3.7.0 + Please share bugs, suggestions, and feature requests at: + ... + 2. │ └─base::withCallingHandlers(...) + 3. └─spinifex::play_tour_path(tour_path = tpath, data = dat_std, angle = 1) + 4. └─spinifex (local) render_type(frames = tour_df, ...) + 5. ├─plotly::ggplotly(p = gg, tooltip = "tooltip") + 6. └─plotly:::ggplotly.ggplot(p = gg, tooltip = "tooltip") + 7. └─plotly::gg2list(...) + + [ FAIL 3 | WARN 4 | SKIP 0 | PASS 80 ] + Error: Test failures + Execution halted + ``` + +# sport + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/gogonzo/sport +* Source code: https://github.com/cran/sport +* Date/Publication: 2024-01-08 23:50:02 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "sport")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > + > test_check("sport") + Loading required package: sport + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 238 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test_output.R:30:3'): Scale is labelled 'r' ─────────────────────── + p$labels$y not identical to "r". + target is NULL, current is character + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 238 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 7504 marked UTF-8 strings + ``` + +# spotoroo + +
+ +* Version: 0.1.4 +* GitHub: https://github.com/TengMCing/spotoroo +* Source code: https://github.com/cran/spotoroo +* Date/Publication: 2023-08-21 05:50:02 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::cloud_details(, "spotoroo")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(spotoroo) + > + > test_check("spotoroo") + + -------------------------------- SPOTOROO 0.1.4 -------------------------------- + + ... + i Actually got a with text: + argument is of length zero + ── Failure ('test-plot_spotoroo.R:64:3'): plot_spotoroo() works ──────────────── + Expected `plot_spotoroo(result, type = "timeline")` to run without any errors. + i Actually got a with text: + argument is of length zero + + [ FAIL 2 | WARN 5 | SKIP 0 | PASS 65 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Clustering-hot-spots.Rmd’ + ... + + ──────────────────────────────────────────────────────────────────────────────── + + > plot_spotoroo(result, type = "def") + + > plot_spotoroo(result, type = "timeline") + + When sourcing ‘Clustering-hot-spots.R’: + Error: argument is of length zero + Execution halted + + ‘Clustering-hot-spots.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Clustering-hot-spots.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘utils’ + All declared Imports should be used. + ``` + +# SqueakR + +
+ +* Version: 1.3.0 +* GitHub: https://github.com/osimon81/SqueakR +* Source code: https://github.com/cran/SqueakR +* Date/Publication: 2022-06-28 09:20:04 UTC +* Number of recursive dependencies: 145 + +Run `revdepcheck::cloud_details(, "SqueakR")` for more info + +
+ +## Newly broken + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘SqueakR.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘SqueakR.Rmd’ + ... + $ experimenters : NULL + $ experimental_data: list() + + > my_new_data <- add_timepoint_data(data_path = "../inst/extdata/Example_Mouse_Data.xlsx", + + t1 = 5, t2 = 25) + Adding call features Excel file to workspace... + + When sourcing ‘SqueakR.R’: + Error: `path` does not exist: ‘../inst/extdata/Example_Mouse_Data.xlsx’ + Execution halted + + ‘SqueakR.Rmd’ using ‘UTF-8’... failed + ``` + +* checking installed package size ... NOTE + ``` + installed size is 8.8Mb + sub-directories of 1Mb or more: + doc 8.2Mb + ``` + +# stability + +
+ +* Version: 0.5.0 +* GitHub: https://github.com/myaseen208/stability +* Source code: https://github.com/cran/stability +* Date/Publication: 2018-10-02 17:50:03 UTC +* Number of recursive dependencies: 47 + +Run `revdepcheck::cloud_details(, "stability")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘stability-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ammi_biplot + > ### Title: Additive Main Effects and Multiplicative Interaction (AMMI) + > ### Biplot + > ### Aliases: ammi_biplot ammi_biplot.default + > + > ### ** Examples + > + ... + > ammi_biplot( + + .data = ge_data + + , .y = Yield + + , .rep = Rep + + , .gen = Gen + + , .env = Env + + ) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ammi_biplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# statgenGWAS + +
+ +* Version: 1.0.9 +* GitHub: https://github.com/Biometris/statgenGWAS +* Source code: https://github.com/cran/statgenGWAS +* Date/Publication: 2022-10-13 15:30:43 UTC +* Number of recursive dependencies: 71 + +Run `revdepcheck::cloud_details(, "statgenGWAS")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("statgenGWAS") + + } + + test_GWAS.R................... 0 tests + test_GWAS.R................... 0 tests + ... + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <86> + 3: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <90> + 4: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for + 5: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <86> + 6: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, : + conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <90> + Execution halted + ``` + +## In both + +* checking C++ specification ... NOTE + ``` + Specified C++11: please drop specification unless essential + ``` + +* checking installed package size ... NOTE + ``` + installed size is 15.2Mb + sub-directories of 1Mb or more: + data 7.0Mb + libs 7.2Mb + ``` + +# statgenHTP + +
+ +* Version: 1.0.6.1 +* GitHub: https://github.com/Biometris/statgenHTP +* Source code: https://github.com/cran/statgenHTP +* Date/Publication: 2023-04-14 08:20:02 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "statgenHTP")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘statgenHTP-Ex.R’ failed + The error most likely occurred in: + + > ### Name: removeSerieOut + > ### Title: Replace outliers for series of observations by NA + > ### Aliases: removeSerieOut + > + > ### ** Examples + > + > ## Run the function to fit P-splines on a subset of genotypes. + ... + 18. │ └─ggplot2:::`+.gg`(...) + 19. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 20. │ ├─ggplot2::ggplot_add(object, p, objectname) + 21. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 22. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 23. └─base::.handleSimpleError(...) + 24. └─purrr (local) h(simpleError(msg, call)) + 25. └─cli::cli_abort(...) + 26. └─rlang::abort(...) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if ( requireNamespace("tinytest", quietly=TRUE) ){ + + tinytest::test_package("statgenHTP") + + } + + test_TP.R..................... 0 tests + test_TP.R..................... 0 tests + ... + test_detectSerieOut.R......... 16 tests 1 fails Error in eval(expr, envir = e) : object 'serieOut1' not found + Calls: ... lapply -> FUN -> eval -> eval -> expect_inherits -> fun + In addition: Warning messages: + 1: 125 failed to parse. + 2: Ignoring unknown labels: + • `colour = ""` + 3: The following genotypes have less than 3 plotIds and are skipped in the outlier detection: + G12 + + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Overview_HTP.Rmd’ + ... + > outVator <- detectSerieOut(corrDat = spatCorrectedVator, + + predDat = predDat, coefDat = coefDat, trait = "EffpsII_corr", + + genotypes = sub .... [TRUNCATED] + + When sourcing ‘Overview_HTP.R’: + Error: ℹ In index: 1. + ℹ With name: y. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘Overview_HTP.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Overview_HTP.Rmd’ using rmarkdown + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘asreml’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 9.0Mb + sub-directories of 1Mb or more: + data 7.5Mb + ``` + +# sugrrants + +
+ +* Version: 0.2.9 +* GitHub: https://github.com/earowang/sugrrants +* Source code: https://github.com/cran/sugrrants +* Date/Publication: 2024-03-12 05:20:03 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "sugrrants")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘sugrrants-Ex.R’ failed + The error most likely occurred in: + + > ### Name: frame_calendar + > ### Title: Rearrange a temporal data frame to a calendar-based data format + > ### using linear algebra + > ### Aliases: frame_calendar prettify + > + > ### ** Examples + > + ... + + frame_calendar(x = Time, y = Hourly_Counts, date = Date, nrow = 4) + > + > # ggplot + > p1 <- calendar_df %>% + + ggplot(aes(x = .Time, y = .Hourly_Counts, group = Date)) + + + geom_line() + > prettify(p1, size = 3, label.padding = unit(0.15, "lines")) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: prettify ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘frame-calendar.Rmd’ + ... + > p1 <- centre_calendar %>% ggplot(aes(x = .Time, y = .Hourly_Counts, + + group = Date)) + geom_line() + + > p1 + + > prettify(p1) + + When sourcing ‘frame-calendar.R’: + Error: argument is of length zero + Execution halted + + ‘frame-calendar.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘frame-calendar.Rmd’ using rmarkdown + ``` + +# superb + +
+ +* Version: 0.95.15 +* GitHub: https://github.com/dcousin3/superb +* Source code: https://github.com/cran/superb +* Date/Publication: 2024-08-17 19:00:02 UTC +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "superb")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘superb-Ex.R’ failed + The error most likely occurred in: + + > ### Name: GRD + > ### Title: Generate random data + > ### Aliases: GRD + > + > ### ** Examples + > + > # Simplest example using all the default arguments: + ... + Difficulty; levels: 1, 2, 3, 4, 5 + 2.Within-Subject Factors ( 1 repeated measures ): + 3.Subjects per group ( 500 total subjects ): + 100 + ------------------------------------------------------------ + > # show the mean performance as a function of difficulty: + > superbPlot(dta, BSFactors = "Difficulty", variables="DV") + Error in superbPlot(dta, BSFactors = "Difficulty", variables = "DV") : + superb::ERROR: The function superbPlot.bar is not a known function for making plots with superbPlot. Exiting... + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > test_check("superb") + Loading required package: superb + [ FAIL 48 | WARN 0 | SKIP 0 | PASS 93 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Error ('test_compatibility.R:36:2'): TESTS (1/1) ──────────────────────────── + ... + 1. ├─testthat::expect_message(...) at test_superbPlot.R:810:5 + 2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages) + 3. │ ├─testthat (local) .capture(...) + 4. │ │ └─base::withCallingHandlers(...) + 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 6. └─superb::superbPlot(...) + + [ FAIL 48 | WARN 0 | SKIP 0 | PASS 93 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘CustomizingSuperbPlots.Rmd’ + ... + > mylabels <- c("Verbal", "Numerical", "Spatial", "Creativity", + + "Intrapersonal", "Interpersonal") + + > pltA <- superbPlot(dtaA, WSFactors = "Domain(6)", + + variables = mylabels, adjustments = list(purpose = "difference", + + decorrelation = .... [TRUNCATED] + + ... + ‘Vignette7.Rmd’ using ‘UTF-8’... failed + ‘Vignette8.Rmd’ using ‘UTF-8’... failed + ‘Vignette9.Rmd’ using ‘UTF-8’... failed + ‘VignetteA.Rmd’ using ‘UTF-8’... failed + ‘VignetteB.Rmd’ using ‘UTF-8’... failed + ‘VignetteC.Rmd’ using ‘UTF-8’... failed + ‘VignetteD.Rmd’ using ‘UTF-8’... OK + ‘VignetteE.Rmd’ using ‘UTF-8’... failed + ‘VignetteF.Rmd’ using ‘UTF-8’... failed + ‘VignetteG.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘CustomizingSuperbPlots.Rmd’ using rmarkdown + + Quitting from lines 91-107 [unnamed-chunk-4] (CustomizingSuperbPlots.Rmd) + Error: processing vignette 'CustomizingSuperbPlots.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.raincloud is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘CustomizingSuperbPlots.Rmd’ + + --- re-building ‘TheMakingOf.Rmd’ using rmarkdown + + ... + --- failed re-building ‘Vignette1.Rmd’ + + --- re-building ‘Vignette2.Rmd’ using rmarkdown + + Quitting from lines 39-48 [unnamed-chunk-2] (Vignette2.Rmd) + Error: processing vignette 'Vignette2.Rmd' failed with diagnostics: + superb::ERROR: The function superbPlot.line is not a known function for making plots with superbPlot. Exiting... + --- failed re-building ‘Vignette2.Rmd’ + + --- re-building ‘Vignette3.Rmd’ using rmarkdown + ``` + +# surveyexplorer + +
+ +* Version: 0.2.0 +* GitHub: NA +* Source code: https://github.com/cran/surveyexplorer +* Date/Publication: 2024-06-07 09:50:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "surveyexplorer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘surveyexplorer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: multi_freq + > ### Title: Generate an UpSet plot for multiple-choice questions + > ### Aliases: multi_freq + > + > ### ** Examples + > + > + ... + + > + > #Basic Upset plot + > + > #Use `group_by` to partition the question into several groups + > multi_freq(berlinbears, question = dplyr::starts_with('will_eat'), group_by + + = gender) + Error in as.unit(e2) : object is not coercible to a unit + Calls: ... polylineGrob -> is.unit -> unit.c -> Ops.unit -> as.unit + Execution halted + ``` + +# survivalAnalysis + +
+ +* Version: 0.3.0 +* GitHub: NA +* Source code: https://github.com/cran/survivalAnalysis +* Date/Publication: 2022-02-11 14:00:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::cloud_details(, "survivalAnalysis")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘survivalAnalysis-Ex.R’ failed + The error most likely occurred in: + + > ### Name: kaplan_meier_plot + > ### Title: Kaplan Meier plots from survival results. + > ### Aliases: kaplan_meier_plot + > + > ### ** Examples + > + > library(magrittr) + ... + + > survival::aml %>% + + analyse_survival(vars(time, status), x) %>% + + kaplan_meier_plot(break.time.by="breakByMonth", + + xlab=".OS.months", + + risk.table=TRUE, + + ggtheme=ggplot2::theme_bw(10)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘multivariate.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘univariate.Rmd’ + ... + ECOG 2-3 vs. ECOG 1-2 1.41 2.0 2.82 <0.001 + ECOG 1-2 vs. ECOG 2-3 0.35 0.5 0.71 <0.001 + + + + > kaplan_meier_plot(result) + + When sourcing ‘univariate.R’: + Error: argument is of length zero + Execution halted + + ‘multivariate.Rmd’ using ‘UTF-8’... OK + ‘univariate.Rmd’ using ‘UTF-8’... failed + ``` + +# survminer + +
+ +* Version: 0.4.9 +* GitHub: https://github.com/kassambara/survminer +* Source code: https://github.com/cran/survminer +* Date/Publication: 2021-03-09 09:50:03 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "survminer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘survminer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: BRCAOV.survInfo + > ### Title: Breast and Ovarian Cancers Survival Information + > ### Aliases: BRCAOV.survInfo + > + > ### ** Examples + > + > data(BRCAOV.survInfo) + ... + The following object is masked from ‘package:survminer’: + + myeloma + + > fit <- survfit(Surv(times, patient.vital_status) ~ admin.disease_code, + + data = BRCAOV.survInfo) + > ggsurvplot(fit, data = BRCAOV.survInfo, risk.table = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ggsurvplot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(survminer) + Loading required package: ggplot2 + Loading required package: ggpubr + > + > test_check("survminer") + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] + ... + 4. └─survminer (local) ``(...) + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Informative_Survival_Plots.Rmd’ + ... + + + > fit <- survfit(Surv(times, patient.vital_status) ~ + + admin.disease_code, data = BRCAOV.survInfo) + + > ggsurvplot(fit, data = BRCAOV.survInfo, risk.table = TRUE) + + ... + > ggsurvplot(fit, data = lung, pval = TRUE, pval.method = TRUE) + + When sourcing ‘Specifiying_weights_in_log-rank_comparisons.R’: + Error: argument is of length zero + Execution halted + + ‘Informative_Survival_Plots.Rmd’ using ‘UTF-8’... failed + ‘Playing_with_fonts_and_texts.Rmd’ using ‘UTF-8’... failed + ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ using ‘UTF-8’... failed + ‘ggforest-show-interactions-hazard-ratio.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Informative_Survival_Plots.Rmd’ using rmarkdown + + Quitting from lines 66-72 [unnamed-chunk-4] (Informative_Survival_Plots.Rmd) + Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Informative_Survival_Plots.Rmd’ + + --- re-building ‘Playing_with_fonts_and_texts.Rmd’ using rmarkdown + + ... + --- failed re-building ‘Playing_with_fonts_and_texts.Rmd’ + + --- re-building ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ using rmarkdown + + Quitting from lines 98-99 [unnamed-chunk-4] (Specifiying_weights_in_log-rank_comparisons.Rmd) + Error: processing vignette 'Specifiying_weights_in_log-rank_comparisons.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ + + --- re-building ‘ggforest-show-interactions-hazard-ratio.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + doc 5.6Mb + ``` + +# survParamSim + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/yoshidk6/survParamSim +* Source code: https://github.com/cran/survParamSim +* Date/Publication: 2022-06-03 08:10:02 UTC +* Number of recursive dependencies: 122 + +Run `revdepcheck::cloud_details(, "survParamSim")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘survParamSim.Rmd’ + ... + + "Lev+5FU")), depth = as.nu .... [TRUNCATED] + + > survfit.colon <- survfit(Surv(time, status) ~ rx, + + data = colon2) + + > survminer::ggsurvplot(survfit.colon) + + When sourcing ‘survParamSim.R’: + Error: argument is of length zero + Execution halted + + ‘survParamSim.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘survParamSim.Rmd’ using rmarkdown + + Quitting from lines 53-58 [plot_raw_data] (survParamSim.Rmd) + Error: processing vignette 'survParamSim.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘survParamSim.Rmd’ + + SUMMARY: processing the following file failed: + ‘survParamSim.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# survstan + +
+ +* Version: 0.0.7.1 +* GitHub: https://github.com/fndemarqui/survstan +* Source code: https://github.com/cran/survstan +* Date/Publication: 2024-04-12 16:50:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::cloud_details(, "survstan")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘LRT.Rmd’ + ... + > ipass <- ipass %>% mutate(arm = as.factor(ipass$arm), + + arm = ifelse(arm == 1, "gefitinib", "carboplatin/paclitaxel")) + + > km <- survfit(Surv(time, status) ~ arm, data = ipass) + + > ggsurv(km) + + When sourcing ‘LRT.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘LRT.Rmd’ using ‘UTF-8’... failed + ‘survstan.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘LRT.Rmd’ using rmarkdown + + Quitting from lines 31-42 [unnamed-chunk-2] (LRT.Rmd) + Error: processing vignette 'LRT.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘LRT.Rmd’ + + --- re-building ‘survstan.Rmd’ using rmarkdown + --- finished re-building ‘survstan.Rmd’ + + SUMMARY: processing the following file failed: + ‘LRT.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 80.3Mb + sub-directories of 1Mb or more: + libs 79.7Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘RcppParallel’ ‘rstantools’ + All declared Imports should be used. + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# SVMMaj + +
+ +* Version: 0.2.9.2 +* GitHub: NA +* Source code: https://github.com/cran/SVMMaj +* Date/Publication: 2024-08-19 08:20:13 UTC +* Number of recursive dependencies: 57 + +Run `revdepcheck::cloud_details(, "SVMMaj")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘SVMMaj-Ex.R’ failed + The error most likely occurred in: + + > ### Name: print.q.svmmaj + > ### Title: SVM-Maj Algorithm + > ### Aliases: print.q.svmmaj svmmaj svmmaj.default + > + > ### ** Examples + > + > + ... + + > model3 <- svmmaj( + + diabetes$X, diabetes$y, weight.obs = weight.obs, + + spline.knots = 3, spline.degree = 2 + + ) + > plotWeights(model3, plotdim = c(2, 4)) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: plotWeights ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘paper.Rnw’ + ... + + TP FP Precision + negative 0.741 0.259 0.879 + positive 0.817 0.183 0.636 + + > plotWeights(model.spline) + + When sourcing ‘paper.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘paper.Rnw’... failed + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘paper.Rnw’ using Sweave + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + Scale for y is already present. + Adding another scale for y, which will replace the existing scale. + + Error: processing vignette 'paper.Rnw' failed with diagnostics: + chunk 20 (label = splineweightsplot) + ... + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + + --- failed re-building ‘paper.Rnw’ + + SUMMARY: processing the following file failed: + ‘paper.Rnw’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# Sysrecon + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/Sysrecon +* Date/Publication: 2023-02-20 08:50:02 UTC +* Number of recursive dependencies: 58 + +Run `revdepcheck::cloud_details(, "Sysrecon")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Sysrecon-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Sysrecon + > ### Title: Sysrecon + > ### Aliases: Sysrecon + > + > ### ** Examples + > + > + ... + Warning in fortify(data, ...) : + Arguments in `...` must be used. + ✖ Problematic arguments: + • as.Date = as.Date + • yscale_mapping = yscale_mapping + • hang = hang + ℹ Did you misspell an argument name? + Error in as.unit(value) : object is not coercible to a unit + Calls: Sysrecon ... assemble_guides -> guides_build -> [<- -> [<-.unit -> as.unit + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 38 marked UTF-8 strings + ``` + +# tabledown + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/masiraji/tabledown +* Source code: https://github.com/cran/tabledown +* Date/Publication: 2024-05-02 13:40:03 UTC +* Number of recursive dependencies: 164 + +Run `revdepcheck::cloud_details(, "tabledown")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tabledown-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggreliability_plotly + > ### Title: A Function for Creating Item Response Theory based reliability + > ### plot based on plotly. + > ### Aliases: ggreliability_plotly + > + > ### ** Examples + > + ... + Iteration: 17, Log-Lik: -5351.363, Max-Change: 0.00011 + Iteration: 18, Log-Lik: -5351.363, Max-Change: 0.00054 + Iteration: 19, Log-Lik: -5351.363, Max-Change: 0.00012 + Iteration: 20, Log-Lik: -5351.363, Max-Change: 0.00035 + Iteration: 21, Log-Lik: -5351.363, Max-Change: 0.00010 + > + > plot <- ggreliability_plotly(data, model) + Error in pm[[2]] : subscript out of bounds + Calls: ggreliability_plotly -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 551 marked UTF-8 strings + ``` + +# tcgaViz + +
+ +* Version: 1.0.2 +* GitHub: NA +* Source code: https://github.com/cran/tcgaViz +* Date/Publication: 2023-04-04 15:40:02 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "tcgaViz")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Tutorial.Rmd’ + ... + # `P-value adjusted` , Significance + + > plot(df, stats = stats) + + When sourcing ‘Tutorial.R’: + Error: ℹ In index: 1. + ℹ With name: value. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘Tutorial.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘Tutorial.Rmd’ using rmarkdown + + Quitting from lines 35-43 [plot] (Tutorial.Rmd) + Error: processing vignette 'Tutorial.Rmd' failed with diagnostics: + ℹ In index: 1. + ℹ With name: value. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + --- failed re-building ‘Tutorial.Rmd’ + + SUMMARY: processing the following file failed: + ‘Tutorial.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# TCIU + +
+ +* Version: 1.2.6 +* GitHub: https://github.com/SOCR/TCIU +* Source code: https://github.com/cran/TCIU +* Date/Publication: 2024-05-17 23:40:21 UTC +* Number of recursive dependencies: 163 + +Run `revdepcheck::cloud_details(, "TCIU")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TCIU-Ex.R’ failed + The error most likely occurred in: + + > ### Name: fmri_image + > ### Title: interactive graph object of the fMRI image + > ### Aliases: fmri_image + > + > ### ** Examples + > + > fmri_generate = fmri_simulate_func(dim_data = c(64, 64, 40), mask = mask) + > fmri_image(fmri_generate$fmri_data, option='manually', voxel_location = c(40,22,33), time = 4) + Error in pm[[2]] : subscript out of bounds + Calls: fmri_image ... add_trace -> add_data -> ggplotly -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tciu-LT-kimesurface.Rmd’ + ... + > require(ggplot2) + + > sample_save[[1]] + + > sample_save[[2]] + + When sourcing ‘tciu-LT-kimesurface.R’: + ... + + > fmri_image(fmri_generate$fmri_data, option = "manually", + + voxel_location = c(40, 22, 33), time = 4) + + When sourcing ‘tciu-fMRI-analytics.R’: + Error: subscript out of bounds + Execution halted + + ‘tciu-LT-kimesurface.Rmd’ using ‘UTF-8’... failed + ‘tciu-fMRI-analytics.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘tciu-LT-kimesurface.Rmd’ using rmarkdown + + Quitting from lines 159-160 [unnamed-chunk-5] (tciu-LT-kimesurface.Rmd) + Error: processing vignette 'tciu-LT-kimesurface.Rmd' failed with diagnostics: + unused arguments (list(1, 2), list(list("black", 0.727272727272727, 1, "butt", FALSE, TRUE), list("white", "black", 0.727272727272727, 1, TRUE), list("", "plain", "black", 16, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(4, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 4, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 4, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, + NULL, 1, -90, NULL, c(0, 0, 0, 4), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(3.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 3.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 3.2, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 3.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, + NULL, NULL, c(0, 3.2, 0, 3.2), NULL, TRUE), list("grey20", NULL, NULL, NULL, FALSE, TRUE), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 4, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), c(8, 8, 8, 8), 16, NULL, NULL, NULL, 1.2, NULL, NULL, 8, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, + NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, "bold", "black", 14, 0, NULL, NULL, NULL, NULL, NULL, FALSE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), list(), 16, list("grey92", NA, NULL, NULL, TRUE), list(), 8, NULL, NULL, list("white", NULL, NULL, NULL, FALSE, TRUE), NULL, list(NULL, 0.5, NULL, NULL, FALSE, TRUE), NULL, list(), NULL, list(), FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0.5, 1, NULL, + ... + Quitting from lines 184-185 [unnamed-chunk-5] (tciu-fMRI-analytics.Rmd) + Error: processing vignette 'tciu-fMRI-analytics.Rmd' failed with diagnostics: + subscript out of bounds + --- failed re-building ‘tciu-fMRI-analytics.Rmd’ + + SUMMARY: processing the following files failed: + ‘tciu-LT-kimesurface.Rmd’ ‘tciu-fMRI-analytics.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 14.1Mb + sub-directories of 1Mb or more: + data 1.5Mb + doc 12.0Mb + ``` + +# tcpl + +
+ +* Version: 3.1.0 +* GitHub: https://github.com/USEPA/CompTox-ToxCast-tcpl +* Source code: https://github.com/cran/tcpl +* Date/Publication: 2023-10-06 19:50:02 UTC +* Number of recursive dependencies: 117 + +Run `revdepcheck::cloud_details(, "tcpl")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 20. │ └─grid:::grid.draw.grob(x$children[[i]], recording = FALSE) + 21. │ └─grDevices::recordGraphics(drawGrob(x), list(x = x), getNamespace("grid")) + 22. └─grid:::drawGrob(x) + 23. ├─grid::drawDetails(x, recording = FALSE) + 24. └─grid:::drawDetails.polyline(x, recording = FALSE) + 25. └─grid:::grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) + + [ FAIL 2 | WARN 4 | SKIP 3 | PASS 55 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Data_processing-Archive_tcpl_v2.Rmd’ + ... + Loaded L4 AEID2 (7 rows; 0.03 secs) + Processed L5 AEID2 (7 rows; 0.08 secs) + Writing level 5 data for 2 ids... + Completed delete cascade for 2 ids (0.03 secs) + Writing level 5 complete. (0.03 secs) + Loaded L5 AEID1 (6 rows; 0.11 secs) + + When sourcing ‘Data_processing-Archive_tcpl_v2.R’: + Error: attempt to apply non-function + Execution halted + + ‘Assay_Registration.Rmd’ using ‘UTF-8’... OK + ‘Data_processing-Archive_tcpl_v2.Rmd’ using ‘UTF-8’... failed + ‘Data_processing.Rmd’ using ‘UTF-8’... OK + ‘Data_retrieval.Rmd’ using ‘UTF-8’... OK + ‘Introduction_Appendices.Rmd’ using ‘UTF-8’... OK + ``` + +# tern + +
+ +* Version: 0.9.5 +* GitHub: https://github.com/insightsengineering/tern +* Source code: https://github.com/cran/tern +* Date/Publication: 2024-06-21 04:40:06 UTC +* Number of recursive dependencies: 109 + +Run `revdepcheck::cloud_details(, "tern")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tern-Ex.R’ failed + The error most likely occurred in: + + > ### Name: g_km + > ### Title: Kaplan-Meier plot + > ### Aliases: g_km kaplan_meier + > + > ### ** Examples + > + > library(dplyr) + ... + + control_surv = control_surv_timepoint(conf_level = 0.9), + + col = c("grey25", "grey50", "grey75"), + + annot_at_risk_title = FALSE, + + lty = 1:3, + + font_size = 8 + + ) + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 9.8Mb + sub-directories of 1Mb or more: + R 1.5Mb + doc 4.5Mb + help 3.3Mb + ``` + +# thematic + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/rstudio/thematic +* Source code: https://github.com/cran/thematic +* Date/Publication: 2024-07-29 15:50:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "thematic")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘thematic-Ex.R’ failed + The error most likely occurred in: + + > ### Name: sequential_gradient + > ### Title: Control parameters of the sequential colorscale + > ### Aliases: sequential_gradient + > + > ### ** Examples + > + > + > # Gradient from fg to accent + > fg <- sequential_gradient(1, 0) + > thematic_on("black", "white", "salmon", sequential = fg) + > ggplot2::qplot(1:10, 1:10, color = 1:10) + Warning: `qplot()` was deprecated in ggplot2 3.4.0. + Error in adjust_color(user_default$colour, bg, fg, accent) : + Internal error: adjust_color() expects an input of length 1 + Calls: ... -> -> update_defaults -> adjust_color + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(thematic) + > + > test_check("thematic") + [ FAIL 9 | WARN 1 | SKIP 7 | PASS 27 ] + + ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ + ... + 10. └─base::Map(...) + 11. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 12. └─thematic (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) + 13. ├─ggplot2::update_geom_defaults(...) + 14. │ └─ggplot2:::update_defaults(geom, "Geom", new, env = parent.frame()) + 15. └─thematic:::adjust_color(user_default$colour, bg, fg, accent) + + [ FAIL 9 | WARN 1 | SKIP 7 | PASS 27 ] + Error: Test failures + Execution halted + ``` + +# Thermistor + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/Thermistor +* Date/Publication: 2024-04-05 15:43:02 UTC +* Number of recursive dependencies: 28 + +Run `revdepcheck::cloud_details(, "Thermistor")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Thermistor-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_voltageCurve + > ### Title: Plot the V-DeltaT Curve + > ### Aliases: plot_voltageCurve + > + > ### ** Examples + > + > ### only target curve + ... + > ThVal <- CompValues$ThVal + > ThBeta <- CompValues$ThBeta + > Vnew <- voltageCurve(Tdata, R_id, Res, ThVal, ThBeta) + > plot_voltageCurve(Tdata, OnlyTarget = FALSE, Pdata = Vnew) + Warning in ggplot2::geom_line(ggplot2::aes(x = xid, y = Vdata, colour = "target", : + Ignoring unknown aesthetics: shape + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# tidybayes + +
+ +* Version: 3.0.6 +* GitHub: https://github.com/mjskay/tidybayes +* Source code: https://github.com/cran/tidybayes +* Date/Publication: 2023-08-12 23:30:02 UTC +* Number of recursive dependencies: 200 + +Run `revdepcheck::cloud_details(, "tidybayes")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tidybayes-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compare_levels + > ### Title: Compare the value of draws of some variable from a Bayesian + > ### model for different levels of a factor + > ### Aliases: compare_levels + > ### Keywords: manip + > + > ### ** Examples + ... + 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) + 13. │ └─l$compute_geom_2(d, theme = plot$theme) + 14. │ └─ggplot2 (local) compute_geom_2(..., self = self) + 15. │ └─self$geom$use_defaults(...) + 16. └─base::.handleSimpleError(...) + 17. └─rlang (local) h(simpleError(msg, call)) + 18. └─handlers[[1L]](cnd) + 19. └─cli::cli_abort(...) + 20. └─rlang::abort(...) + Execution halted + ``` + +## In both + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This is necessary because some tests fail otherwise; see https://github.com/hadley/testthat/issues/144 + > Sys.setenv("R_TESTS" = "") + > + > library(testthat) + > library(tidybayes) + > + > test_check("tidybayes") + ... + • test.geom_interval/grouped-intervals-h-stat.svg + • test.geom_pointinterval/grouped-pointintervals-h-stat.svg + • test.stat_dist_slabinterval/ccdfintervalh-using-args.svg + • test.stat_eye/one-parameter-horizontal-eye-mode-hdi.svg + • test.stat_eye/one-parameter-horizontal-half-eye.svg + • test.stat_eye/one-parameter-vertical-eye.svg + • test.stat_eye/one-parameter-vertical-halfeye.svg + • test.stat_eye/two-parameter-factor-horizontal-eye-fill.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tidy-brms.Rmd’ + ... + + ]) %>% median_qi(condition_mean = b_Intercept + r_condition, + + .width = c(0.95, 0 .... [TRUNCATED] + + When sourcing ‘tidy-brms.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ... + + When sourcing ‘tidybayes.R’: + Error: error in evaluating the argument 'object' in selecting a method for function 'sampling': object 'ABC_stan' not found + Execution halted + + ‘tidy-brms.Rmd’ using ‘UTF-8’... failed + ‘tidy-posterior.Rmd’ using ‘UTF-8’... failed + ‘tidy-rstanarm.Rmd’ using ‘UTF-8’... failed + ‘tidybayes-residuals.Rmd’ using ‘UTF-8’... failed + ‘tidybayes.Rmd’ using ‘UTF-8’... failed + ``` + +# tidycat + +
+ +* Version: 0.1.2 +* GitHub: https://github.com/guyabel/tidycat +* Source code: https://github.com/cran/tidycat +* Date/Publication: 2021-08-02 04:20:01 UTC +* Number of recursive dependencies: 70 + +Run `revdepcheck::cloud_details(, "tidycat")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tidycat-Ex.R’ failed + The error most likely occurred in: + + > ### Name: tidy_categorical + > ### Title: Expand broom::tidy() Outputs for Categorical Parameter Estimates + > ### Aliases: tidy_categorical + > + > ### ** Examples + > + > # strip ordering in factors (currently ordered factor not supported) + ... + > ggplot(data = d0, + + mapping = aes(x = level, colour = reference, + + y = estimate, ymin = conf.low, ymax = conf.high)) + + + facet_row(facets = vars(variable), scales = "free_x", space = "free") + + + geom_hline(yintercept = 0, linetype = "dashed") + + + geom_pointrange() + + + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + Error in space$x : $ operator is invalid for atomic vectors + Calls: ... -> draw_panels -> -> init_gtable + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘intro.Rmd’ + ... + + > library(ggforce) + + > ggplot(data = d0, mapping = aes(x = level, y = estimate, + + colour = reference, ymin = conf.low, ymax = conf.high)) + + + facet_col(facets = .... [TRUNCATED] + + When sourcing ‘intro.R’: + Error: $ operator is invalid for atomic vectors + Execution halted + + ‘intro.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘intro.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘tidyr’ + All declared Imports should be used. + ``` + +# tidyCDISC + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/Biogen-Inc/tidyCDISC +* Source code: https://github.com/cran/tidyCDISC +* Date/Publication: 2023-03-16 14:20:02 UTC +* Number of recursive dependencies: 141 + +Run `revdepcheck::cloud_details(, "tidyCDISC")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(tidyCDISC) + > library(shinyjs) + + Attaching package: 'shinyjs' + + ... + 6. ├─plotly::config(...) + 7. │ └─plotly:::modify_list(p$x$config, args) + 8. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...) + 9. │ │ └─base::stopifnot(is.list(x), is.list(val)) + 10. │ └─x %||% list() + 11. └─plotly::layout(...) + + [ FAIL 1 | WARN 1 | SKIP 15 | PASS 91 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.5Mb + sub-directories of 1Mb or more: + R 1.5Mb + data 2.0Mb + doc 1.8Mb + ``` + +# tidydr + +
+ +* Version: 0.0.5 +* GitHub: https://github.com/YuLab-SMU/tidydr +* Source code: https://github.com/cran/tidydr +* Date/Publication: 2023-03-08 09:20:02 UTC +* Number of recursive dependencies: 79 + +Run `revdepcheck::cloud_details(, "tidydr")` for more info + +
+ +## Newly broken + +* checking whether package ‘tidydr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel -# inTextSummaryTable (default access) - -# inventorize (unknown) - -``` -#
-# -# * Version: 1.1.1 -# * GitHub: NA -# * Source code: https://github.com/cran/inventorize -# * Date/Publication: 2022-05-31 22:20:09 UTC -# * Number of recursive dependencies: 71 -# -# Run `revdepcheck::cloud_details(, "inventorize")` for more info -# -#
-# -# ## Newly broken -# -# * checking whether package ‘inventorize’ can be installed ... ERROR -# ``` -# Installation failed. -# See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details. -# ``` -# -# ## Installation -# -# ### Devel -# -# ``` -# * installing *source* package ‘inventorize’ ... -# ** package ‘inventorize’ successfully unpacked and MD5 sums checked -# ** using staged installation -# ** R -# ** byte-compile and prepare package for lazy loading -# Error in pm[[2]] : subscript out of bounds -# Error: unable to load R code in package ‘inventorize’ -# Execution halted -# ERROR: lazy loading failed for package ‘inventorize’ -# * removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’ -# -# -# ``` -# ### CRAN -# -# ``` -# * installing *source* package ‘inventorize’ ... -# ** package ‘inventorize’ successfully unpacked and MD5 sums checked -# ** using staged installation -# ** R -# ** byte-compile and prepare package for lazy loading -# Warning in qgamma(service_level, alpha, beta) : NaNs produced -# Warning in qgamma(service_level, alpha, beta) : NaNs produced -# ** help -# *** installing help indices -# ** building package indices -# ** testing if installed package can be loaded from temporary location -# ** testing if installed package can be loaded from final location -# ** testing if installed package keeps a record of temporary installation path -# * DONE (inventorize) -# -# -# ``` ``` -# karel (gganimate) - -# kDGLM (plotly) - -# latentcor (plotly) - -# lcars (device issue) - -# lemon (resolve theme) - -# lfproQC (plotly) - -# LMoFit (saved to disk) - -# manydata (plot slots) - -# MARVEL (ggnewscale) - -# MBNMAdose (cannot reproduce) - -# MBNMAtime (ggdist) - -# MetaNet (ggnewscale) - -# metR (fixed in dev) - -# migraph (missing labels) - -# MiMIR (plotly) +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in get(x, envir = ns, inherits = FALSE) : + object 'len0_null' not found +Error: unable to load R code in package ‘tidydr’ +Execution halted +ERROR: lazy loading failed for package ‘tidydr’ +* removing ‘/tmp/workdir/tidydr/new/tidydr.Rcheck/tidydr’ -# miRetrieve (plotly) - -# misspi (plotly) - -# mizer (cannot reproduce) - -# mlr3spatiotempcv (patchwork) - -# mlr3viz (patchwork) - -# modeltime.resample (plotly) - -# move (false positive) - -# mtb (missing labels) - -# neatmaps (plotly) - -# NetFACS (false positive) - -# NeuralSens (ggnewscale) - -# NHSRplotthedots (missing labels) - -# NIMAA (plotly) - -# OBIC (patchwork) - -# OmicNavigator (plotly) - -# oncomsm (patchwork) - -# pafr (missing labels) - -# patchwork (patchwork) - -# pathviewr (missing labels) - -# pcutils (patchwork) - -# pdxTrees (gganimate) - -# personalized (plotly) - -# phylepic (ggnewscale) - -# Plasmidprofiler (plotly) - -# platetools (faulty tests) - -# plotDK (missing labels) - -# plotly (plotly) - -# pmartR (unknown) ``` -#
-# -# * Version: 2.4.5 -# * GitHub: https://github.com/pmartR/pmartR -# * Source code: https://github.com/cran/pmartR -# * Date/Publication: 2024-05-21 15:50:02 UTC -# * Number of recursive dependencies: 149 -# -# Run `revdepcheck::cloud_details(, "pmartR")` for more info -# -#
-# -# ## Newly broken -# -# * checking tests ... ERROR -# ``` -# Running ‘testthat.R’ -# Running the tests in ‘tests/testthat.R’ failed. -# Complete output: -# > library(testthat) -# > library(pmartR) -# > -# > test_check("pmartR") -# [ FAIL 1 | WARN 1 | SKIP 11 | PASS 2375 ] -# -# ══ Skipped tests (11) ══════════════════════════════════════════════════════════ -# ... -# • plots/plot-spansres-color-high-color-low.svg -# • plots/plot-spansres.svg -# • plots/plot-statres-anova-volcano.svg -# • plots/plot-statres-anova.svg -# • plots/plot-statres-combined-volcano.svg -# • plots/plot-statres-combined.svg -# • plots/plot-statres-gtest.svg -# • plots/plot-totalcountfilt.svg -# Error: Test failures -# Execution halted -# ``` -# -# ## In both -# -# * checking installed package size ... NOTE -# ``` -# installed size is 10.4Mb -# sub-directories of 1Mb or more: -# R 1.5Mb -# help 1.5Mb -# libs 6.3Mb -# ``` -``` - -# pmxTools (ggdist) - -# posterior (ggdist) - -# PPQplan (plotly) - -# ppseq (plotly) - -# precrec (patchwork) - -# priorsense (ggdist) - -# ProAE (ggnewscale) - -# probably (missing labels) - -# processmapR (plotly) - -# psborrow (missing labels) - -# r2dii.plot (missing labels) - -# Radviz (accessing defaults) - -# rassta (plotly) - -# REddyProc (false positive) - -# redist (patchwork) - -# reReg (length 0 width) - -# reservr (patchwork) - -# rKOMICS (unknown) +### CRAN ``` -#
-# -# * Version: 1.3 -# * GitHub: NA -# * Source code: https://github.com/cran/rKOMICS -# * Date/Publication: 2023-06-29 22:40:03 UTC -# * Number of recursive dependencies: 128 -# -# Run `revdepcheck::cloud_details(, "rKOMICS")` for more info -# -#
-# -# ## Newly broken -# -# * checking examples ... ERROR -# ``` -# Running examples in ‘rKOMICS-Ex.R’ failed -# The error most likely occurred in: -# -# > ### Name: msc.pca -# > ### Title: Prinicple Component Analysis based on MSC -# > ### Aliases: msc.pca -# > -# > ### ** Examples -# > -# > data(matrices) -# ... -# 11. │ └─base::withCallingHandlers(...) -# 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) -# 13. └─l$compute_geom_2(d, theme = plot$theme) -# 14. └─ggplot2 (local) compute_geom_2(..., self = self) -# 15. └─self$geom$use_defaults(...) -# 16. └─ggplot2 (local) use_defaults(..., self = self) -# 17. └─ggplot2:::check_aesthetics(new_params, nrow(data)) -# 18. └─cli::cli_abort(...) -# 19. └─rlang::abort(...) -# Execution halted -# ``` -# -# ## In both -# -# * checking installed package size ... NOTE -# ``` -# installed size is 24.8Mb -# sub-directories of 1Mb or more: -# extdata 24.0Mb -# ``` -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘example.Rnw’ using Sweave -# Loading required package: viridisLite -# Warning: Removed 95 rows containing non-finite outside the scale range -# (`stat_boxplot()`). -# Warning: Removed 89 rows containing non-finite outside the scale range -# (`stat_boxplot()`). -# Warning: Removed 149 rows containing non-finite outside the scale range -# (`stat_boxplot()`). -# Warning: Removed 286 rows containing non-finite outside the scale range -# ... -# l.5 \usepackage -# {xcolor}^^M -# ! ==> Fatal error occurred, no output PDF file produced! -# --- failed re-building ‘example.Rnw’ -# -# SUMMARY: processing the following file failed: -# ‘example.Rnw’ -# -# Error: Vignette re-building failed. -# Execution halted -# ``` -``` - -# RKorAPClient (missing labels) - -# RNAseqQC (patchwork) - -# roahd (plotly) +* installing *source* package ‘tidydr’ ... +** package ‘tidydr’ successfully unpacked and MD5 sums checked +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +** help +*** installing help indices +** building package indices +** installing vignettes +** testing if installed package can be loaded from temporary location +** testing if installed package can be loaded from final location +** testing if installed package keeps a record of temporary installation path +* DONE (tidydr) -# romic (plotly) -# roptions (plotly) - -# santaR (plot slots) - -# scdtb (missing labels) - -# scoringutils (ggdist) - -# scUtils (missing labels) - -# SCVA (plotly) - -# SDMtune (missing labels) - -# SeaVal (plotly) - -# sgsR (missing labels) - -# SHAPforxgboost (ggforce) - -# SHELF (unknown) - -``` -#
-# -# * Version: 1.10.0 -# * GitHub: https://github.com/OakleyJ/SHELF -# * Source code: https://github.com/cran/SHELF -# * Date/Publication: 2024-05-07 14:20:03 UTC -# * Number of recursive dependencies: 126 -# -# Run `revdepcheck::cloud_details(, "SHELF")` for more info -# -#
-# -# ## Newly broken -# -# * checking re-building of vignette outputs ... NOTE -# ``` -# Error(s) in re-building vignettes: -# --- re-building ‘Dirichlet-elicitation.Rmd’ using rmarkdown -# ``` ``` - -# shinipsum (plot slots) - -# SimNPH (missing labels) - -# smallsets (patchwork) - -# spbal (empty sf) - -# spinifex (plotly) - -# sport (missing labels) - -# SqueakR (false positive) - -# statgenGWAS (device issue) - -# surveyexplorer (ggupset) - -# Sysrecon (patchwork) - -# tabledown (plotly) - -# TCIU (plotly) - -# tensorEVD (ggnewscale) - -# thematic (thematic) - -# tidybayes (ggdist) - -# tidycat (ggforce) - -# tidyCDISC (plotly) - -# tidydr (uses internals) - -# tidysdm (patchwork) - -# tidytreatment (ggdist) - -# timetk (plotly) - -# tinyarray (patchwork) - -# tornado (length 0 width) - -# TOSTER (ggdist) - -# TreatmentPatterns (plotly) - -# trelliscopejs (plotly) - -# tricolore (ggtern) - -# triptych (patchwork) - -# tsnet (ggdist) - -# umiAnalyzer (plotly) - -# valr (missing labels) - -# vivaldi (plotly) - -# vivid (ggnewscale) - -# vvshiny (plotly) - -# wilson (plotly) - -# xaringanthemer (default access) - -# yamlet (missing labels) +# tidysdm + +
+ +* Version: 0.9.5 +* GitHub: https://github.com/EvolEcolGroup/tidysdm +* Source code: https://github.com/cran/tidysdm +* Date/Publication: 2024-06-23 19:40:02 UTC +* Number of recursive dependencies: 180 + +Run `revdepcheck::cloud_details(, "tidysdm")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘a0_tidysdm_overview.Rmd’ + ... + > climate_vars <- names(climate_present) + + > lacerta_thin <- lacerta_thin %>% bind_cols(terra::extract(climate_present, + + lacerta_thin, ID = FALSE)) + + > lacerta_thin %>% plot_pres_vs_bg(class) + + When sourcing ‘a0_tidysdm_overview.R’: + Error: object is not a unit + Execution halted + + ‘a0_tidysdm_overview.Rmd’ using ‘UTF-8’... failed + ‘a1_palaeodata_application.Rmd’ using ‘UTF-8’... OK + ‘a2_tidymodels_additions.Rmd’ using ‘UTF-8’... OK + ‘a3_troubleshooting.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘a0_tidysdm_overview.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + data 2.5Mb + doc 2.0Mb + ``` + +# tidySEM + +
+ +* Version: 0.2.7 +* GitHub: https://github.com/cjvanlissa/tidySEM +* Source code: https://github.com/cran/tidySEM +* Date/Publication: 2024-06-04 09:46:01 UTC +* Number of recursive dependencies: 229 + +Run `revdepcheck::cloud_details(, "tidySEM")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tidySEM-Ex.R’ failed + The error most likely occurred in: + + > ### Name: edit_graph + > ### Title: Edit graph elements + > ### Aliases: edit_graph edit_nodes edit_edges + > + > ### ** Examples + > + > p <- prepare_graph(layout = get_layout("x", rows = 1)) + > p <- edit_graph(p, {colour = "blue"}, element = "nodes") + > plot(p) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(tidySEM) + Loading required package: OpenMx + To take full advantage of multiple cores, use: + mxOption(key='Number of Threads', value=parallel::detectCores()) #now + Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx) + Registered S3 method overwritten by 'tidySEM': + ... + 4. └─tidySEM:::.plot_edges_internal(p, df_edges) + 5. └─ggplot2:::`+.gg`(p, do.call(geom_path, argslist)) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 17 | WARN 1 | SKIP 6 | PASS 65 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Plotting_graphs.Rmd’ + ... + + > suppressWarnings({ + + HS.model <- " visual =~ x1 + x2 + x3\n textual =~ x4 + x5 + x6\n speed =~ x7 + x8 + x9 " + + .... [TRUNCATED] + + > p <- graph_sem(model = fit, text_size = 2, fix_coord = TRUE) + + ... + + ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK + ‘Plotting_graphs.Rmd’ using ‘UTF-8’... failed + ‘SMART_LCA_checklist.Rmd’ using ‘UTF-8’... OK + ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK + ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK + ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK + ‘lca_lcga.Rmd’ using ‘UTF-8’... OK + ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK + ‘sem_graph.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Generating_syntax.Rmd’ using rmarkdown + --- finished re-building ‘Generating_syntax.Rmd’ + + --- re-building ‘Plotting_graphs.Rmd’ using rmarkdown + + Quitting from lines 77-80 [unnamed-chunk-5] (Plotting_graphs.Rmd) + Error: processing vignette 'Plotting_graphs.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘Plotting_graphs.Rmd’ + ... + Quitting from lines 48-51 [unnamed-chunk-3] (sem_graph.Rmd) + Error: processing vignette 'sem_graph.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘sem_graph.Rmd’ + + SUMMARY: processing the following files failed: + ‘Plotting_graphs.Rmd’ ‘sem_graph.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# tidytreatment + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/bonStats/tidytreatment +* Source code: https://github.com/cran/tidytreatment +* Date/Publication: 2022-02-21 09:00:07 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "tidytreatment")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘use-tidytreatment-BART.Rmd’ + ... + + by = ".row") %>% ggplot() + stat_halfeye(aes(x = z, y = fit)) + + + facet_wrap(~c1, l .... [TRUNCATED] + + When sourcing ‘use-tidytreatment-BART.R’: + Error: Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, + Execution halted + + ‘use-tidytreatment-BART.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘use-tidytreatment-BART.Rmd’ using rmarkdown + + Quitting from lines 163-177 [plot-tidy-bart] (use-tidytreatment-BART.Rmd) + Error: processing vignette 'use-tidytreatment-BART.Rmd' failed with diagnostics: + Problem while setting up geom aesthetics. + ℹ Error occurred in the 1st layer. + Caused by error in `use_defaults()`: + ! unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, + ... + NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list("white", NA, NULL, NULL, TRUE), list(NULL, "grey20", NULL, NULL, TRUE), NULL, NULL, NULL, list("grey92", + NULL, NULL, NULL, FALSE, "grey92", TRUE), NULL, list(NULL, 0.5, NULL, NULL, FALSE, NULL, TRUE), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, TRUE), "topleft", + NULL, NULL, list("grey85", "grey20", NULL, NULL, TRUE), NULL, NULL, "on", "inside", list(NULL, NULL, "grey10", 0.8, NULL, NULL, NULL, NULL, c(4.4, 4.4, 4.4, 4.4), NULL, TRUE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + --- failed re-building ‘use-tidytreatment-BART.Rmd’ + + SUMMARY: processing the following file failed: + ‘use-tidytreatment-BART.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package which this enhances but not available for checking: ‘bartMachine’ + ``` + +# timeplyr + +
+ +* Version: 0.8.2 +* GitHub: https://github.com/NicChr/timeplyr +* Source code: https://github.com/cran/timeplyr +* Date/Publication: 2024-08-17 13:40:02 UTC +* Number of recursive dependencies: 83 + +Run `revdepcheck::cloud_details(, "timeplyr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘timeplyr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: time_ggplot + > ### Title: Quick time-series ggplot + > ### Aliases: time_ggplot + > + > ### ** Examples + > + > library(dplyr) + ... + > data.table::setDTthreads(threads = 2L) + > collapse::set_collapse(nthreads = 1L) + > ## End(Don't show) + > # It's as easy as this + > AirPassengers %>% + + ts_as_tibble() %>% + + time_ggplot(time, value) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: %>% ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# timetk + +
+ +* Version: 2.9.0 +* GitHub: https://github.com/business-science/timetk +* Source code: https://github.com/cran/timetk +* Date/Publication: 2023-10-31 22:30:02 UTC +* Number of recursive dependencies: 205 + +Run `revdepcheck::cloud_details(, "timetk")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 7. └─timetk:::plot_time_series.grouped_df(...) + 8. ├─timetk::plot_time_series(...) + 9. └─timetk:::plot_time_series.data.frame(...) + 10. ├─plotly::ggplotly(g, dynamicTicks = TRUE) + 11. └─plotly:::ggplotly.ggplot(g, dynamicTicks = TRUE) + 12. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 406 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2750 marked UTF-8 strings + ``` + +# tinyarray + +
+ +* Version: 2.4.2 +* GitHub: https://github.com/xjsun1221/tinyarray +* Source code: https://github.com/cran/tinyarray +* Date/Publication: 2024-06-13 14:20:02 UTC +* Number of recursive dependencies: 243 + +Run `revdepcheck::cloud_details(, "tinyarray")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tinyarray-Ex.R’ failed + The error most likely occurred in: + + > ### Name: box_surv + > ### Title: box_surv + > ### Aliases: box_surv + > + > ### ** Examples + > + > if(requireNamespace("ggpubr",quietly = TRUE)) { + + k = box_surv(log2(exp_hub1+1),exprSet_hub1,meta1);k[[1]] + + }else{ + + warning("Package 'ggpubr' needed for this function to work. + + Please install it by install.packages('ggpubr')") + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: box_surv ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘ComplexHeatmap’ + ``` + +# tipmap + +
+ +* Version: 0.5.2 +* GitHub: https://github.com/Boehringer-Ingelheim/tipmap +* Source code: https://github.com/cran/tipmap +* Date/Publication: 2023-08-14 10:30:03 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "tipmap")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘introduction.Rmd’ + ... + + MAP Prior MCMC sample: + mean sd 2.5% 50% 97.5% + theta_resp_pred 1.43 0.356 0.661 1.44 2.1 + + > plot(map_mcmc)$forest_model + + When sourcing ‘introduction.R’: + Error: argument is of length zero + Execution halted + + ‘expert_elicitation.Rmd’ using ‘UTF-8’... OK + ‘introduction.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘expert_elicitation.Rmd’ using rmarkdown + ``` + +# tornado + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/bertcarnell/tornado +* Source code: https://github.com/cran/tornado +* Date/Publication: 2024-01-21 17:30:02 UTC +* Number of recursive dependencies: 114 + +Run `revdepcheck::cloud_details(, "tornado")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tornado-Ex.R’ failed + The error most likely occurred in: + + > ### Name: importance.cv.glmnet + > ### Title: Plot Variable Importance for a GLMNET model + > ### Aliases: importance.cv.glmnet + > + > ### ** Examples + > + > if (requireNamespace("glmnet", quietly = TRUE)) + ... + + form <- formula(mpg ~ cyl*wt*hp) + + mf <- model.frame(form, data = mtcars) + + mm <- model.matrix(mf, mf) + + gtest <- glmnet::cv.glmnet(x = mm, y = mtcars$mpg, family = "gaussian") + + imp <- importance(gtest, mtcars, form, nperm = 50) + + plot(imp) + + } + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > if (require(testthat)) + + { + + library(tornado) + + + + test_check("tornado") + + } + Loading required package: testthat + ... + 2. └─tornado:::plot.tornado_plot(torn, plot = FALSE, xlabel = "Probability of Class 1") + 3. └─ggplot2:::`+.gg`(...) + 4. └─ggplot2:::add_ggplot(e1, e2, e2name) + 5. ├─ggplot2::ggplot_add(object, p, objectname) + 6. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 7. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 28 | WARN 14 | SKIP 0 | PASS 86 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘tornadoVignette.Rmd’ + ... + > lm1 <- lm(mpg ~ cyl * wt * hp, data = mtcars) + + > torn1 <- tornado::tornado(lm1, type = "PercentChange", + + alpha = 0.1) + + > plot(torn1, xlabel = "MPG", geom_bar_control = list(width = 0.4)) + + When sourcing ‘tornadoVignette.R’: + Error: argument is of length zero + Execution halted + + ‘tornadoVignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘tornadoVignette.Rmd’ using rmarkdown + + Quitting from lines 106-109 [lm1] (tornadoVignette.Rmd) + Error: processing vignette 'tornadoVignette.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘tornadoVignette.Rmd’ + + SUMMARY: processing the following file failed: + ‘tornadoVignette.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# TOSTER + +
+ +* Version: 0.8.3 +* GitHub: NA +* Source code: https://github.com/cran/TOSTER +* Date/Publication: 2024-05-08 16:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "TOSTER")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TOSTER-Ex.R’ failed + The error most likely occurred in: + + > ### Name: dataTOSTone + > ### Title: TOST One Sample T-Test + > ### Aliases: dataTOSTone + > + > ### ** Examples + > + > library("TOSTER") + ... + N Mean Median SD SE + ───────────────────────────────────────────────────────────────────────── + Sepal.Width 150 3.057333 3.000000 0.4358663 0.03558833 + ───────────────────────────────────────────────────────────────────────── + + Error in use_defaults(..., self = self) : + unused argument (theme = list(list("black", 0.727272727272727, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.727272727272727, 1, TRUE), list("", "plain", "black", 16, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.727272727272727, 0.727272727272727, 1, 1, "", 5.62335685623357, 2.18181818181818, 19, TRUE), 8, c(8, 8, 8, 8), NULL, NULL, list(NULL, NULL, "#333333", NULL, NULL, NULL, NULL, + NULL, c(10, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 4, 0), NULL, TRUE), NULL, list(NULL, NULL, "#333333", NULL, NULL, NULL, 90, NULL, c(0, 10, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 4), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, "#333333", NULL, NULL, NULL, NULL, NULL, c(5, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NU + Calls: ... -> -> -> + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(TOSTER) + + Attaching package: 'TOSTER' + + The following object is masked from 'package:testthat': + ... + 26. └─base::Map(...) + 27. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) + 28. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) + 29. └─layer$compute_geom_2(key, single_params, theme) + 30. └─ggplot2 (local) compute_geom_2(..., self = self) + 31. └─self$geom$use_defaults(...) + + [ FAIL 8 | WARN 0 | SKIP 0 | PASS 1034 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘IntroTOSTt.Rmd’ + ... + mean of x mean of y + 0.75 2.33 + + + > plot(res1, type = "cd") + + When sourcing ‘IntroTOSTt.R’: + ... + Error: unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(7, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, "bold", NULL, 11, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(), NULL, list + Execution halted + + ‘IntroTOSTt.Rmd’ using ‘UTF-8’... failed + ‘IntroductionToTOSTER.Rmd’ using ‘UTF-8’... OK + ‘SMD_calcs.Rmd’ using ‘UTF-8’... OK + ‘correlations.Rmd’ using ‘UTF-8’... OK + ‘robustTOST.Rmd’ using ‘UTF-8’... failed + ‘the_ftestTOSTER.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘IntroTOSTt.Rmd’ using rmarkdown + ``` + +# TreatmentPatterns + +
+ +* Version: 2.6.9 +* GitHub: https://github.com/darwin-eu/TreatmentPatterns +* Source code: https://github.com/cran/TreatmentPatterns +* Date/Publication: 2024-09-02 12:40:06 UTC +* Number of recursive dependencies: 142 + +Run `revdepcheck::cloud_details(, "TreatmentPatterns")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + 22. ├─testthat::expect_s3_class(output$charAgePlot$html, "html") at test-CharacterizationPlots.R:50:9 + 23. │ └─testthat::quasi_label(enquo(object), arg = "object") + 24. │ └─rlang::eval_bare(expr, quo_get_env(quo)) + 25. ├─output$charAgePlot + 26. └─shiny:::`$.shinyoutput`(output, charAgePlot) + 27. └─.subset2(x, "impl")$getOutput(name) + + [ FAIL 1 | WARN 39 | SKIP 21 | PASS 138 ] + Error: Test failures + Execution halted + ``` + +# TreatmentSelection + +
+ +* Version: 2.1.1 +* GitHub: NA +* Source code: https://github.com/cran/TreatmentSelection +* Date/Publication: 2017-08-11 18:55:47 UTC +* Number of recursive dependencies: 30 + +Run `revdepcheck::cloud_details(, "TreatmentSelection")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TreatmentSelection-Ex.R’ failed + The error most likely occurred in: + + > ### Name: compare.trtsel + > ### Title: compare the performance of two treatment selection markers + > ### Aliases: compare.trtsel + > + > ### ** Examples + > + > + ... + > # Plot treatment effect curves with pointwise confidence intervals + > ## use more bootstraps in practice + > compare(x = trtsel.Y1, x2 = trtsel.Y2, + + bootstraps = 10, plot = TRUE, + + ci = "horizontal", conf.bands = TRUE) + Bootstrap bias-correction will be implemented to correct for over-optimism bias in estimation. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: compare ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# TreeDep + +
+ +* Version: 0.1.3 +* GitHub: NA +* Source code: https://github.com/cran/TreeDep +* Date/Publication: 2018-12-02 17:50:03 UTC +* Number of recursive dependencies: 32 + +Run `revdepcheck::cloud_details(, "TreeDep")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘TreeDep-Ex.R’ failed + The error most likely occurred in: + + > ### Name: TreeDep_plot + > ### Title: TreeDep_plot - Generates a plot for selected variables and + > ### dates. + > ### Aliases: TreeDep_plot + > + > ### ** Examples + > + ... + + start_day = 25, + + stop_day = 3) + Warning: Removed 12 rows containing missing values or values outside the scale range + (`geom_line()`). + Warning: Removed 12 rows containing missing values or values outside the scale range + (`geom_line()`). + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +# TreeDist + +
+ +* Version: 2.9.1 +* GitHub: https://github.com/ms609/TreeDist +* Source code: https://github.com/cran/TreeDist +* Date/Publication: 2024-09-07 09:20:02 UTC +* Number of recursive dependencies: 229 + +Run `revdepcheck::cloud_details(, "TreeDist")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘treespace.Rmd’ + ... + [1] "Epoch: 3 finished. 212 datapoints changed bestmatch" + [1] "Epoch: 4 started" + [1] "Epoch: 4 finished. 203 datapoints changed bestmatch" + [1] "Epoch: 5 started" + [1] "Epoch: 5 finished. 165 datapoints changed bestmatch" + [1] "---- Esom Training Finished ----" + + ... + + ‘Generalized-RF.Rmd’ using ‘UTF-8’... OK + ‘Robinson-Foulds.Rmd’ using ‘UTF-8’... OK + ‘Using-TreeDist.Rmd’ using ‘UTF-8’... OK + ‘compare-treesets.Rmd’ using ‘UTF-8’... OK + ‘different-leaves.Rmd’ using ‘UTF-8’... OK + ‘information.Rmd’ using ‘UTF-8’... OK + ‘landscapes.Rmd’ using ‘UTF-8’... OK + ‘treespace.Rmd’ using ‘UTF-8’... failed + ‘using-distances.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Generalized-RF.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.7Mb + sub-directories of 1Mb or more: + doc 1.2Mb + libs 5.9Mb + ``` + +# treeheatr + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/trang1618/treeheatr +* Source code: https://github.com/cran/treeheatr +* Date/Publication: 2020-11-19 21:00:03 UTC +* Number of recursive dependencies: 97 + +Run `revdepcheck::cloud_details(, "treeheatr")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘treeheatr-Ex.R’ failed + The error most likely occurred in: + + > ### Name: draw_tree + > ### Title: Draws the conditional decision tree. + > ### Aliases: draw_tree + > + > ### ** Examples + > + > x <- compute_tree(penguins, target_lab = 'species') + > draw_tree(x$dat, x$fit, x$term_dat, x$layout) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: draw_tree ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘explore.Rmd’ + ... + + > library(treeheatr) + + > penguins <- na.omit(penguins) + + > heat_tree(penguins, target_lab = "species") + + When sourcing ‘explore.R’: + Error: argument is of length zero + Execution halted + + ‘explore.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘explore.Rmd’ using rmarkdown + + Quitting from lines 33-36 [unnamed-chunk-2] (explore.Rmd) + Error: processing vignette 'explore.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘explore.Rmd’ + + SUMMARY: processing the following file failed: + ‘explore.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# trelliscopejs + +
+ +* Version: 0.2.6 +* GitHub: https://github.com/hafen/trelliscopejs +* Source code: https://github.com/cran/trelliscopejs +* Date/Publication: 2021-02-01 08:00:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "trelliscopejs")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(trelliscopejs) + > + > test_check("trelliscopejs") + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ] + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ... + 4. └─base::lapply(...) + 5. └─trelliscopejs (local) FUN(X[[i]], ...) + 6. ├─base::do.call(plotly::ggplotly, c(list(p = q), plotly_args)) + 7. ├─plotly (local) ``(p = ``) + 8. └─plotly:::ggplotly.ggplot(p = ``) + 9. └─plotly::gg2list(...) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ] + Error: Test failures + Execution halted + ``` + +# tricolore + +
+ +* Version: 1.2.4 +* GitHub: https://github.com/jschoeley/tricolore +* Source code: https://github.com/cran/tricolore +* Date/Publication: 2024-05-15 15:00:02 UTC +* Number of recursive dependencies: 108 + +Run `revdepcheck::cloud_details(, "tricolore")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘tricolore-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ColorKeySextant + > ### Title: Sextant Scheme Legend + > ### Aliases: ColorKeySextant + > ### Keywords: internal + > + > ### ** Examples + > + ... + 3. ├─ggtern::ggplot_build(x) + 4. └─ggtern:::ggplot_build.ggplot(x) + 5. └─ggtern:::layers_add_or_remove_mask(plot) + 6. └─ggint$plot_theme(plot) + 7. └─ggplot2:::validate_theme(theme) + 8. └─base::mapply(...) + 9. └─ggplot2 (local) ``(...) + 10. └─cli::cli_abort(...) + 11. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘choropleth_maps_with_tricolore.Rmd’ + ... + + > plot_educ <- ggplot(euro_example) + geom_sf(aes(fill = rgb, + + geometry = geometry), size = 0.1) + scale_fill_identity() + + > plot_educ + + When sourcing ‘choropleth_maps_with_tricolore.R’: + Error: The `tern.axis.ticks.length.major` theme element must be a + object. + Execution halted + + ‘choropleth_maps_with_tricolore.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown + + Quitting from lines 61-72 [unnamed-chunk-4] (choropleth_maps_with_tricolore.Rmd) + Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics: + The `tern.axis.ticks.length.major` theme element must be a + object. + --- failed re-building ‘choropleth_maps_with_tricolore.Rmd’ + + SUMMARY: processing the following file failed: + ‘choropleth_maps_with_tricolore.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 2 marked UTF-8 strings + ``` + +# triptych + +
+ +* Version: 0.1.3 +* GitHub: https://github.com/aijordan/triptych +* Source code: https://github.com/cran/triptych +* Date/Publication: 2024-06-13 15:50:02 UTC +* Number of recursive dependencies: 64 + +Run `revdepcheck::cloud_details(, "triptych")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘triptych-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot.triptych + > ### Title: Plot methods for the triptych classes + > ### Aliases: plot.triptych autoplot.triptych plot.triptych_murphy + > ### autoplot.triptych_murphy plot.triptych_reliability + > ### autoplot.triptych_reliability plot.triptych_roc autoplot.triptych_roc + > ### plot.triptych_mcbdsc autoplot.triptych_mcbdsc + > + > ### ** Examples + > + > data(ex_binary, package = "triptych") + > tr <- triptych(ex_binary) + > + > dplyr::slice(tr, 1, 3, 6, 9) |> autoplot() + Error in identicalUnits(x) : object is not a unit + Calls: ... assemble_guides -> guides_build -> unit.c -> identicalUnits + Execution halted + ``` + +# tsnet + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/bsiepe/tsnet +* Source code: https://github.com/cran/tsnet +* Date/Publication: 2024-02-28 11:30:02 UTC +* Number of recursive dependencies: 77 + +Run `revdepcheck::cloud_details(, "tsnet")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(7, 0, 0, 0), NULL, FALSE), list(NULL, NULL, NULL, NULL, NULL, + 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 7, 0, 0), NULL, FALSE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "grey30", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, + NULL, c(0, 2.2, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, c(0, 0, 0, 2.2), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, c(0, 2.2, 0, 2.2), NULL, TRUE), list("grey70", 0.5, NULL, NULL, FALSE, "grey70", TRUE), NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, list(), list("gray70", 0.5, NULL, NULL, + FALSE, "gray70", FALSE), NULL, NULL, list("gray70", 0.5, NULL, NULL, FALSE, "gray70", FALSE), NULL, NULL, NULL, NULL, list(NULL, NA, NULL, NULL, TRUE), NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 0, NULL, NULL, NULL, NULL, NULL, TRUE), NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, list(), 2, list("white", + NA, NULL, NULL, TRUE), list(), NULL, NULL, NULL, list("grey87", NULL, NULL, NULL, FALSE, "grey87", TRUE), list(), list(), NULL, NULL, NULL, NULL, FALSE, list(NULL, "white", NULL, NULL, TRUE), list(NULL, NULL, NULL, 1.2, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, NULL, 0, 1, NULL, NULL, c(0, 0, 5.5, 0), NULL, TRUE), list(NULL, NULL, NULL, 0.8, 1, 1, NULL, NULL, c(5.5, 0, 0, 0), NULL, TRUE), "panel", list(NULL, NULL, NULL, 1.2, 0.5, 0.5, NULL, NULL, NULL, NULL, + TRUE), "topleft", NULL, NULL, list("gray90", NA, NULL, NULL, FALSE), NULL, NULL, "on", "inside", list(NULL, NULL, "black", 0.8, NULL, NULL, NULL, NULL, c(6, 6, 6, 6), NULL, FALSE), NULL, NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, NULL, -90, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, 90, NULL, NULL, NULL, TRUE), NULL, 2.75, 2.75)) + + [ FAIL 1 | WARN 14 | SKIP 0 | PASS 108 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 163.4Mb + sub-directories of 1Mb or more: + libs 162.3Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# UBayFS + +
+ +* Version: 1.0 +* GitHub: https://github.com/annajenul/UBayFS +* Source code: https://github.com/cran/UBayFS +* Date/Publication: 2023-03-07 10:50:02 UTC +* Number of recursive dependencies: 188 + +Run `revdepcheck::cloud_details(, "UBayFS")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘BFS_UBayFS.Rmd’ + ... + ( 21,23,28 ) + ( 21,27,28 ) + ( 21,23,24 ) + + > plot(model) + [1] "Warning: multiple optimal feature sets, plotting first feature set." + + ... + ( 2,3,7,8,14,22,23,26,27,28 ) + + > plot(model) + + When sourcing ‘UBayFS.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘BFS_UBayFS.Rmd’ using ‘UTF-8’... failed + ‘UBayFS.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + ... + --- re-building ‘BFS_UBayFS.Rmd’ using rmarkdown + + Quitting from lines 147-150 [unnamed-chunk-8] (BFS_UBayFS.Rmd) + Error: processing vignette 'BFS_UBayFS.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘BFS_UBayFS.Rmd’ + + --- re-building ‘UBayFS.Rmd’ using rmarkdown + ... + Quitting from lines 306-309 [unnamed-chunk-12] (UBayFS.Rmd) + Error: processing vignette 'UBayFS.Rmd' failed with diagnostics: + invalid line type: must be length 2, 4, 6 or 8 + --- failed re-building ‘UBayFS.Rmd’ + + SUMMARY: processing the following files failed: + ‘BFS_UBayFS.Rmd’ ‘UBayFS.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +# Umatrix + +
+ +* Version: 4.0.1 +* GitHub: NA +* Source code: https://github.com/cran/Umatrix +* Date/Publication: 2024-08-17 06:30:17 UTC +* Number of recursive dependencies: 98 + +Run `revdepcheck::cloud_details(, "Umatrix")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘Umatrix-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plotMatrix + > ### Title: plotMatrix + > ### Aliases: plotMatrix + > + > ### ** Examples + > + > data("Hepta") + ... + 4. └─ggplot2:::ggplot_build.ggplot(x) + 5. └─layout$setup(data, plot$data, plot$plot_env) + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 10. └─ggplot2:::check_logical(expand) + 11. └─ggplot2:::stop_input_type(...) + 12. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +# umiAnalyzer + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/sfilges/umiAnalyzer +* Source code: https://github.com/cran/umiAnalyzer +* Date/Publication: 2021-11-25 08:40:02 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::cloud_details(, "umiAnalyzer")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘umiAnalyzer-Ex.R’ failed + The error most likely occurred in: + + > ### Name: AmpliconPlot + > ### Title: Generate Amplicon plots + > ### Aliases: AmpliconPlot + > + > ### ** Examples + > + > library(umiAnalyzer) + ... + > + > main = system.file('extdata', package = 'umiAnalyzer') + > samples <- list.dirs(path = main, full.names = FALSE, recursive = FALSE) + > simsen <- createUmiExperiment(experimentName = 'example',mainDir = main,sampleNames = samples) + > simsen <- filterUmiObject(simsen) + > + > amplicon_plot <- AmpliconPlot(simsen) + Error in pm[[2]] : subscript out of bounds + Calls: AmpliconPlot -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +# UnalR + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/estadisticaun/UnalR +* Source code: https://github.com/cran/UnalR +* Date/Publication: 2024-05-25 17:20:05 UTC +* Number of recursive dependencies: 168 + +Run `revdepcheck::cloud_details(, "UnalR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘UnalR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: Plot.Apiladas + > ### Title: Cree un gráfico de barras apiladas dinámico/estático y flexible + > ### Aliases: Plot.Apiladas + > + > ### ** Examples + > + > ## Don't show: + ... + + legend.direction = "vertical"), gg.Bar = list(width = 0.6, color = "#000000"), + + gg.Texto = list(subtitle = "»»»", tag = "®", caption = "Información Disponible desde 2009-1"))) + Warning: + ¡Ha ingresado un dataframe que no está de forma condensada, es decir, + para cada categoría existe más de un valor para un mismo punto del eje X! + Se sumará los valores por defectos para dichos puntos que gocen de +1 valor + + Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(UnalR) + > + > test_check("UnalR") + Starting 2 test processes + [ FAIL 2 | WARN 4 | SKIP 1 | PASS 50 ] + + ... + 7. └─UnalR::Plot.Series(...) + 8. └─ggplot2:::`+.gg`(...) + 9. └─ggplot2:::add_ggplot(e1, e2, e2name) + 10. ├─ggplot2::ggplot_add(object, p, objectname) + 11. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 12. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 2 | WARN 4 | SKIP 1 | PASS 50 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 7.0Mb + sub-directories of 1Mb or more: + R 2.3Mb + data 2.0Mb + help 2.6Mb + ``` + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 312859 marked UTF-8 strings + ``` + +# unmconf + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/unmconf +* Date/Publication: 2024-09-09 22:00:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "unmconf")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘unmconf.Rmd’ + ... + 9 -1.05 1 5.63 -0.447 1 1 1.55 TRUE TRUE + 10 0.620 0 1.66 -1.71 1 1 1.37 TRUE TRUE + + > bayesplot::mcmc_intervals(unm_mod, prob_outer = 0.95, + + regex_pars = "(beta|lambda|gamma|delta|zeta).+") + geom_point(aes(value, + + name), .... [TRUNCATED] + + When sourcing ‘unmconf.R’: + Error: argument is of length zero + Execution halted + + ‘unmconf.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘unmconf.Rmd’ using rmarkdown + ``` + +# usmap + +
+ +* Version: 0.7.1 +* GitHub: https://github.com/pdil/usmap +* Source code: https://github.com/cran/usmap +* Date/Publication: 2024-03-21 04:20:02 UTC +* Number of recursive dependencies: 91 + +Run `revdepcheck::cloud_details(, "usmap")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘usmap-Ex.R’ failed + The error most likely occurred in: + + > ### Name: .east_north_central + > ### Title: East North Central census division + > ### Aliases: .east_north_central + > ### Keywords: datasets + > + > ### ** Examples + > + > plot_usmap(include = .east_north_central, labels = TRUE) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: plot_usmap ... ggplot_add.list -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘spelling.R’ + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + ... + • data/statepov.svg + • plot/arizona-county-map-with-labels-and-fill.svg + • plot/example-data-state-map-with-custom-linewidth.svg + • plot/new-england-state-map-with-labels-excluding-maine.svg + • plot/southeastern-states-map-with-labels.svg + • plot/state-map-with-labels.svg + • plot/state-map-with-major-rivers.svg + • plot/state-population-map-with-blue-outlines.svg + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘usmap1.Rmd’ + ... + + > knitr::opts_chunk$set(collapse = TRUE, comment = "#>") + + > usmap::plot_usmap() + + When sourcing ‘usmap1.R’: + Error: argument is of length zero + ... + + > usmap::plot_usmap("states", labels = TRUE) + + When sourcing ‘usmap3.R’: + Error: argument is of length zero + Execution halted + + ‘usmap1.Rmd’ using ‘UTF-8’... failed + ‘usmap2.Rmd’ using ‘UTF-8’... failed + ‘usmap3.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘usmap1.Rmd’ using rmarkdown + + Quitting from lines 26-27 [unnamed-chunk-1] (usmap1.Rmd) + Error: processing vignette 'usmap1.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘usmap1.Rmd’ + + --- re-building ‘usmap2.Rmd’ using rmarkdown + + ... + Quitting from lines 26-27 [unnamed-chunk-1] (usmap3.Rmd) + Error: processing vignette 'usmap3.Rmd' failed with diagnostics: + argument is of length zero + --- failed re-building ‘usmap3.Rmd’ + + SUMMARY: processing the following files failed: + ‘usmap1.Rmd’ ‘usmap2.Rmd’ ‘usmap3.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 17 marked UTF-8 strings + ``` + +# vannstats + +
+ +* Version: 1.3.4.14 +* GitHub: NA +* Source code: https://github.com/cran/vannstats +* Date/Publication: 2023-04-15 04:30:02 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::cloud_details(, "vannstats")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vannstats-Ex.R’ failed + The error most likely occurred in: + + > ### Name: qq + > ### Title: Simplified Normal (Q-Q) Plot + > ### Aliases: qq + > + > ### ** Examples + > + > data <- mtcars + > + > qq(data,mpg,cyl) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: qq ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# vDiveR + +
+ +* Version: 1.2.1 +* GitHub: NA +* Source code: https://github.com/cran/vDiveR +* Date/Publication: 2024-01-09 20:20:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "vDiveR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vDiveR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: plot_entropy + > ### Title: Entropy plot + > ### Aliases: plot_entropy + > + > ### ** Examples + > + > plot_entropy(proteins_1host) + Scale for colour is already present. + Adding another scale for colour, which will replace the existing scale. + Scale for linetype is already present. + Adding another scale for linetype, which will replace the existing scale. + Error in grid.Call.graphics(C_lines, x$x, x$y, index, x$arrow) : + invalid line type: must be length 2, 4, 6 or 8 + Calls: ... drawDetails -> drawDetails.polyline -> grid.Call.graphics + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘DT’ ‘maps’ ‘readr’ + All declared Imports should be used. + ``` + +# venn + +
+ +* Version: 1.12 +* GitHub: https://github.com/dusadrian/venn +* Source code: https://github.com/cran/venn +* Date/Publication: 2024-01-08 11:40:05 UTC +* Number of recursive dependencies: 56 + +Run `revdepcheck::cloud_details(, "venn")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘venn-Ex.R’ failed + The error most likely occurred in: + + > ### Name: venn + > ### Title: Draw and display a Venn diagram + > ### Aliases: venn + > ### Keywords: functions + > + > ### ** Examples + > + ... + > + > + > # producing a ggplot2 graphics + > venn(x, ilabels = "counts", ggplot = TRUE) + > + > # increasing the border size + > venn(x, ilabels = "counts", ggplot = TRUE, size = 1.5) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: venn ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# vimpclust + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/vimpclust +* Date/Publication: 2021-01-08 09:30:03 UTC +* Number of recursive dependencies: 53 + +Run `revdepcheck::cloud_details(, "vimpclust")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘sparsewkm.Rmd’ + ... + restecg 3.1e-02 0.000 0.000 0.000 0.000 + exang 2.3e-01 0.182 0.138 0.106 0.046 + slope 3.2e-01 0.231 0.188 0.151 0.077 + thal 1.2e-01 0.058 0.023 0.000 0.000 + + > plot(res, what = "weights.features") + + When sourcing ‘sparsewkm.R’: + Error: invalid line type: must be length 2, 4, 6 or 8 + Execution halted + + ‘groupsparsewkm.Rmd’ using ‘UTF-8’... OK + ‘sparsewkm.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘groupsparsewkm.Rmd’ using rmarkdown + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘mclust’ ‘rlang’ + All declared Imports should be used. + ``` + +# vip + +
+ +* Version: 0.4.1 +* GitHub: https://github.com/koalaverse/vip +* Source code: https://github.com/cran/vip +* Date/Publication: 2023-08-21 09:20:02 UTC +* Number of recursive dependencies: 104 + +Run `revdepcheck::cloud_details(, "vip")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vip-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vi + > ### Title: Variable importance + > ### Aliases: vi vi.default + > + > ### ** Examples + > + > # + ... + 8 drat 0.0265 0.0564 + 9 carb 0.00898 0.00885 + 10 disp -0.000824 0.00744 + > + > # Plot variable importance scores + > vip(vis, include_type = TRUE, all_permutations = TRUE, + + geom = "point", aesthetics = list(color = "forestgreen", size = 3)) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: vip ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > if (requireNamespace("tinytest", quietly = TRUE)) { + + home <- length(unclass(packageVersion("vip"))[[1L]]) == 4 + + tinytest::test_package("vip", at_home = home) + + } + + Attaching package: 'vip' + + ... + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 0 tests + test_pkg_nnet.R............... 1 tests OK + test_pkg_nnet.R............... 2 tests OK + test_pkg_nnet.R............... 3 tests OK Error in if (new_name %in% existing) { : argument is of length zero + Calls: ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking package dependencies ... NOTE + ``` + Packages which this enhances but not available for checking: + 'C50', 'caret', 'Cubist', 'earth', 'gbm', 'glmnet', 'h2o', + 'lightgbm', 'mixOmics', 'mlr', 'mlr3', 'neuralnet', 'parsnip', + 'partykit', 'pls', 'randomForest', 'ranger', 'RSNNS', 'sparklyr', + 'tidymodels', 'workflows', 'xgboost' + ``` + +* checking Rd cross-references ... NOTE + ``` + Packages unavailable to check Rd xrefs: ‘randomForest’, ‘glmnet’, ‘C50’, ‘Cubist’, ‘caret’, ‘partykit’, ‘earth’, ‘gbm’, ‘h2o’, ‘sparklyr’, ‘ranger’, ‘xgboost’, ‘lightgbm’ + ``` + +# VirtualPop + +
+ +* Version: 2.0.2 +* GitHub: https://github.com/willekens/VirtualPop +* Source code: https://github.com/cran/VirtualPop +* Date/Publication: 2024-03-18 10:30:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "VirtualPop")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Piecewise_exponential.Rmd’ + ... + > H <- VirtualPop::H_pw(x, breakpoints, rates) + + > dd <- data.frame(x = x, y = exp(-H)) + + > p <- survminer::ggsurvplot(KM, data = data.frame(pw_sample), + + conf.int = TRUE, ggtheme = theme_bw()) + + When sourcing ‘Piecewise_exponential.R’: + Error: argument is of length zero + Execution halted + + ‘MultistateLH.Rmd’ using ‘UTF-8’... OK + ‘Piecewise_exponential.Rmd’ using ‘UTF-8’... failed + ‘Tutorial.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘MultistateLH.Rmd’ using knitr + --- finished re-building ‘MultistateLH.Rmd’ + + --- re-building ‘Piecewise_exponential.Rmd’ using knitr + ``` + +# viscomp + +
+ +* Version: 1.0.0 +* GitHub: https://github.com/georgiosseitidis/viscomp +* Source code: https://github.com/cran/viscomp +* Date/Publication: 2023-01-16 09:50:02 UTC +* Number of recursive dependencies: 137 + +Run `revdepcheck::cloud_details(, "viscomp")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘viscomp-Ex.R’ failed + The error most likely occurred in: + + > ### Name: loccos + > ### Title: Leaving One Component Combination Out Scatter plot + > ### Aliases: loccos + > + > ### ** Examples + > + > data(nmaMACE) + > loccos(model = nmaMACE, combination = c("B")) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: loccos ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +# vivaldi + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/GreshamLab/vivaldi +* Source code: https://github.com/cran/vivaldi +* Date/Publication: 2023-03-21 20:10:02 UTC +* Number of recursive dependencies: 102 + +Run `revdepcheck::cloud_details(, "vivaldi")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vivaldi-Ex.R’ failed + The error most likely occurred in: + + > ### Name: snv_location + > ### Title: snv_location + > ### Aliases: snv_location + > + > ### ** Examples + > + > # Example 1: + ... + 6 m2 PB1 234 G A minor 0.010 0.990 + 7 m2 PB1 266 G A minor 0.022 0.978 + 8 m2 PB2 199 A G minor 0.043 0.957 + 9 m2 PB2 88 G A major 0.055 0.945 + 10 m2 PB2 180 C T minor 0.011 0.989 + > + > snv_location(df) + Error in pm[[2]] : subscript out of bounds + Calls: snv_location -> -> ggplotly.ggplot -> gg2list + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/tests.html + > # * https://testthat.r-lib.org/reference/test_package.html#special-files + ... + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-snv_location.R:13:3'): expect output ───────────────────────── + Expected `snv_location(df)` to run without any errors. + i Actually got a with text: + subscript out of bounds + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 29 ] + Error: Test failures + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘vignette.Rmd’ + ... + |a_3_fb | 96| + |a_3_iv | 94| + |b_1_fb | 82| + |b_1_iv | 91| + + > snv_location(DF_filt_SNVs) + + When sourcing ‘vignette.R’: + Error: subscript out of bounds + Execution halted + + ‘vignette.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘vignette.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.8Mb + sub-directories of 1Mb or more: + doc 5.4Mb + extdata 1.1Mb + ``` + +# voiceR + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/voiceR +* Date/Publication: 2023-09-12 20:30:02 UTC +* Number of recursive dependencies: 179 + +Run `revdepcheck::cloud_details(, "voiceR")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘voiceR-Ex.R’ failed + The error most likely occurred in: + + > ### Name: comparisonPlots + > ### Title: Create boxplots for extracted audio features + > ### Aliases: comparisonPlots + > + > ### ** Examples + > + > comparisonPlots(testAudioData, by = "Condition") + Error in if (new_name %in% existing) { : argument is of length zero + Calls: comparisonPlots ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 4. └─(function() {... + 5. └─ggplot2:::`+.gg`(...) + 6. └─ggplot2:::add_ggplot(e1, e2, e2name) + 7. ├─ggplot2::ggplot_add(object, p, objectname) + 8. └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 9. └─ggplot2:::new_layer_names(object, names(plot$layers)) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 30 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.0Mb + sub-directories of 1Mb or more: + Audios 1.1Mb + data 6.5Mb + ``` + +# volcano3D + +
+ +* Version: 2.0.9 +* GitHub: https://github.com/KatrionaGoldmann/volcano3D +* Source code: https://github.com/cran/volcano3D +* Date/Publication: 2023-05-17 11:00:02 UTC +* Number of recursive dependencies: 166 + +Run `revdepcheck::cloud_details(, "volcano3D")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘volcano3D-Ex.R’ failed + The error most likely occurred in: + + > ### Name: boxplot_trio + > ### Title: Boxplot to compare groups + > ### Aliases: boxplot_trio + > ### Keywords: hplot + > + > ### ** Examples + > + ... + 11. │ └─ggplot2:::`+.gg`(...) + 12. │ └─ggplot2:::add_ggplot(e1, e2, e2name) + 13. │ ├─ggplot2::ggplot_add(object, p, objectname) + 14. │ └─ggplot2:::ggplot_add.Layer(object, p, objectname) + 15. │ └─ggplot2:::new_layer_names(object, names(plot$layers)) + 16. └─base::.handleSimpleError(...) + 17. └─purrr (local) h(simpleError(msg, call)) + 18. └─cli::cli_abort(...) + 19. └─rlang::abort(...) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘Vignette.rmd’ + ... + > plot1 <- boxplot_trio(syn_polar, value = "COBL", text_size = 7, + + test = "polar_padj", my_comparisons = list(c("Lymphoid", + + "Myeloid" .... [TRUNCATED] + + When sourcing ‘Vignette.R’: + Error: ℹ In index: 1. + ℹ With name: row. + Caused by error in `if (new_name %in% existing) ...`: + ! argument is of length zero + Execution halted + + ‘Vignette.rmd’ using ‘UTF-8’... failed + ‘Vignette_2x3.Rmd’ using ‘UTF-8’... OK + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘Vignette.rmd’ using rmarkdown + ``` + +# voluModel + +
+ +* Version: 0.2.2 +* GitHub: https://github.com/hannahlowens/voluModel +* Source code: https://github.com/cran/voluModel +* Date/Publication: 2024-08-20 22:50:01 UTC +* Number of recursive dependencies: 133 + +Run `revdepcheck::cloud_details(, "voluModel")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘voluModel-Ex.R’ failed + The error most likely occurred in: + + > ### Name: pointCompMap + > ### Title: Comparative point mapping + > ### Aliases: pointCompMap + > ### Keywords: plotting + > + > ### ** Examples + > + ... + 6. └─ggplot2 (local) setup(..., self = self) + 7. └─self$coord$setup_params(data) + 8. └─ggplot2 (local) setup_params(..., self = self) + 9. └─ggproto_parent(Coord, self)$setup_params(data) + 10. └─ggplot2 (local) setup_params(..., self = self) + 11. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 12. └─ggplot2:::check_logical(expand) + 13. └─ggplot2:::stop_input_type(...) + 14. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘a_Introduction.Rmd’ using rmarkdown + + Quitting from lines 44-58 [show points] (a_Introduction.Rmd) + Error: processing vignette 'a_Introduction.Rmd' failed with diagnostics: + `expand` must be a logical vector, not the number 0.05. + --- failed re-building ‘a_Introduction.Rmd’ + + --- re-building ‘b_RasterProcessing.Rmd’ using rmarkdown + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘a_Introduction.Rmd’ + ... + + returnclass = "sf")[1] + + > pointMap(occs = occurrences, ptCol = "orange", landCol = "black", + + spName = "Steindachneria argentea", ptSize = 3, land = land) + Using decimalLongitude and decimalLatitude + as x and y coordinates, respectively. + + ... + + When sourcing ‘e_GLMWorkflow.R’: + Error: invalid font type + Execution halted + + ‘a_Introduction.Rmd’ using ‘UTF-8’... failed + ‘b_RasterProcessing.Rmd’ using ‘UTF-8’... OK + ‘c_DataSampling.Rmd’ using ‘UTF-8’... failed + ‘d_Visualization.Rmd’ using ‘UTF-8’... failed + ‘e_GLMWorkflow.Rmd’ using ‘UTF-8’... failed + ``` + +# vsd + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/vsd +* Date/Publication: 2021-05-11 09:40:02 UTC +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "vsd")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘vsd-Ex.R’ failed + The error most likely occurred in: + + > ### Name: vsd + > ### Title: Visualizing Survival Data + > ### Aliases: vsd vsd.formula vsd.Surv vsd.coxph vsd.survfit vsd.survfitcox + > ### vsd.flexsurvreg + > + > ### ** Examples + > + ... + • `linetype = "Strata"` + • `shape = "Strata"` + + > + > # parametric models are also supported with flexsurv + > vsd(flexsurv::flexsurvreg(Surv(rectime, censrec) ~ group, data = flexsurv::bc, dist = 'gengamma'), + + .include = c("par")) + Error in if (new_name %in% existing) { : argument is of length zero + Calls: vsd ... add_ggplot -> ggplot_add -> ggplot_add.Layer -> new_layer_names + Execution halted + ``` + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘flexsurv’ + All declared Imports should be used. + ``` + +# vvshiny + +
+ +* Version: 0.1.1 +* GitHub: NA +* Source code: https://github.com/cran/vvshiny +* Date/Publication: 2023-07-19 15:30:02 UTC +* Number of recursive dependencies: 135 + +Run `revdepcheck::cloud_details(, "vvshiny")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > # This file is part of the standard setup for testthat. + > # It is recommended that you do not modify it. + > # + > # Where should you do additional test configuration? + > # Learn more about the roles of various files in: + > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview + > # * https://testthat.r-lib.org/articles/special-files.html + ... + 1. ├─vvshiny::ggplotly_with_legend(p, color = "grp", mapping_table = list(grp = "Group")) at test-ggplotly_with_legend.R:15:3 + 2. │ ├─plotly::ggplotly(plot) %>% ... + 3. │ ├─plotly::ggplotly(plot) + 4. │ └─plotly:::ggplotly.ggplot(plot) + 5. │ └─plotly::gg2list(...) + 6. └─plotly::layout(...) + + [ FAIL 1 | WARN 2 | SKIP 0 | PASS 60 ] + Error: Test failures + Execution halted + ``` + +# walker + +
+ +* Version: 1.0.10 +* GitHub: https://github.com/helske/walker +* Source code: https://github.com/cran/walker +* Date/Publication: 2024-08-30 06:40:02 UTC +* Number of recursive dependencies: 106 + +Run `revdepcheck::cloud_details(, "walker")` for more info + +
+ +## Newly broken + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘walker.Rmd’ + ... + For each parameter, n_eff is a crude measure of effective sample size, + and Rhat is the potential scale reduction factor on split chains (at + convergence, Rhat=1). + + > mcmc_areas(as.matrix(fit$stanfit), regex_pars = c("sigma_y", + + "sigma_rw1")) + + When sourcing ‘walker.R’: + Error: argument is of length zero + Execution halted + + ‘walker.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘walker.Rmd’ using rmarkdown + ``` + +## In both + +* checking installed package size ... NOTE + ``` + installed size is 161.5Mb + sub-directories of 1Mb or more: + libs 160.1Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. + ``` + +# WVPlots + +
+ +* Version: 1.3.8 +* GitHub: https://github.com/WinVector/WVPlots +* Source code: https://github.com/cran/WVPlots +* Date/Publication: 2024-04-22 20:40:07 UTC +* Number of recursive dependencies: 78 + +Run `revdepcheck::cloud_details(, "WVPlots")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘WVPlots-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ScatterHist + > ### Title: Plot a scatter plot with marginals. + > ### Aliases: ScatterHist + > + > ### ** Examples + > + > + ... + 10. └─ggplot2:::ggplot_build.ggplot(x) + 11. └─layout$setup(data, plot$data, plot$plot_env) + 12. └─ggplot2 (local) setup(..., self = self) + 13. └─self$coord$setup_params(data) + 14. └─ggplot2 (local) setup_params(..., self = self) + 15. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 16. └─ggplot2:::check_logical(expand) + 17. └─ggplot2:::stop_input_type(...) + 18. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘tinytest.R’ + Running the tests in ‘tests/tinytest.R’ failed. + Complete output: + > + > if (requireNamespace("tinytest", quietly=TRUE) ) { + + if (requireNamespace('data.table', quietly = TRUE)) { + + # don't multi-thread during CRAN checks + + data.table::setDTthreads(1) + + } + + tinytest::test_package("WVPlots") + ... + 18. └─ggplot2:::ggplot_build.ggplot(x) + 19. └─layout$setup(data, plot$data, plot$plot_env) + 20. └─ggplot2 (local) setup(..., self = self) + 21. └─self$coord$setup_params(data) + 22. └─ggplot2 (local) setup_params(..., self = self) + 23. └─ggplot2:::parse_coord_expand(expand = self$expand %||% TRUE) + 24. └─ggplot2:::check_logical(expand) + 25. └─ggplot2:::stop_input_type(...) + 26. └─rlang::abort(message, ..., call = call, arg = arg) + Execution halted + ``` + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘WVPlots_concept.Rmd’ + ... + > frm$absY <- abs(frm$y) + + > frm$posY = frm$y > 0 + + > WVPlots::ScatterHist(frm, "x", "y", smoothmethod = "lm", + + title = "Example Linear Fit") + + ... + > frm$posY = frm$y > 0 + + > WVPlots::ScatterHist(frm, "x", "y", title = "Example Fit") + + When sourcing ‘WVPlots_examples.R’: + Error: `expand` must be a logical vector, not the number 0. + Execution halted + + ‘WVPlots_concept.Rmd’ using ‘UTF-8’... failed + ‘WVPlots_examples.Rmd’ using ‘UTF-8’... failed + ``` + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘WVPlots_concept.Rmd’ using rmarkdown + ``` + +# xaringanthemer + +
+ +* Version: 0.4.2 +* GitHub: https://github.com/gadenbuie/xaringanthemer +* Source code: https://github.com/cran/xaringanthemer +* Date/Publication: 2022-08-20 18:40:02 UTC +* Number of recursive dependencies: 75 + +Run `revdepcheck::cloud_details(, "xaringanthemer")` for more info + +
+ +## Newly broken + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(xaringanthemer) + > + > test_check("xaringanthemer") + [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] + + ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ + ... + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-ggplot2.R:267:3'): theme_xaringan_restore_defaults() restores defaults ── + res$after_restore$line_colour (`actual`) not equal to res$original$colour (`expected`). + + `actual` is a character vector ('#0088ff') + `expected` is an S3 object of class , a call + + [ FAIL 1 | WARN 18 | SKIP 1 | PASS 308 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking running R code from vignettes ... ERROR + ``` + Errors in running code in vignettes: + when running code in ‘xaringanthemer.Rmd’ + ... + Warning in file(con, "r") : + cannot open file './../man/fragments/_quick-intro.Rmd': No such file or directory + + Quitting from lines 43-43 [unnamed-chunk-2] (xaringanthemer.Rmd) + + When tangling ‘xaringanthemer.Rmd’: + Error: cannot open the connection + Execution halted + + ‘ggplot2-themes.Rmd’ using ‘UTF-8’... OK + ‘template-variables.Rmd’ using ‘UTF-8’... OK + ‘xaringanthemer.Rmd’ using ‘UTF-8’... failed + ``` + +# yamlet + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/bergsmat/yamlet +* Source code: https://github.com/cran/yamlet +* Date/Publication: 2024-03-29 13:30:02 UTC +* Number of recursive dependencies: 103 + +Run `revdepcheck::cloud_details(, "yamlet")` for more info + +
+ +## Newly broken + +* checking examples ... ERROR + ``` + Running examples in ‘yamlet-Ex.R’ failed + The error most likely occurred in: + + > ### Name: ggplot_add.ggplot_isometric + > ### Title: Add Isometry to Plot Object + > ### Aliases: ggplot_add.ggplot_isometric + > ### Keywords: internal + > + > ### ** Examples + > + ... + ismtrc> library(magrittr) + + ismtrc> library(ggplot2) + + ismtrc> data.frame(x = 1:5, y = 3:7) %>% + ismtrc+ ggplot(aes(x, y)) + geom_point() + isometric() + Error in ggplot_add.ggplot_isometric(object, p, objectname) : + "x" %in% names(plot$labels) is not TRUE + Calls: example ... ggplot_add -> ggplot_add.ggplot_isometric -> stopifnot + Execution halted + ``` + +* checking tests ... ERROR + ``` + Running ‘testthat.R’ + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(yamlet) + + Attaching package: 'yamlet' + + The following object is masked from 'package:stats': + + ... + ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ + • empty test (2): 'test-yamlet.R:1346:1', 'test-yamlet.R:1351:1' + + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-yamlet.R:843:1'): ggplot.resolved is stable ────────────────── + `print(x %>% ggplot(map) + geom_point())` did not produce any warnings. + + [ FAIL 1 | WARN 0 | SKIP 2 | PASS 516 ] + Error: Test failures + Execution halted + ``` + +## In both + +* checking re-building of vignette outputs ... NOTE + ``` + Error(s) in re-building vignettes: + --- re-building ‘scripted-html.Rmd’ using rmarkdown + ``` diff --git a/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg b/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg index b38125acd3..78e321d395 100644 --- a/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg +++ b/tests/testthat/_snaps/coord_sf/coord-sf-with-custom-guides.svg @@ -47,27 +47,27 @@ -80 -° -W -79 -° -W -78 -° -W -77 -° -W -76 -° -W -75 -° -W -40 -° -N +80 +° +W +79 +° +W +78 +° +W +77 +° +W +76 +° +W +75 +° +W +40 +° +N 35 ° N diff --git a/tests/testthat/_snaps/guides.md b/tests/testthat/_snaps/guides.md index 62d1e41d24..be7c84d7f3 100644 --- a/tests/testthat/_snaps/guides.md +++ b/tests/testthat/_snaps/guides.md @@ -1,3 +1,14 @@ +# dots are checked when making guides + + Ignoring unknown argument to `guide_axis()`: `foo`. + +--- + + Arguments in `...` must be used. + x Problematic argument: + * foo = "bar" + i Did you misspell an argument name? + # Using non-position guides for position scales results in an informative error `guide_legend()` cannot be used for x, xmin, xmax, or xend. diff --git a/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg b/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg index f5ad2b2273..8902fa04cd 100644 --- a/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg +++ b/tests/testthat/_snaps/guides/axis-guides-negative-rotation.svg @@ -70,16 +70,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -91,16 +91,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -112,27 +112,27 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 diff --git a/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg b/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg index fb7d39a9d3..1d83ebc1e2 100644 --- a/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg +++ b/tests/testthat/_snaps/guides/axis-guides-vertical-negative-rotation.svg @@ -70,16 +70,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -91,16 +91,16 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 @@ -112,27 +112,27 @@ -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 -1,000 -2,000 -3,000 -4,000 -5,000 -6,000 -7,000 -8,000 -9,000 -10,000 +1,000 +2,000 +3,000 +4,000 +5,000 +6,000 +7,000 +8,000 +9,000 +10,000 diff --git a/tests/testthat/_snaps/labels.md b/tests/testthat/_snaps/labels.md index e1f6ed4140..49efe59a72 100644 --- a/tests/testthat/_snaps/labels.md +++ b/tests/testthat/_snaps/labels.md @@ -5,6 +5,18 @@ Output [1] "A plot showing class on a discrete x-axis and count on a continuous y-axis using a bar layer." +# get_alt_text checks dots + + Arguments in `...` must be used. + x Problematic argument: + * foo = "bar" + i Did you misspell an argument name? + +# warnings are thrown for unknown labels + + Ignoring unknown labels: + * `foo = "bar"` + # plot.tag.position rejects invalid input The `plot.tag.position` theme element must be a object. diff --git a/tests/testthat/_snaps/plot.md b/tests/testthat/_snaps/plot.md index 6035364389..157ebb6635 100644 --- a/tests/testthat/_snaps/plot.md +++ b/tests/testthat/_snaps/plot.md @@ -8,6 +8,13 @@ `data` cannot be a function. i Have you misspelled the `data` argument in `ggplot()` +--- + + Arguments in `...` must be used. + x Problematic argument: + * foobar = "nonsense" + i Did you misspell an argument name? + # construction have user friendly errors Cannot use `+` with a single argument. diff --git a/tests/testthat/_snaps/utilities.md b/tests/testthat/_snaps/utilities.md index 6b2e0e8e8c..37138df4e9 100644 --- a/tests/testthat/_snaps/utilities.md +++ b/tests/testthat/_snaps/utilities.md @@ -50,3 +50,19 @@ Only one of `boundary` and `center` may be specified. +# summary method gives a nice summary + + Code + summary(p) + Output + data: manufacturer, model, displ, year, cyl, trans, drv, cty, hwy, fl, + class [234x11] + mapping: x = ~displ, y = ~hwy, colour = ~drv + scales: x, xmin, xmax, xend, xintercept, xmin_final, xmax_final, xlower, xmiddle, xupper, x0, colour + faceting: ~year, ~cyl + ----------------------------------- + geom_point: na.rm = FALSE + stat_identity: na.rm = FALSE + position_identity + + diff --git a/tests/testthat/helper-plot-data.R b/tests/testthat/helper-plot-data.R index bc1f81f2c9..13e36d861a 100644 --- a/tests/testthat/helper-plot-data.R +++ b/tests/testthat/helper-plot-data.R @@ -5,7 +5,7 @@ cdata <- function(plot) { lapply(pieces$data, function(d) { dapply(d, "PANEL", function(panel_data) { scales <- pieces$layout$get_scales(panel_data$PANEL[1]) - panel_params <- plot$coordinates$setup_panel_params(scales$x, scales$y) + panel_params <- plot$coordinates$setup_panel_params(scales$x, scales$y, params = pieces$layout$coord_params) plot$coordinates$transform(panel_data, panel_params) }) }) diff --git a/tests/testthat/test-coord-.R b/tests/testthat/test-coord-.R index 76a174454c..6a50369bbc 100644 --- a/tests/testthat/test-coord-.R +++ b/tests/testthat/test-coord-.R @@ -75,3 +75,19 @@ test_that("coords append a column to the layout correctly", { expect_equal(test$COORD, c(1, 2, 1)) }) +test_that("coord expand takes a vector", { + + base <- ggplot() + lims(x = c(0, 10), y = c(0, 10)) + + p <- ggplot_build(base + coord_cartesian(expand = c(TRUE, FALSE, FALSE, TRUE))) + pp <- p$layout$panel_params[[1]] + expect_equal(pp$x.range, c(-0.5, 10)) + expect_equal(pp$y.range, c(0, 10.5)) + + p <- ggplot_build(base + coord_cartesian(expand = c(top = FALSE, left = FALSE))) + pp <- p$layout$panel_params[[1]] + expect_equal(pp$x.range, c(0, 10.5)) + expect_equal(pp$y.range, c(-0.5, 10)) + +}) + diff --git a/tests/testthat/test-guides.R b/tests/testthat/test-guides.R index f0057a7452..23df1f75e2 100644 --- a/tests/testthat/test-guides.R +++ b/tests/testthat/test-guides.R @@ -87,6 +87,15 @@ test_that("show.legend handles named vectors", { expect_equal(n_legends(p), 1) }) +test_that("dots are checked when making guides", { + expect_snapshot_warning( + new_guide(foo = "bar", super = GuideAxis) + ) + expect_snapshot_warning( + guide_legend(foo = "bar") + ) +}) + test_that("axis_label_overlap_priority always returns the correct number of elements", { expect_identical(axis_label_priority(0), numeric(0)) expect_setequal(axis_label_priority(1), seq_len(1)) diff --git a/tests/testthat/test-labels.R b/tests/testthat/test-labels.R index c659e39cf5..60f5165c1b 100644 --- a/tests/testthat/test-labels.R +++ b/tests/testthat/test-labels.R @@ -104,6 +104,15 @@ test_that("alt text can take a function", { expect_snapshot(get_alt_text(p)) }) +test_that("get_alt_text checks dots", { + expect_snapshot_warning(get_alt_text(ggplot(), foo = "bar")) +}) + +test_that("warnings are thrown for unknown labels", { + p <- ggplot(mtcars, aes(mpg, disp)) + geom_point() + labs(foo = 'bar') + expect_snapshot_warning(ggplot_build(p)) +}) + test_that("plot.tag.position rejects invalid input", { p <- ggplot(mtcars, aes(mpg, disp)) + geom_point() + labs(tag = "Fig. A)") diff --git a/tests/testthat/test-plot.R b/tests/testthat/test-plot.R index dc1b507c13..2cccf79034 100644 --- a/tests/testthat/test-plot.R +++ b/tests/testthat/test-plot.R @@ -1,6 +1,7 @@ test_that("ggplot() throws informative errors", { expect_snapshot_error(ggplot(mapping = letters)) expect_snapshot_error(ggplot(data)) + expect_snapshot_warning(ggplot(foobar = "nonsense")) }) test_that("construction have user friendly errors", { diff --git a/tests/testthat/test-stat-summary.R b/tests/testthat/test-stat-summary.R index 825efd981c..abc2ffe5dd 100644 --- a/tests/testthat/test-stat-summary.R +++ b/tests/testthat/test-stat-summary.R @@ -40,8 +40,16 @@ test_that("stat_summary(_bin) work with lambda expressions", { }) +test_that("stat_summary_bin takes user's `width` argument (#4647)", { + p <- ggplot(mtcars, aes(mpg, disp)) + + stat_summary_bin( + fun.data = mean_se, na.rm = TRUE, + binwidth = 1, width = 2 + ) - + ld <- layer_data(p) + expect_equal(unique(ld$width), 2) +}) test_that("stat_summary_(2d|hex) work with lambda expressions", { diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R index 5c6ff47b26..a602eb22c7 100644 --- a/tests/testthat/test-utilities.R +++ b/tests/testthat/test-utilities.R @@ -192,3 +192,16 @@ test_that("expose/ignore_data() can round-trip a data.frame", { expect_equal(test, df[, c("a", "c", "b", "d")]) }) + +test_that("summary method gives a nice summary", { + # This test isn't important enough to break anything on CRAN + skip_on_cran() + + p <- ggplot(mpg, aes(displ, hwy, colour = drv)) + + geom_point() + + scale_x_continuous() + + scale_colour_brewer() + + facet_grid(year ~ cyl) + + expect_snapshot(summary(p)) +}) diff --git a/vignettes/articles/faq-annotation.Rmd b/vignettes/articles/faq-annotation.Rmd index a36ddfb670..b92e93e9e1 100644 --- a/vignettes/articles/faq-annotation.Rmd +++ b/vignettes/articles/faq-annotation.Rmd @@ -39,7 +39,7 @@ You should use `annotate(geom = "text")` instead of `geom_text()` for annotation In the following visualisation we have annotated a histogram with a red line and red text to mark the mean. Note that both the line and the text appears pixellated/fuzzy. ```{r} -#| fig.alt = "Histogram of highway miles per gallon for 234 cars. A red line is +#| fig.alt: "Histogram of highway miles per gallon for 234 cars. A red line is #| placed at the position 23.44 and is adorned with the label 'mean 23.44'. #| Both the line and the text appear pixellated due to overplotting." mean_hwy <- round(mean(mpg$hwy), 2) @@ -62,7 +62,7 @@ This is because `geom_text()` draws the geom once per each row of the data frame ```{r} -#| fig.alt = "Histogram of highway miles per gallon for 234 cars. A red line is +#| fig.alt: "Histogram of highway miles per gallon for 234 cars. A red line is #| placed at the position 23.44 and is adorned with the label 'mean = 23.44'. #| Both the line and the text appear crisp." ggplot(mpg, aes(x = hwy)) + @@ -91,7 +91,7 @@ Set `vjust = "inward"` and `hjust = "inward"` in `geom_text()`. Suppose you have the following data frame and visualization. The labels at the edges of the plot are cut off slightly. ```{r} -#| fig.alt = "A plot showing the words 'two', 'three' and 'four' arranged +#| fig.alt: "A plot showing the words 'two', 'three' and 'four' arranged #| diagonally. The 'two' and 'four' labels have been clipped to the panel's #| edge and are not displayed completely." df <- tibble::tribble( @@ -108,7 +108,7 @@ ggplot(df, aes(x = x, y = y, label = name)) + You could manually extend axis limits to avoid this, but a more straightforward approach is to set `vjust = "inward"` and `hjust = "inward"` in `geom_text()`. ```{r} -#| fig.alt = "A plot showing the words 'two', 'three' and 'four' arranged +#| fig.alt: "A plot showing the words 'two', 'three' and 'four' arranged #| diagonally. The 'two' and 'four' labels are aligned to the top-right and #| bottom-left relative to their anchor points, and are displayed in their #| entirety." @@ -129,7 +129,7 @@ Either calculate the counts ahead of time and place them on bars using `geom_tex Suppose you have the following bar plot and you want to add the number of cars that fall into each `drv` level on their respective bars. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train." ggplot(mpg, aes(x = drv)) + geom_bar() @@ -139,7 +139,7 @@ One option is to calculate the counts with `dplyr::count()` and then pass them t Note that we expanded the y axis limit to get the numbers to fit on the plot. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The count values are displayed on top of the bars as text." mpg %>% dplyr::count(drv) %>% @@ -152,7 +152,7 @@ mpg %>% Another option is to let `ggplot()` do the counting for you, and access these counts with `after_stat(count)` that is mapped to the labels to be placed on the plot with `stat_count()`. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The count values are displayed on top of the bars as text." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -173,7 +173,7 @@ First calculate the counts for each segment (e.g. with `dplyr::count()`) and the Suppose you have the following stacked bar plot. ```{r} -#| fig.alt = "A stacked bar chart showing the number of cars for each of seven +#| fig.alt: "A stacked bar chart showing the number of cars for each of seven #| types of cars. The fill colour of the bars indicate the type of drive #| train." ggplot(mpg, aes(x = class, fill = drv)) + @@ -190,7 +190,7 @@ mpg %>% You can then pass this result directly to `ggplot()`, draw the segments with appropriate heights with `y = n` in the `aes`thetic mapping and `geom_col()` to draw the bars, and finally place the counts on the plot with `geom_text()`. ```{r} -#| fig.alt = "A stacked bar chart showing the number of cars for each of seven +#| fig.alt: "A stacked bar chart showing the number of cars for each of seven #| types of cars. The fill colour of the bars indicate the type of drive #| train. In the middle of each filled part, the count value is displayed as #| text." @@ -214,7 +214,7 @@ Either calculate the proportions ahead of time and place them on bars using `geo Suppose you have the following bar plot but you want to display the proportion of cars that fall into each `drv` level, instead of the count. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train." ggplot(mpg, aes(x = drv)) + geom_bar() @@ -223,7 +223,7 @@ ggplot(mpg, aes(x = drv)) + One option is to calculate the proportions with `dplyr::count()` and then use `geom_col()` to draw the bars ```{r} -#| fig.alt = "A bar chart showing the proportion of cars for each of three types +#| fig.alt: "A bar chart showing the proportion of cars for each of three types #| of drive train." mpg %>% dplyr::count(drv) %>% @@ -236,7 +236,7 @@ Another option is to let `ggplot()` do the calculation of proportions for you, a Note that we also need to the `group = 1` mapping for this option. ```{r} -#| fig.alt = "A bar chart showing the proportion of cars for each of three types +#| fig.alt: "A bar chart showing the proportion of cars for each of three types #| of drive train." ggplot(mpg, aes(x = drv, y = ..prop.., group = 1)) + geom_bar() diff --git a/vignettes/articles/faq-axes.Rmd b/vignettes/articles/faq-axes.Rmd index f9868cdf8e..a6996dbe36 100644 --- a/vignettes/articles/faq-axes.Rmd +++ b/vignettes/articles/faq-axes.Rmd @@ -37,7 +37,7 @@ Set the angle of the text in the `axis.text.x` or `axis.text.y` components of th In the following plot the labels on the x-axis are overlapping. ```{r msleep-order-sleep-total} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis for the orders overlap and are unreadable." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -47,7 +47,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Rotate axis labels: We can do this by components of the `theme()`, specifically the `axis.text.x` component. Applying some vertical and horizontal justification to the labels centers them at the axis ticks. The `angle` can be set as desired within the 0 to 360 degree range, here we set it to 90 degrees. ```{r msleep-order-sleep-total-rotate} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The x-axis labels are oriented #| vertically and are readable." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -58,7 +58,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Flip the axes: Use the y-axis for long labels. ```{r msleep-order-sleep-total-flip} -#| fig.alt = "A boxplot showing the total amount of sleep on the x-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the x-axis for 19 #| taxonomical orders of mammals on the y-axis. The y-axis labels are oriented #| horizontally and are readable." ggplot(msleep, aes(y = order, x = sleep_total)) + @@ -68,7 +68,7 @@ ggplot(msleep, aes(y = order, x = sleep_total)) + - Dodge axis labels: Add a `scale_*()` layer, e.g. `scale_x_continuous()`, `scale_y_discrete()`, etc., and customise the `guide` argument with the `guide_axis()` function. In this case we want to customise the x-axis, and the variable on the x-axis is discrete, so we'll use `scale_x_continuous()`. In the `guide` argument we use the `guide_axis()` and specify how many rows to dodge the labels into with `n.dodge`. This is likely a trial-and-error exercise, depending on the lengths of your labels and the width of your plot. In this case we've settled on 3 rows to render the labels. ```{r msleep-order-sleep-total-dodge} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis are dodged to three levels so that they remain readable." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -79,7 +79,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Omit overlapping labels: Alternatively, you can set `guide_axis(check.overlap = TRUE)` to omit axis labels that overlap. ggplot2 will prioritize the first, last, and middle labels. Note that this option might be more preferable for axes representing variables that have an inherent ordering that is obvious to the audience of the plot, so that it's trivial to guess what the missing labels are. (This is not the case for the following plot.) ```{r msleep-order-sleep-total-check-overlap} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. Several of the x-axis labels #| have been omitted, but the one that remain are readable and don't overlap." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -100,7 +100,7 @@ Add a `theme()` layer and set relevant arguments, e.g. `axis.title.x`, `axis.tex Suppose we want to remove the axis labels entirely. ```{r ref.label="msleep-order-sleep-total"} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The horizontal labels on the #| x-axis for the orders overlap and are unreadable." ``` @@ -108,7 +108,7 @@ Suppose we want to remove the axis labels entirely. - Remove x or y axis labels: If you want to modify just one of the axes, you can do so by modifying the components of the `theme()`, setting the elements you want to remove to `element_blank()`. You would replace `x` with `y` for applying the same update to the y-axis. Note the distinction between `axis.title` and `axis.ticks` -- `axis.title` is the name of the variable and `axis.text` is the text accompanying each of the ticks. ```{r} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The annotation on the x-axis #| is abent." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -123,7 +123,7 @@ ggplot(msleep, aes(x = order, y = sleep_total)) + - Remove all axis labels: You can use `theme_void()` to remove all theming elements. Note that this might remove more features than you like. For finer control over the theme, see below. ```{r} -#| fig.alt = "A boxplot showing the total amount of sleep on the y-axis for 19 +#| fig.alt: "A boxplot showing the total amount of sleep on the y-axis for 19 #| taxonomical orders of mammals on the x-axis. The plot has no axes, #| gridlines or background panel." ggplot(msleep, aes(x = order, y = sleep_total)) + @@ -162,7 +162,7 @@ sales <- tribble( You can create a line plot of these data and facet by `year` to group the quarters for each year together. ```{r} -#| fig.alt = "A line plot with two panels showing value on the y-axis and four +#| fig.alt: "A line plot with two panels showing value on the y-axis and four #| quarters on the x-axis. The left panel is labelled '2020' and the right #| panel is labelled '2021'." ggplot(sales, aes(x = quarter, y = value, group = 1)) + @@ -175,7 +175,7 @@ However it might be preferable to plot all points in a single plot and indicate To achieve this, map the `interaction()` of `quarter` and `year` to the `x` aesthetic. ```{r} -#| fig.alt = "A line plot with one panel showing value on the y-axis and eight +#| fig.alt: "A line plot with one panel showing value on the y-axis and eight #| quarters on the x-axis. The years are appended after each quarter label." ggplot(sales, aes(x = interaction(quarter, year), y = value, group = 1)) + geom_line() @@ -186,7 +186,7 @@ To clean this up (1) clip the plotting area with `coord_cartesian()`, (2) remove Note that the x-coordinates of the year labels are manually assigned here, but if you had many more years, you might write some logic to calculate their placement. ```{r} -#| fig.alt = "A line plot with one panel showing value on the y-axis and eight +#| fig.alt: "A line plot with one panel showing value on the y-axis and eight #| quarters on the x-axis. The years are shown in the middle of the first four #| and last four quarters. The line touches the panel on the left and right." ggplot(sales, aes(x = interaction(quarter, year), y = value, group = 1)) + @@ -205,7 +205,7 @@ This approach works with other geoms as well. For example, you might can create a bar plot representing the same data using the following. ```{r} -#| fig.alt = "A bar chart with one panel showing value on the y-axis and eight +#| fig.alt: "A bar chart with one panel showing value on the y-axis and eight #| quarters on the x-axis. The years are shown in the middle of the first four #| and last four quarters. The outer bars touch the panel on the left and #| right." @@ -225,7 +225,7 @@ If it's undesirable to have the bars flush against the edges of the plot, a simi However note that the space between the bars for 2020 Q4 and 2021 Q1 is greater than the space between the other bars. ```{r} -#| fig.alt = "A bar chart showing value on the y-axis and eight +#| fig.alt: "A bar chart showing value on the y-axis and eight #| quarters on the x-axis. The chart appears as a single panel. The years are #| shown in the middle of the first four and last four quarters. The outer bars #| do not touch the panel on the left and right." @@ -255,7 +255,7 @@ Add a `scale_*()` layer, e.g. `scale_x_continuous()`, `scale_y_discrete()`, etc. Suppose you want to give more informative labels for the type of drive train. ```{r} -#| fig.alt = "A horizontal bar chart showing the number of cars on the x-axis +#| fig.alt: "A horizontal bar chart showing the number of cars on the x-axis #| for each of three types of drive trains on the y-axis. The three drive trains #| are labelled from top-to-bottom as 'r', 'f' and '4'." ggplot(mpg, aes(y = drv)) + @@ -265,7 +265,7 @@ ggplot(mpg, aes(y = drv)) + - Use the `labels` argument in the appropriate `scale_*()` function. You can find a list of these functions [here](https://ggplot2.tidyverse.org/reference/index.html#section-scales). Type of drive train (`drv`) is a discrete variable on the y-axis, so we'll adjust the labels in `scale_y_discrete()`. One option is to list the labels in the same order as the levels. Note that we start from the bottom and go up, just like we would if the variable was numeric/continuous. ```{r} -#| fig.alt = "A horizontal bar chart showing the number of cars on the x-axis +#| fig.alt: "A horizontal bar chart showing the number of cars on the x-axis #| for each of three types of drive trains on the y-axis. The three drive trains #| are labelled from top-to-bottom as 'Rear wheel drive', 'Front wheel drive' #| and 'Four wheel drive'." @@ -279,7 +279,7 @@ ggplot(mpg, aes(y = drv)) + - Another approach is to use a named list. This approach not only makes the relabelling more explicit, but it also means you don't need to worry about the order of the levels. ```{r} -#| fig.alt = "A horizontal bar chart showing the number of cars on the x-axis +#| fig.alt: "A horizontal bar chart showing the number of cars on the x-axis #| for each of three types of drive trains on the y-axis. The three drive trains #| are labelled from top-to-bottom as 'Rear wheel drive', 'Front wheel drive' #| and 'Four wheel drive'." @@ -308,7 +308,7 @@ You will first need to add a `scale_*()` layer (e.g. `scale_x_continuous()`, `sc By default, large numbers on the axis labels in the following plot are shown in scientific notation. ```{r} -#| fig.alt = "A scatter plot showing the median sale price of housing in Texas +#| fig.alt: "A scatter plot showing the median sale price of housing in Texas #| on the x-axis and the total volume of sales on the y-axis. The labels of #| both axes are in scientific notation, for example: '1e+09'." ggplot(txhousing, aes(x = median, y = volume)) + @@ -319,7 +319,7 @@ The [**scales**](https://scales.r-lib.org/) package offers a large number of fun Use `scales::label_number()` to force decimal display of numbers rather than using scientific notation or use `scales::label_comma()` to insert a comma every three digits. ```{r} -#| fig.alt = "A scatter plot showing the median sale price of housing in Texas +#| fig.alt: "A scatter plot showing the median sale price of housing in Texas #| on the x-axis and the total volume of sales on the y-axis. The labels of #| the y-axis are written out in full, with commas marking groups of three #| zeroes. The x-axis labels are written out in full, with spaces marking @@ -345,7 +345,7 @@ You will first need to add a `scale_*()` layer (e.g. `scale_x_continuous()`, `sc Suppose you want to increase/decrease the number of decimal spaces shown in the axis text in the following plot. ```{r} -#| fig.alt = "A scatter plot showing the difference in longitude on the x-axis +#| fig.alt: "A scatter plot showing the difference in longitude on the x-axis #| and difference in latitude on the y-axis for seal movements. The x-axis #| labels have one digit after the decimal place. The y-axis labels have two #| digits after the decimal place." @@ -357,7 +357,7 @@ The [**scales**](https://scales.r-lib.org/) package offers a large number of fun Use `scales::label_number()` where the `accuracy` argument indicates the number to round to, e.g. 0.1 to show 1 decimal place, 0.0001 to show 4 decimal places, etc. ```{r} -#| fig.alt = "A scatter plot showing the difference in longitude on the x-axis +#| fig.alt: "A scatter plot showing the difference in longitude on the x-axis #| and difference in latitude on the y-axis for seal movements. The x-axis #| labels have one digit after the decimal place. The y-axis labels have four #| digits after the decimal place." @@ -383,7 +383,7 @@ You will first need to add a `scale_*()` layer (e.g. `scale_x_continuous()`, `sc The variable on the y-axis of the following line plot (`psavert`) indicates the personal savings rate, which is in percentages. ```{r} -#| fig.alt = "A lineplot showing the personal savings rate over time from 1967 +#| fig.alt: "A lineplot showing the personal savings rate over time from 1967 #| to 2015." ggplot(economics, aes(x = date, y = psavert, group = 1)) + geom_line() @@ -392,7 +392,7 @@ ggplot(economics, aes(x = date, y = psavert, group = 1)) + With `scales::label_percent()` you can add `%`s after the numbers shown on the axis to make the units more clear. ```{r} -#| fig.alt = "A lineplot showing the personal savings rate over time from 1967 +#| fig.alt: "A lineplot showing the personal savings rate over time from 1967 #| to 2015. The y-axis labels are appended by percentage signs." ggplot(economics, aes(x = date, y = psavert, group = 1)) + geom_line() + @@ -414,7 +414,7 @@ You can either use `bquote()` to parse mathematical expressions or use the [**gg In the following plot `cty` is squared and `hwy` is log transformed. ```{r} -#| fig.alt = "A scatter plot showing the squared city miles per gallon on the +#| fig.alt: "A scatter plot showing the squared city miles per gallon on the #| x-axis versus the logarithm of highway miles per gallon on the y-axis for #| 234 cars." ggplot(mpg, aes(x = cty^2, y = log(hwy))) + @@ -424,7 +424,7 @@ ggplot(mpg, aes(x = cty^2, y = log(hwy))) + - Use `bquote()` function to parse mathematical expressions. ```{r} -#| fig.alt = "A scatter plot showing the squared city miles per gallon on the +#| fig.alt: "A scatter plot showing the squared city miles per gallon on the #| x-axis versus the base 10 logarithm of highway miles per gallon on the #| y-axis for 234 cars. In the axis titles, the base 10 is indicated in #| subscript on the y-axis and the power 2 is indicated in superscript on @@ -440,7 +440,7 @@ ggplot(mpg, aes(x = cty^2, y = log(hwy, base = 10))) + - If you're already familiar with Markdown and HTML, you might prefer using the [ggtext](https://wilkelab.org/ggtext/) package instead. In Markdown we can write the axis labels as `cty2` and `log10(hwy)` for x and y axes, respectively. Then, we tell ggplot2 to interpret the axis labels as Markdown and not as plain text by setting `axis.title.x` and `axis.title.y` to `ggtext::element_markdown()`. ```{r} -#| fig.alt = "A scatter plot showing the squared city miles per gallon on the +#| fig.alt: "A scatter plot showing the squared city miles per gallon on the #| x-axis versus the base 10 logarithm of highway miles per gallon on the #| y-axis for 234 cars. In the axis titles, the base 10 is indicated in #| subscript on the y-axis and the power 2 is indicated in superscript on @@ -472,7 +472,7 @@ Customise the `breaks` and `minor_breaks` in `scale_x_continuous()`, `scale_y_co Suppose you want to customise the major and minor grid lines on both the x and the y axes of the following plot. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis versus +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis versus #| the highway miles per gallon on the y-axis for 234 cars. The distance #| between axis ticks is constant within each axis." ggplot(mpg, aes(x = cty, y = hwy)) + @@ -483,7 +483,7 @@ You can set `breaks` and `minor_breaks` in `scale_x_continuous()` and `scale_y_c For example, on the x-axis we have major and minor grid breaks defined as a sequence and on the y-axis we have explicitly stated where major breaks should appear as a vector (the value stated are randomly selected for illustrative purposes only, they don't follow a best practice) and we have completely turned off minor grid lines by setting `minor_breaks` to `NULL`. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis versus +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis versus #| the highway miles per gallon on the y-axis for 234 cars. The distance #| between axis ticks varies within the y-axis. There are no minor horizontal #| grid lines, and there are three minor vertical gridlines between major @@ -528,7 +528,7 @@ Remove the padding around the data entirely using by setting `expand = c(0, 0)` - Remove all padding: Suppose you want to remove the padding around the heat map so it's flush against the axes. ```{r} -#| fig.alt = "A heatmap showing a 2D density estimate of the waiting and +#| fig.alt: "A heatmap showing a 2D density estimate of the waiting and #| eruption times of the Old Faithful geyser. The heatmap does not touch the #| panel edges." ggplot(faithfuld, aes(waiting, eruptions)) + @@ -538,7 +538,7 @@ ggplot(faithfuld, aes(waiting, eruptions)) + Since both x and y variables are continuous, we set `expand = c(0, 0)` in both `scale_x_continuous()` and `scale_y_continuous()`. ```{r} -#| fig.alt = "A heatmap showing a 2D density estimate of the waiting and +#| fig.alt: "A heatmap showing a 2D density estimate of the waiting and #| eruption times of the Old Faithful geyser. The heatmap touches the panel #| edges." ggplot(faithfuld, aes(waiting, eruptions)) + @@ -550,7 +550,7 @@ ggplot(faithfuld, aes(waiting, eruptions)) + - Remove some of the padding: Suppose you want to remove the padding below the bars and the x-axis only. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. No parts of the bars touch the panel edges." ggplot(mpg, aes(drv)) + geom_bar() @@ -559,7 +559,7 @@ ggplot(mpg, aes(drv)) + You would make this adjustment on `scale_y_continuous()` since that padding is in the vertical direction. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. All bars touch the bottom of the panel, and the highest bar #| touches the top of the panel." ggplot(mpg, aes(drv)) + @@ -574,7 +574,7 @@ The `mult` argument in `expansion()` takes a multiplicative range expansion fact Given a vector of length 2, the lower limit is expanded by `mult[1]` (in this case 0) and the upper limit is expanded by `mult[2]` (in this case 0.05). ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. All bars touch the bottom of the panel, and no bar touches #| the top of the panel." ggplot(mpg, aes(drv)) + diff --git a/vignettes/articles/faq-bars.Rmd b/vignettes/articles/faq-bars.Rmd index 345ff68c1b..3cbacf4d79 100644 --- a/vignettes/articles/faq-bars.Rmd +++ b/vignettes/articles/faq-bars.Rmd @@ -42,7 +42,7 @@ If assigning color based on another variable, map the variable to the `fill` `ae You can set all bars to be a given color with the `fill` argument of `geom_bar()`. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. All bars are blue." ggplot(mpg, aes(x = drv)) + geom_bar(fill = "blue") @@ -51,7 +51,7 @@ ggplot(mpg, aes(x = drv)) + Alternatively, if the colors should be based on a variable, this should be should happen in the `aes()` mapping. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. From left-to-right, the bars appear red, green and blue." ggplot(mpg, aes(x = drv, fill = drv)) + geom_bar() @@ -61,7 +61,7 @@ And if you want to then customize the colors, one option is `scale_fill_manual() See other `scale_fill_*()` functions for more options for color choices. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. From left-to-right, the bars are purple, orange and dark #| blue." ggplot(mpg, aes(x = drv, fill = drv)) + @@ -85,12 +85,11 @@ By default, the `width` of bars is `0.9` (90% of the resolution of the data). You can set this argument to a lower value to get bars that are narrower with more space between them. ```{r} -#| fig.alt = c( -#| "A bar chart showing the number of cars for each of three types -#| of drive train. The bars are somewhat narrower than the default.", -#| "A bar chart showing the number of cars for each of three types +#| fig.alt: +#| - "A bar chart showing the number of cars for each of three types +#| of drive train. The bars are somewhat narrower than the default." +#| - "A bar chart showing the number of cars for each of three types #| of drive train. The bars are very narrow." -#| ) ggplot(mpg, aes(x = drv)) + geom_bar(width = 0.5) @@ -111,7 +110,7 @@ Adjust the `expand` argument in `scale_y_continuous()`, e.g. add `scale_y_contin By default ggplot2 expands the axes so the geoms aren't flush against the edges of the plot. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. No parts of the bars touch the panel edges." ggplot(mpg, aes(x = drv)) + geom_bar() @@ -120,7 +119,7 @@ ggplot(mpg, aes(x = drv)) + To remove the spacing between the bars and the x-axis, but keep the spacing between the bars and the top of the plot, use the following. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The bottom of the bars touch the x-axis." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -131,7 +130,7 @@ To achieve the opposite, switch the values in `mult`. Note that the tallest bar is now flush against top of the plot. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The top of the highest bar touches the top of the panel." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -142,7 +141,7 @@ To adjust spacing around the x-axis, adjust the `expand` argument in `scale_x_di Note that this places the bars flush against the left side and leaves some space on the right side. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The left of the leftmost bar touches the y-axis." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -152,7 +151,7 @@ ggplot(mpg, aes(x = drv)) + The default look of a bar plot can be achieved with the following. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. No parts of the bars touch the panel edges." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -173,7 +172,7 @@ Set `position = position_dodge2(preserve = "single")` in `geom_bar()`. In the following plot the bars have differing widths within each level of `drv` as there are differing levels of `class` represented. ```{r} -#| fig.alt = "A grouped bar chart showing car counts dodged and filled by 7 +#| fig.alt: "A grouped bar chart showing car counts dodged and filled by 7 #| types of cars for each of three types of drive train. The left group has #| 5 narrower bars, the middle group has 4 bars and the right group has 3 wider #| bars." @@ -184,7 +183,7 @@ ggplot(mpg, aes(x = drv, fill = class)) + You can use `position_dodge2()` with `preserve = "single"` to address this. ```{r} -#| fig.alt = "A grouped bar chart showing car counts dodged and filled by 7 +#| fig.alt: "A grouped bar chart showing car counts dodged and filled by 7 #| types of cars for each of three types of drive train. From left-to-right, #| each groups has respectively 5, 4 and 3 equally wide bars." ggplot(mpg, aes(x = drv, fill = class)) + @@ -207,7 +206,7 @@ If you also want to show percentages on the axis, use `scales::label_percent()`. The following plot is useful for comparing counts but not as useful for comparing proportions, which is what you need if you want to be able to make statements like "in this sample, it's more likely to have a two-seater car that has rear-wheel drive than an SUV that has rear-wheel drive". ```{r} -#| fig.alt = "A horizontal stacked bar chart showing car counts for 7 types of +#| fig.alt: "A horizontal stacked bar chart showing car counts for 7 types of #| cars, stacked and filled by 3 types of drive train." ggplot(mpg, aes(y = class, fill = drv)) + geom_bar() @@ -216,7 +215,7 @@ ggplot(mpg, aes(y = class, fill = drv)) + `position = "fill"` will generate a bar plot with bars of equal length and the stacks in each bar will show the proportion of `drv` for that particular `class`. ```{r} -#| fig.alt = "A horizontal filled bar chart showing proportions of cars for 7 +#| fig.alt: "A horizontal filled bar chart showing proportions of cars for 7 #| types of cars. The fill colour represents 3 types of drive train. Every #| stacked bar spans the width of the panel." ggplot(mpg, aes(y = class, fill = drv)) + @@ -226,7 +225,7 @@ ggplot(mpg, aes(y = class, fill = drv)) + If you want to show percentages instead of proportions on the x-axis, you can define this in `scale_x_continuous()` with `scales::label_percent()`. ```{r} -#| fig.alt = "A horizontal filled bar chart showing percentages of cars for 7 +#| fig.alt: "A horizontal filled bar chart showing percentages of cars for 7 #| types of cars. The fill colour represents 3 types of drive train. Every #| stacked bar spans the width of the panel." ggplot(mpg, aes(y = class, fill = drv)) + @@ -271,7 +270,7 @@ poll_longer Then, you can pass this result to `ggplot()` and create a bar for each `party` on the `y` (or `x`, if you prefer vertical bars) axis and fill the bars in with number of responses for each `opinion`. ```{r} -#| fig.alt = "A horizontal stacked bar chart showing opinion counts for 3 +#| fig.alt: "A horizontal stacked bar chart showing opinion counts for 3 #| parties, stacked and filled by 3 types of opinions." ggplot(poll_longer, aes(y = party, fill = opinion, x = n)) + geom_col() @@ -280,7 +279,7 @@ ggplot(poll_longer, aes(y = party, fill = opinion, x = n)) + To plot proportions (relative frequencies) instead of counts, use `position = "fill"` in `geom_col()`. ```{r} -#| fig.alt = "A horizontal filled bar chart showing proportions of opinions for +#| fig.alt: "A horizontal filled bar chart showing proportions of opinions for #| 3 parties. The fill colour represents 3 types of opinion. Every #| stacked bar spans the width of the panel." ggplot(poll_longer, aes(y = party, fill = opinion, x = n)) + @@ -315,7 +314,7 @@ You can do this with `tidyr::pivot_longer()`. Then, pass the resulting longer data frame to `ggplot()` group responses for each question together. ```{r} -#| fig.alt = "A grouped bar chart showing the number of responses to three +#| fig.alt: "A grouped bar chart showing the number of responses to three #| questions. Within each question, two bars denote an 'Agree' or 'Disagree' #| response." survey %>% @@ -342,7 +341,7 @@ One option for calculating group means is using `dplyr::group_by()` followed by Then, you can pass the resulting data frame to `ggplot()` and plot bars using `geom_col()`. ```{r} -#| fig.alt = "A bar chart showing the average highway miles per gallon for +#| fig.alt: "A bar chart showing the average highway miles per gallon for #| three types of drive train." mpg %>% group_by(drv) %>% @@ -354,7 +353,7 @@ mpg %>% Alternatively, you can use `stat_summary()` to let ggplot2 calculate and plot the means. ```{r} -#| fig.alt = "A bar chart showing the average highway miles per gallon for +#| fig.alt: "A bar chart showing the average highway miles per gallon for #| three types of drive train." ggplot(mpg, aes(x = drv, y = hwy)) + stat_summary(fun = "mean", geom = "bar") @@ -379,7 +378,7 @@ Also note that this will result in a deceiving bar plot, which should be avoided In the following plot the y-axis is limited to 20 to 120, and hence the bars are not showing up. ```{r} -#| fig.alt = "A plot with axes and a panel, but no other geometry." +#| fig.alt: "A plot with axes and a panel, but no other geometry." ggplot(mpg, aes(x = drv)) + geom_bar() + ylim(c(20, 120)) @@ -388,7 +387,7 @@ ggplot(mpg, aes(x = drv)) + In order to obtain a bar plot with limited y-axis, you need to instead set the limits in `coord_cartesian()`. ```{r} -#| fig.alt = "A bar chart showing the number of cars for each of three types +#| fig.alt: "A bar chart showing the number of cars for each of three types #| of drive train. The y-axis starts at 20, and all bars touch the x-axis." ggplot(mpg, aes(x = drv)) + geom_bar() + @@ -400,7 +399,7 @@ If you're using a bar plot to display values that could not take the value of 0, For example, if you have the following data and plot. ```{r} -#| fig.alt = "A bar chart showing numbers for 3 arbitrary categories. The +#| fig.alt: "A bar chart showing numbers for 3 arbitrary categories. The #| numbers are far away from the x-axis and visually appear broadly similar #| in height." df <- tibble::tribble( @@ -417,14 +416,13 @@ ggplot(df, aes(x = x, y = y)) + Also suppose that you want to cut off the bars at `y = 1000` since you know that the variable you're plotting cannot take a value less than 1000, you might use `geom_point()` instead. ```{r} -#| fig.alt = c( -#| "A bar chart showing numbers for 3 arbitrary categories. The y-axis starts +#| fig.alt: +#| - "A bar chart showing numbers for 3 arbitrary categories. The y-axis starts #| at 1000 and the bars all look different in height. This is not a recommended -#| way of plotting this data.", -#| "A scatter plot with 3 points showing numbers for 3 arbitrary categories. +#| way of plotting this data." +#| - "A scatter plot with 3 points showing numbers for 3 arbitrary categories. #| The y-axis starts at 1000 and the points have visually different values. #| This is a better way of plotting this data." -#| ) # don't do this ggplot(df, aes(x = x, y = y)) + geom_col() + diff --git a/vignettes/articles/faq-customising.Rmd b/vignettes/articles/faq-customising.Rmd index 5c8ed1b44f..0112d64627 100644 --- a/vignettes/articles/faq-customising.Rmd +++ b/vignettes/articles/faq-customising.Rmd @@ -40,7 +40,7 @@ By default your legend label will be the name of the variable that is mapped to You can change the title of your legend using `labs()`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend with the title 'Drive #| train'." @@ -52,16 +52,16 @@ ggplot(mpg, aes(x = hwy, y = cty, color = drv)) + If a legend is drawn for multiple aesthetics, you'll want to update the title for all of them. ```{r} -#| fig.alt = c( -#| "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: +#| - "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The point shapes and colours #| indicate three types of drive train. The shapes and colours are displayed in -#| separate legends titled 'drv' and 'Drive train' respectively.", -#| "A scatter plot showing the highway miles per gallon on the x-axis +#| separate legends titled 'drv' and 'Drive train' respectively." +#| - "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The point shapes and colours #| indicate three types of drive train. The shapes and colours are displayed in #| a single legend titled 'Drive train'." -#| ) +#| # not this ggplot(mpg, aes(x = hwy, y = cty, color = drv, shape = drv)) + geom_point() + @@ -89,7 +89,7 @@ You can supply a unit object to this argument, e.g. `unit(1.0, "cm")` for 1 cm s See the documentation for `grid::unit()` for more options for units. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the bottom of the #| plot in a horizontal orientation. Legend elements are spaced widely apart." @@ -104,7 +104,7 @@ ggplot(mpg, aes(x = hwy, y = cty, color = drv)) + For vertical legends changing `legend.spacing.y` changes the space between the legend title and the keys, but not between the keys, e.g. see the large space between the legend title and keys. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. In the legend, there is a large space between the title and keys." @@ -116,7 +116,7 @@ ggplot(mpg, aes(x = hwy, y = cty, color = drv)) + In order to change the space between the legend keys, you can first make the key size bigger with `legend.key.size` and then remove the grey background color with `legend.key`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. In the legend, elements are placed widely apart and the title is @@ -133,7 +133,7 @@ Note that the legend title is no longer aligned with the keys with this approach You can also shift it over with the `hjust` setting of `legend.title`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. In the legend, elements are placed widely apart and the title is @@ -161,7 +161,7 @@ The `labels` argument of `scale_*` functions takes named vectors, which what we Using named lists allows you to declare explicitly which label is assigned to which level, without having to keep track of level order. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by three #| types of drive train, which is displayed in a legend at the right of the #| plot. The legend items are name '4-wheel drive', 'Front-wheel drive' and @@ -191,7 +191,7 @@ You can use the following for 14 pts text for legend key labels and 10 pts text (Note that this doesn't result in a visually pleasing legend, by default ggplot2 uses a larger font size for the legend title than the legend text.) ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by seven #| types of cars, which is displayed in the legend on the right of the plot. #| The labels in the legend have a larger font size than the title." @@ -206,7 +206,7 @@ ggplot(mpg, aes(x = hwy, y = cty, color = class)) + For further customization of legend text, see the documentation for `element_text()`, e.g. you can change font colors or font face as well. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by seven #| types of cars, which is displayed in the legend on the right of the plot. #| The labels in the legends have a large, red font. The title has a smaller, @@ -235,7 +235,7 @@ You can set the background colour of the plot with `panel.background` in `theme( In the following example the border is made thicker with `linewidth = 3` to ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The panel background of the plot #| is light blue and is outlined in red with a thick stroke." ggplot(mpg, aes(x = hwy, y = cty)) + @@ -246,7 +246,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + If you want to change the colour of the plotting area but not the panel where the panel, you can so the same thing with `plot.background`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The plot background is light blue #| and is outlined in red with a thick stroke. The panel background remains #| grey." @@ -259,7 +259,7 @@ Note that ggplot2 has a variety of [complete themes](https://ggplot2.tidyverse.o For example, if you prefer a more minimal look to your plots, without the grey background, you might try `theme_minimal()`. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. There is no visible panel #| background and grid lines are in light grey." ggplot(mpg, aes(x = hwy, y = cty)) + @@ -270,7 +270,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + And you can continue customization based on one of these themes. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. There is no visible panel #| background and grid lines are in light grey. The plot as a whole is outlined #| by a thick red line." @@ -309,7 +309,7 @@ df <- tibble::tribble( By default, ggplot2 uses grey to represent `NA`s. ```{r} -#| fig.alt = "A stacked bar chart showing two groups on the x-axis and counts +#| fig.alt: "A stacked bar chart showing two groups on the x-axis and counts #| on the y-axis. Within a stacked bar, two different outcomes and 'NA's are #| distinguished by fill colour." ggplot(df, aes(x = group, fill = outcome)) + @@ -319,7 +319,7 @@ ggplot(df, aes(x = group, fill = outcome)) + You can change the color of `NA` with `scale_fill_discrete()` in this case, e.g. make it purple. ```{r} -#| fig.alt = "A stacked bar chart showing two groups on the x-axis and counts +#| fig.alt: "A stacked bar chart showing two groups on the x-axis and counts #| on the y-axis. Within a stacked bar, two different outcomes and 'NA's are #| distinguished by fill colour. The 'NA' fill colour is purple." ggplot(df, aes(x = group, fill = outcome)) + @@ -332,7 +332,7 @@ In the plot below this is shown with `theme_minimal()` to demonstrate how that l Note that while this is possible, setting the colour to transparent as such wouldn't be recommended in this particular case as it gives the appearance of a floating bar. ```{r} -#| fig.alt = "A stacked bar chart showing two groups on the x-axis and counts +#| fig.alt: "A stacked bar chart showing two groups on the x-axis and counts #| on the y-axis. Within a stacked bar, two different outcomes and 'NA's are #| distinguished by fill colour. The 'NA' fill colour is transparent, giving #| the appearance that one of the stacked bars is floating." @@ -359,7 +359,7 @@ You can change it with the `base_size` argument in the theme you're using. See the [complete theme documentation](https://ggplot2.tidyverse.org/reference/ggtheme.html) for more high level options you can set. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The points are coloured by seven #| types of car. All text sizes in the axes and legend are large." ggplot(mpg, aes(x = hwy, y = cty, color = class)) + @@ -389,7 +389,7 @@ Font characteristics of plot titles and subtitles can be controlled with the `pl You can use the following for 20 pts text for the plot title and 15 pts text for the plot subtitle. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The plot has a large title #| displaying 'This is the plot title' and a less large subtitle displaying #| 'And this is the subtitle' at the top of the plot." @@ -408,7 +408,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + For further customization of plot title and subtitle, see the documentation for `element_text()`, e.g. you can change font colors or font face as well. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The plot has a large red title #| displaying 'This is the plot title' and a less large subtitle in bold and #| italic displaying 'And this is the subtitle' at the top of the plot." @@ -439,7 +439,7 @@ In both cases, set font size in the `size` argument of `element_text()`, e.g. `a Font characteristics of axis labels can be controlled with `axis.title.x` or `axis.title.y` (or `axis.title` if you the same settings for both axes). ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The x-axis title displays #| 'This is HUGE' in a large font size, and the y-axis title displays #| 'This is small' in a smaller font size." @@ -458,7 +458,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + For further customization of plot title and subtitle, see the documentation for `element_text()`, e.g. you can change font colors or font face as well. ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. The x-axis title displays #| 'This is HUGE' in a large, red font, and the y-axis title displays #| 'This is tiny' in a smaller, bold and italic font." @@ -477,7 +477,7 @@ ggplot(mpg, aes(x = hwy, y = cty)) + You can also change the size of the axis text (e.g. numbers at the axis ticks) using `axis.text` (or `axis.text.x` and `axis.text.y` if you want to set different sizes). ```{r} -#| fig.alt = "A scatter plot showing the highway miles per gallon on the x-axis +#| fig.alt: "A scatter plot showing the highway miles per gallon on the x-axis #| and city miles per gallon on the y-axis. Both the x and the y axis titles #| display 'The axis labels are the same size' in a large font. Both axis #| labels are displayed in a larger, blue font." @@ -497,10 +497,10 @@ ggplot(mpg, aes(x = hwy, y = cty)) + ### What is the default size of `geom_text()` and how can I change the font size of `geom_text()`? -The default font size of `geom_text()` is 3.88. +The default font size of `geom_text()` is about 3.87. ```{r} -GeomLabel$default_aes$size +get_geom_defaults(geom_text)$size ``` You can change the size using the `size` argument in `geom_text()` for a single plot. If you want to use the same updated size, you can set this with `update_geom_defaults()`, e.g. `update_geom_defaults("text", list(size = 6))`. @@ -518,7 +518,7 @@ Please refer to ["Font size" section of the aesthetic specifications](https://gg Suppose you have the following data frame and visualization. ```{r} -#| fig.alt = "A plot showing text at diagonal positions with the labels 'two', +#| fig.alt: "A plot showing text at diagonal positions with the labels 'two', #| 'three' and 'four'." df <- tibble::tribble( ~x, ~y, ~name, @@ -534,7 +534,7 @@ ggplot(df, aes(x = x, y = y, label = name)) + You can set the size of the text with the following. ```{r} -#| fig.alt = "A plot showing larger text at diagonal positions with the labels +#| fig.alt: "A plot showing larger text at diagonal positions with the labels #| 'two', 'three' and 'four'." ggplot(df, aes(x = x, y = y, label = name)) + geom_text(size = 6) @@ -543,7 +543,7 @@ ggplot(df, aes(x = x, y = y, label = name)) + Or you can map it to the `size` `aes`thetic. In the following size is determined by the `x` value with `scale_size_identity()`. ```{r} -#| fig.alt = "A plot showing text at diagonal positions with the labels 'two', +#| fig.alt: "A plot showing text at diagonal positions with the labels 'two', #| 'three' and 'four' that increase in size from left to right." ggplot(df, aes(x = x, y = y, label = name)) + geom_text(aes(size = x)) + diff --git a/vignettes/articles/faq-faceting.Rmd b/vignettes/articles/faq-faceting.Rmd index 93ec538a9e..bb7112edbb 100644 --- a/vignettes/articles/faq-faceting.Rmd +++ b/vignettes/articles/faq-faceting.Rmd @@ -37,7 +37,7 @@ The simplest answer is that you should use `facet_wrap()` when faceting by a sin `facet_wrap()` is most commonly used to facet by a plot by a single categorical variable. ```{r} -#| fig.alt = "A histogram showing the city miles per gallon distribution for +#| fig.alt: "A histogram showing the city miles per gallon distribution for #| three types of drive train, each in their own panel in a 1-row, 3-column #| layout." ggplot(mpg, aes(x = cty)) + @@ -48,7 +48,7 @@ ggplot(mpg, aes(x = cty)) + And `facet_grid()` is commonly used to facet by a plot by two categorical variables. ```{r} -#| fig.alt = "A histogram showing the city miles per gallon distribution. The +#| fig.alt: "A histogram showing the city miles per gallon distribution. The #| plot has twelve panels in a 4-row, 3-column layout, showing three types of #| drive train in the horizontal direction, and four numbers of cylinders #| in the vertical direction. Several panels have no data." @@ -63,7 +63,7 @@ You can also use `facet_wrap()` with to facet by two categorical variables. This will only create facets for combinations of the levels of variables for which data exists. ```{r} -#| fig.alt = "A histogram showing the city miles per gallon distribution. The +#| fig.alt: "A histogram showing the city miles per gallon distribution. The #| plot has nine panels in a 3-row, 3-column layout, showing all existing #| combinations of three types of drive train, and four numbers of cylinders." ggplot(mpg, aes(x = cty)) + @@ -78,12 +78,11 @@ Similarly, you can also use `facet_grid()` to facet by a single categorical vari In the formula notation, you use a `.` to indicate that no faceting should be done along that axis, i.e. `cyl ~ .` facets across the y-axis (within a column) while `. ~ cyl` facets across the x-axis (within a row). ```{r out.width = "50%"} -#| fig.alt = c( -#| "A histogram showing the city miles per gallon distribution. The plot has -#| four panels in a 4-row, 1-column layout, showing four numbers of cylinders.", -#| "A histogram showing the city miles per gallon distribution. The plot has +#| fig.alt: +#| - "A histogram showing the city miles per gallon distribution. The plot has +#| four panels in a 4-row, 1-column layout, showing four numbers of cylinders." +#| - "A histogram showing the city miles per gallon distribution. The plot has #| four panels in a 1-row, 4-column layout, showing four numbers of cylinders." -#| ) ggplot(mpg, aes(x = cty)) + geom_histogram() + facet_grid(cyl ~ .) @@ -107,7 +106,7 @@ Then, add a `geom_vline()` layer to your plot that uses the summarized data. Suppose you have the following plot, and you want to add a vertical line at the mean value of `hwy` (highway mileage) for each pane. ```{r} -#| fig.alt = "A histogram showing the highway miles per gallon distribution for +#| fig.alt: "A histogram showing the highway miles per gallon distribution for #| three types of drive train, each in their own panel in a 1-row, 3-column #| layout." ggplot(mpg, aes(x = hwy)) + @@ -130,7 +129,7 @@ mpg_summary Then, add a `geom_vline()` layer to your plot that uses the summary data. ```{r} -#| fig.alt = "A histogram showing the highway miles per gallon distribution for +#| fig.alt: "A histogram showing the highway miles per gallon distribution for #| three types of drive train, each in their own panel in a 1-row, 3-column #| layout. Each panel has a vertical black line indicating the mean of the #| distribution." @@ -156,7 +155,7 @@ Suppose you have the following faceted plot. By default, both x and y scales are shared across the facets. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout, showing three types of drive train in the #| horizontal direction and four numbers of cylinders in the vertical @@ -170,7 +169,7 @@ ggplot(mpg, aes(x = cty, y = hwy)) + You can control this behaviour with the `scales` argument of faceting functions: varying scales across rows (`"free_x"`), columns (`"free_y"`), or both rows and columns (`"free"`), e.g. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout, showing three types of drive train in the #| horizontal direction and four numbers of cylinders in the vertical @@ -185,7 +184,7 @@ ggplot(mpg, aes(x = cty, y = hwy)) + If you also want to make sure that a particular value or range is included in each of the facets, you can set this with `expand_limits()`, e.g. ensure that 10 is included in the x-axis and values between 20 to 25 are included in the y-axis: ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout, showing three types of drive train in the #| horizontal direction and four numbers of cylinders in the vertical @@ -213,7 +212,7 @@ Set the `strip.text` element in `theme()` to `element_blank()`. Setting `strip.text` to `element_blank()` will remove all facet labels. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout. The strips, or panel layout titles and #| their backgrounds, are missing." @@ -226,7 +225,7 @@ ggplot(mpg, aes(x = cty, y = hwy)) + You can also remove the labels across rows only with `strip.x.text` or across columns only with `strip.y.text`. ```{r} -#| fig.alt = "A scatter plot showing city miles per gallon on the x-axis and +#| fig.alt: "A scatter plot showing city miles per gallon on the x-axis and #| highway miles per gallon on the y-axis. The plot has twelve panels in a #| 4-row, 3-column layout. In the vertical direction, the panels indicate four #| numbers of cylinders. The strips of the horizontal direction are missing." @@ -250,7 +249,7 @@ In the data frame below we have 100 observations, 50 of them come from one group These groups have very long names, and so when you facet the ploy by group, the facet labels (strips) get cut off. ```{r} -#| fig.alt = "A histogram with two panels in a 1-row, 2-column layout of random +#| fig.alt: "A histogram with two panels in a 1-row, 2-column layout of random #| data. The first panel has as title 'A long group name for the first group'. #| The second panel has a title 'A muuuuuuuuuuuuuch longer group name for the #| second group'. However, the second title is clipped to the panel width and @@ -269,7 +268,7 @@ ggplot(df, aes(x = x)) + You can control the maximum width of the facet label by setting the `width` in the `label_wrap_gen()` function, which is then passed to the `labeller` argument of your faceting function. ```{r} -#| fig.alt = "A histogram with two panels in a 1-row, 2-column layout of random +#| fig.alt: "A histogram with two panels in a 1-row, 2-column layout of random #| data. The first panel has as title 'A long group name for the first group' #| in two lines of text. The second panel has a title 'A muuuuuuuuuuuuuch #| longer group name for the second group' in three lines of text. The width @@ -305,7 +304,7 @@ df You can plot `price` versus `time` and facet by `country`, but the resulting plot can be a bit difficult to read due to the shared y-axis label. ```{r warning = FALSE} -#| fig.alt = "A timeseries plot showing price over time for two countries, Japan +#| fig.alt: "A timeseries plot showing price over time for two countries, Japan #| and the US, in two panels in a 2-row, 1-column layout. The countries are #| indicated at the top of each panel. The two y-axes have different ranges." ggplot(df, aes(x = year, y = price)) + @@ -317,7 +316,7 @@ ggplot(df, aes(x = year, y = price)) + With the following you can customize the facet labels first with `as_labeller()`, turn off the default y-axis label, and then place the facet labels where the y-axis label goes (`"outside"` and on the `"left"`). ```{r} -#| fig.alt = "A timeseries plot showing price over time for two countries and +#| fig.alt: "A timeseries plot showing price over time for two countries and #| their currencies, the Japanese Yen and the US Dollar, in two panels in a #| 2-row, 1-column layout. The countries and currency units are indicated at #| the left of each panel. The two y-axes have different ranges." diff --git a/vignettes/articles/faq-reordering.Rmd b/vignettes/articles/faq-reordering.Rmd index 39584e225d..d820c7a50e 100644 --- a/vignettes/articles/faq-reordering.Rmd +++ b/vignettes/articles/faq-reordering.Rmd @@ -44,7 +44,7 @@ Classes are ordered alphabetically. You might prefer them to be ordered by the number of cars in each class. ```{r} -#| fig.alt = "A horizontal bar plot showing counts on the x-axis and seven +#| fig.alt: "A horizontal bar plot showing counts on the x-axis and seven #| types of cars on the y-axis. From bottom to top, the car types are in #| alphabetical order." ggplot(mpg, aes(y = class)) + @@ -54,7 +54,7 @@ ggplot(mpg, aes(y = class)) + To do this, you can use `forcats::fct_infreq()`. ```{r} -#| fig.alt = "A horizontal bar plot showing counts on the x-axis and seven +#| fig.alt: "A horizontal bar plot showing counts on the x-axis and seven #| types of cars on the y-axis. From top to bottom, the car types are ordered #| by increasing number of cars." ggplot(mpg, aes(y = forcats::fct_infreq(class))) + @@ -64,7 +64,7 @@ ggplot(mpg, aes(y = forcats::fct_infreq(class))) + If you'd like to plot the highest value first, you can also reverse the order with `forcats::fct_rev()`. You might also want to simplify the axis label. ```{r} -#| fig.alt = "A horizontal bar plot showing counts on the x-axis and seven +#| fig.alt: "A horizontal bar plot showing counts on the x-axis and seven #| types of cars on the y-axis. From top to bottom, the car types are ordered #| in decreasing number of cars." ggplot(mpg, aes(y = forcats::fct_rev(forcats::fct_infreq(class)))) + @@ -86,7 +86,7 @@ The forcats package offers a variety of options for doing this, such as `forcats Suppose you have the following stacked bar plot of `clarity` of `diamonds` by their `cut`. ```{r} -#| fig.alt = "A stacked bar plot showing counts on the y-axis and five cut +#| fig.alt: "A stacked bar plot showing counts on the y-axis and five cut #| qualities of diamonds on the x-axis. Within every stacked bar, the fill #| colour indicates an ordinal clarity of the diamond. The worst clarity has #| the darkest colour and the best quality has the lightest colour. The best @@ -99,7 +99,7 @@ You can reverse the order `clarity` levels are displayed in the bars with `forca This will also change the order they're presented in the legend so the two orders match. ```{r} -#| fig.alt = "A stacked bar plot showing counts on the y-axis and five cut +#| fig.alt: "A stacked bar plot showing counts on the y-axis and five cut #| qualities of diamonds on the x-axis. Within every stacked bar, the fill #| colour indicates an ordinal clarity of the diamond. The worst clarity has #| the lightest colour and the best quality has the darkest colour. The worst @@ -126,7 +126,7 @@ The order of the boxes is determined by the order of the levels of the variable If the faceting variable is character, this order is alphabetical by default. ```{r} -#| fig.alt = "A boxplot showing the highway miles per gallon on the y-axis for +#| fig.alt: "A boxplot showing the highway miles per gallon on the y-axis for #| seven types of car on the x-axis. The car types on the x-axis are in #| alphabetical order." ggplot(mpg, aes(x = class, y = hwy)) + @@ -138,7 +138,7 @@ You can do this in a data transformation step prior to plotting (e.g. with `dply You might then want to customize the x-axis label as well. ```{r} -#| fig.alt = "A boxplot showing the highway miles per gallon on the y-axis for +#| fig.alt: "A boxplot showing the highway miles per gallon on the y-axis for #| seven types of car on the x-axis. The car types on the x-axis sorted from #| left to right by increasing medians." ggplot(mpg, aes(x = forcats::fct_reorder(class, hwy, .fun = median), y = hwy)) + @@ -163,7 +163,7 @@ The order of the panes is determined by the order of the levels of the variable If the faceting variable is character, this order is alphabetical by default. ```{r} -#| fig.alt = "A scatter plot showing the engine displacement on the x-axis and +#| fig.alt: "A scatter plot showing the engine displacement on the x-axis and #| highway miles per gallon on the y-axis of 234 cars. The plot has three #| panels in a 1-row, 3-column layout for three types of drive train. The drive #| trains are ordered alphabetically in the horizontal direction." @@ -177,7 +177,7 @@ You can use `forcats::fct_relevel()` to reorder the levels of `drv`. You can do this in a data transformation step prior to plotting (e.g. with `dplyr::mutate()`) or you can do it directly in the plotting code as shown below. ```{r} -#| fig.alt = "A scatter plot showing the engine displacement on the x-axis and +#| fig.alt: "A scatter plot showing the engine displacement on the x-axis and #| highway miles per gallon on the y-axis of 234 cars. The plot has three #| panels in a 1-row, 3-column layout for three types of drive train. The drive #| trains are in the order 'r', 'f' and '4' from left to right." @@ -215,7 +215,7 @@ Note that the blue circle is partially covered by the yellow triangle since that Similarly the black asterisk appears on top of the red square. ```{r} -#| fig.alt = "A scatter plot showing four points at the same y-positions but at +#| fig.alt: "A scatter plot showing four points at the same y-positions but at #| four x-positions, of which two are very distinct. Every point has a distinct #| shape and colour. A yellow triangle is plotted on top of a blue circle. #| A black asterisk is plotted on top of a red square." @@ -229,7 +229,7 @@ Suppose you arranged your data in ascending order of the x-coordinates and plott Now the blue circle is over the yellow triangle since 0.01 comes after 0 and similarly the red square is over the black asterisk since 1 comes after 0.99. ```{r} -#| fig.alt = "A scatter plot showing four points at the same y-positions but at +#| fig.alt: "A scatter plot showing four points at the same y-positions but at #| four x-positions, of which two are very distinct. Every point has a distinct #| shape and colour. A blue circle is plotted on top of a yellow triangle. A #| red square is plotted on top of a black asterisk." @@ -245,16 +245,15 @@ df_arranged %>% If you wanted to make sure that the observation identified with an asterisk is always plotted on top, regardless of how the data are arranged in the data frame, you can create an additional layer for that observation. ```{r} -#| fig.alt = c( -#| "A scatter plot showing four points at the same y-positions but at four +#| fig.alt: +#| - "A scatter plot showing four points at the same y-positions but at four #| x-positions, of which two are very distinct. Every point has a distinct shape #| and colour. A yellow triangle is plotted on top of a blue circle. A black -#| asterisk is plotted on top of a red square.", -#| "A scatter plot showing four points at the same y-positions but at four +#| asterisk is plotted on top of a red square." +#| - "A scatter plot showing four points at the same y-positions but at four #| x-positions, of which two are very distinct. Every point has a distinct shape #| and colour. A blue circle is plotted on top of a yellow triangle. A black #| asterisk is plotted on top of a red square." -#| ) ggplot(mapping = aes(x = x, y = y, fill = fill, shape = shape)) + geom_point(data = df %>% filter(shape != "asterisk"), size = 8) + diff --git a/vignettes/extending-ggplot2.Rmd b/vignettes/extending-ggplot2.Rmd index 6ee65ae718..adac6896ea 100644 --- a/vignettes/extending-ggplot2.Rmd +++ b/vignettes/extending-ggplot2.Rmd @@ -86,7 +86,7 @@ stat_chull <- function(mapping = NULL, data = NULL, geom = "polygon", Once we have a layer function we can try our new stat: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hull of all the points is marked by a #| polygon with no fill." ggplot(mpg, aes(displ, hwy)) + @@ -99,7 +99,7 @@ ggplot(mpg, aes(displ, hwy)) + Once we've written this basic object, ggplot2 gives a lot for free. For example, ggplot2 automatically preserves aesthetics that are constant within each group: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hulls of points, grouped and coloured by #| three types of drive train, are marked by polygons with no fill but the #| outline matches the colours of the points." @@ -111,7 +111,7 @@ ggplot(mpg, aes(displ, hwy, colour = drv)) + We can also override the default geom to display the convex hull in a different way: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The points that are part of the convex hull of all #| points are marked with a red outline." ggplot(mpg, aes(displ, hwy)) + @@ -124,7 +124,7 @@ ggplot(mpg, aes(displ, hwy)) + A more complex stat will do some computation. Let's implement a simple version of `geom_smooth()` that adds a line of best fit to a plot. We create a `StatLm` that inherits from `Stat` and a layer function, `stat_lm()`: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. A straight line with a negative slope passes through #| the cloud of points." StatLm <- ggproto("StatLm", Stat, @@ -159,7 +159,7 @@ ggplot(mpg, aes(displ, hwy)) + `StatLm` is inflexible because it has no parameters. We might want to allow the user to control the model formula and the number of points used to generate the grid. To do so, we add arguments to the `compute_group()` method and our wrapper function: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. A wobbly line follows the point cloud over the #| horizontal direction. 20 points are placed on top of the line with constant #| horizontal intervals." @@ -224,13 +224,12 @@ Sometimes you have calculations that should be performed once for the complete d To do this we override the `setup_params()` method. It's passed the data and a list of params, and returns an updated list. ```{r} -#| fig.alt = c( -#| "A line plot showing three kernel density estimates of engine displacement, +#| fig.alt: +#| - "A line plot showing three kernel density estimates of engine displacement, #| coloured for three types of drive trains. The lines are a little bit -#| wobbly.", -#| "A line plot showing three kernel density estimates of engine displacement, +#| wobbly." +#| - "A line plot showing three kernel density estimates of engine displacement, #| coloured for three types of drive trains. The lines are fairly smooth." -#| ) StatDensityCommon <- ggproto("StatDensityCommon", Stat, required_aes = "x", @@ -278,7 +277,7 @@ I recommend using `NULL` as a default value. If you pick important parameters au This stat illustrates another important point. If we want to make this stat usable with other geoms, we should return a variable called `density` instead of `y`. Then we can set up the `default_aes` to automatically map `density` to `y`, which allows the user to override it to use with different geoms: ```{r} -#| fig.alt = "A plot showing the engine displacement versus three types of drive +#| fig.alt: "A plot showing the engine displacement versus three types of drive #| trains. Every drive train is represented by a series of densely packed #| points that imitate a horizontal line, and their colour intensity indicates #| the kernel density estimate of the displacement." @@ -299,7 +298,7 @@ ggplot(mpg, aes(displ, drv, colour = after_stat(density))) + However, using this stat with the area geom doesn't work quite right. The areas don't stack on top of each other: ```{r} -#| fig.alt = "An area plot showing the kernel density estimates of +#| fig.alt: "An area plot showing the kernel density estimates of #| engine displacement. Three areas are shown that indicate the estimates for #| three types of drive trains separately. All areas are floored to the x-axis #| and overlap one another." @@ -310,16 +309,15 @@ ggplot(mpg, aes(displ, fill = drv)) + This is because each density is computed independently, and the estimated `x`s don't line up. We can resolve that issue by computing the range of the data once in `setup_params()`. ```{r} -#| fig.alt = c( -#| "A stacked area plot showing kernel density estimates of engine displacement. +#| fig.alt: +#| - "A stacked area plot showing kernel density estimates of engine displacement. #| Three areas are shown that indicate the estimates for three types of drive #| trains separately. The areas are stacked on top of one another and show -#| no overlap.", -#| "A heatmap showing the density of engine displacement for three types of +#| no overlap." +#| - "A heatmap showing the density of engine displacement for three types of #| drive trains. The heatmap has three rows for the drive trains, but are #| continuous in the horizontal direction. The fill intensity of the heatmap #| shows the kernel density estimates." -#| ) StatDensityCommon <- ggproto("StatDensityCommon", Stat, required_aes = "x", default_aes = aes(y = after_stat(density)), @@ -377,7 +375,7 @@ It's harder to create a new geom than a new stat because you also need to know s It's easiest to start with a simple example. The code below is a simplified version of `geom_point()`: ```{r GeomSimplePoint} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The points are larger than the default." GeomSimplePoint <- ggproto("GeomSimplePoint", Geom, required_aes = c("x", "y"), @@ -441,7 +439,7 @@ Overriding `draw_panel()` is most appropriate if there is one graphic element pe The following code makes a simplified version of `GeomPolygon`: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hulls of points, grouped by 7 types of #| cars, are displayed as multiple polygons with no fill, but the outer line is #| coloured by the type." @@ -512,7 +510,7 @@ You might want to compare this to the real `GeomPolygon`. You'll see it override Sometimes you just want to make a small modification to an existing geom. In this case, rather than inheriting from `Geom` you can inherit from an existing subclass. For example, we might want to change the defaults for `GeomPolygon` to work better with `StatChull`: ```{r} -#| fig.alt = "Scatterplot of engine displacement versus highway miles per +#| fig.alt: "Scatterplot of engine displacement versus highway miles per #| gallon, for 234 cars. The convex hull of all the points is marked by a #| polygon with no fill." GeomPolygonHollow <- ggproto("GeomPolygonHollow", GeomPolygon, @@ -628,12 +626,11 @@ title | `element_text()` | all text in title elements (plot, axes & lege These set default properties that are inherited by more specific settings. These are most useful for setting an overall "background" colour and overall font settings (e.g. family and size). ```{r axis-line-ex} -#| fig.alt = c( -#| "Scatterplot of three observations arranged diagonally. The axis titles 'x' -#| and 'y' are coloured in black", -#| "Scatterplot of three observations arranged diagonally. The axis titles 'x' +#| fig.alt: +#| - "Scatterplot of three observations arranged diagonally. The axis titles 'x' +#| and 'y' are coloured in black" +#| - "Scatterplot of three observations arranged diagonally. The axis titles 'x' #| and 'y' are coloured in red" -#| ) df <- data.frame(x = 1:3, y = 1:3) base <- ggplot(df, aes(x, y)) + geom_point() + @@ -809,11 +806,10 @@ FacetDuplicate <- ggproto("FacetDuplicate", Facet, Now with everything assembled, lets test it out: ```{r} -#| fig.alt = c( -#| "Scatterplot showing horsepower against miles per gallon for 32 cars.", -#| "Scatterplot with two panels showing horsepower against miles per gallon for +#| fig.alt: +#| - "Scatterplot showing horsepower against miles per gallon for 32 cars." +#| - "Scatterplot with two panels showing horsepower against miles per gallon for #| 32 cars. The left and right panels are identical." -#| ) p <- ggplot(mtcars, aes(x = hp, y = mpg)) + geom_point() p p + facet_duplicate() @@ -1005,7 +1001,7 @@ As is very apparent, the `draw_panel` method can become very unwieldy once it be Enough talk - lets see if our new and powerful faceting extension works: ```{r} -#| fig.alt = "Scatterplot with two panels showing horsepower against miles per +#| fig.alt: "Scatterplot with two panels showing horsepower against miles per #| gallon for 32 cars. Both panels show the same datapoints. The left panel is #| titled 'original' and the right panel is titled 'transformed (sqrt)'. On the #| right panel, the miles per gallon are displayed on a square root @@ -1018,7 +1014,7 @@ ggplot(mtcars, aes(x = hp, y = mpg)) + geom_point() + facet_trans('sqrt') As the rendering part of a facet class is often the difficult development step, it is possible to piggyback on the existing faceting classes to achieve a range of new facetings. Below we will subclass `facet_wrap()` to make a `facet_bootstrap()` class that splits the input data into a number of panels at random. ```{r} -#| fig.alt = "Scatterplot with three-by-three panels showing the weight versus +#| fig.alt: "Scatterplot with three-by-three panels showing the weight versus #| the price of about 10.000 diamonds in every panel. The panels are titled 1 #| to 9 and show different points, but are visually similar." diff --git a/vignettes/ggplot2-specs.Rmd b/vignettes/ggplot2-specs.Rmd index d66cb5951b..7829f05f6a 100644 --- a/vignettes/ggplot2-specs.Rmd +++ b/vignettes/ggplot2-specs.Rmd @@ -53,7 +53,7 @@ Line types can be specified with: 4 = dotdash, 5 = longdash, 6 = twodash, as shown below: ```{r} - #| fig.alt = "A series of 6 horizontal lines with different line types. + #| fig.alt: "A series of 6 horizontal lines with different line types. #| From top-to-bottom they are titled 'solid', 'dashed', 'dotted', #| 'dotdash', 'longdash', 'twodash'." lty <- c("solid", "dashed", "dotted", "dotdash", "longdash", "twodash") @@ -76,7 +76,7 @@ Line types can be specified with: three off followed by one on and finally three off. ```{r} - #| fig.alt = "A series of 9 horizontal lines with different line types. + #| fig.alt: "A series of 9 horizontal lines with different line types. #| Each line is titled by two hexadecimal digits that determined the #| lengths of dashes and gaps." lty <- c("11", "18", "1f", "81", "88", "8f", "f1", "f8", "ff") @@ -107,16 +107,15 @@ with this mistake. and can be one of "round", "butt" (the default), or "square". ```{r, out.width = "30%", fig.show = "hold"} - #| fig.alt = c( - #| "A plot showing a line with an angle. A thinner red line is placed over - #| a thicker black line. The black line ends where the red line ends.", - #| "A plot showing a line with an angle. A thinner red line is placed over + #| fig.alt: + #| - "A plot showing a line with an angle. A thinner red line is placed over + #| a thicker black line. The black line ends where the red line ends." + #| - "A plot showing a line with an angle. A thinner red line is placed over #| a thicker black line. The black line ends past where the red line ends, - #| and ends in a semicircle.", - #| "A plot showing a line with an angle. A thinner red line is placed over + #| and ends in a semicircle." + #| - "A plot showing a line with an angle. A thinner red line is placed over #| a thicker black line. The black line ends past where the red line ends, #| and ends in a square shape." - #| ) df <- data.frame(x = 1:3, y = c(4, 1, 9)) base <- ggplot(df, aes(x, y)) + xlim(0.5, 3.5) + ylim(0, 10) base + @@ -136,15 +135,14 @@ with this mistake. "round" (the default), "mitre", or "bevel". ```{r, out.width = "30%", fig.show = "hold"} - #| fig.alt = c( - #| "A plot showing a thin red line on top of a thick black line shaped like - #| the letter 'V'. The corner in the black V-shape is rounded.", - #| "A plot showing a thin red line on top of a thick black line shaped like - #| the letter 'V'. The corner in the black V-shape is sharp.", - #| "A plot showing a thin red line on top of a thick black line shaped like + #| fig.alt: + #| - "A plot showing a thin red line on top of a thick black line shaped like + #| the letter 'V'. The corner in the black V-shape is rounded." + #| - "A plot showing a thin red line on top of a thick black line shaped like + #| the letter 'V'. The corner in the black V-shape is sharp." + #| - "A plot showing a thin red line on top of a thick black line shaped like #| the letter 'V'. A piece of the corner is cut off so that the two #| straight parts are connected by a horizontal part." - #| ) df <- data.frame(x = 1:3, y = c(9, 1, 9)) base <- ggplot(df, aes(x, y)) + ylim(0, 10) base + @@ -175,7 +173,7 @@ Shapes take five types of values: * An __integer__ in $[0, 25]$: ```{r} - #| fig.alt = "A 5-by-5 grid of point symbols annotated by the numbers + #| fig.alt: "A 5-by-5 grid of point symbols annotated by the numbers #| that can be used to represent the symbols. From left to right, the #| first 15 symbols are lines or open shapes, the next 5 symbols are solid #| shapes and the last 5 symbols are filled shaped." @@ -195,7 +193,7 @@ Shapes take five types of values: * The __name__ of the shape: ```{r out.width = "90%", fig.asp = 0.4, fig.width = 8} - #| fig.alt = "An irregular 6-by-7 grid of point symbols annotated by the + #| fig.alt: "An irregular 6-by-7 grid of point symbols annotated by the #| names that can be used to represent the symbols. Broadly, from top to #| bottom, the symbols are circles, squares, diamonds, triangles and #| others. Broadly from left to right, the symbols are solid shapes, @@ -233,7 +231,7 @@ Shapes take five types of values: While `colour` applies to all shapes, `fill` only applies to shapes 21-25, as can be seen above. The size of the filled part is controlled by `size`, the size of the stroke is controlled by `stroke`. Each is measured in mm, and the total size of the point is the sum of the two. Note that the size is constant along the diagonal in the following figure. ```{r} -#| fig.alt = "A plot showing a 4-by-4 grid of red points, the top 12 points with +#| fig.alt: "A plot showing a 4-by-4 grid of red points, the top 12 points with #| black outlines. The size of the points increases horizontally. The stroke of #| the outlines of the points increases vertically. A white diagonal line with #| a negative slope marks that the 'stroke' versus 'size' trade-off has @@ -252,7 +250,7 @@ ggplot(sizes, aes(size, stroke, size = size, stroke = stroke)) + There are only three fonts that are guaranteed to work everywhere: "sans" (the default), "serif", or "mono": ```{r} -#| fig.alt = "A plot showing three text labels arranged vertically. The top +#| fig.alt: "A plot showing three text labels arranged vertically. The top #| label is 'sans' and is displayed in a sans-serif font. The middle label is #| 'serif' and is displayed in a serif font. The bottom label is 'mono' and #| is displayed in a monospaced font." @@ -272,7 +270,7 @@ Both approaches have pros and cons, so you will to need to try both of them and ### Font face ```{r} -#| fig.alt = "A plot showing four text labels arranged vertically. The top +#| fig.alt: "A plot showing four text labels arranged vertically. The top #| label is 'bold.italic' and is displayed in bold and italic. The next three #| labels are 'italic', 'bold' and 'plain' and are displayed in their #| respective styles." @@ -294,7 +292,7 @@ Horizontal and vertical justification have the same parameterisation, either a s * left = 0, center = 0.5, right = 1 ```{r} -#| fig.alt = "A 3-by-3 grid of text on top of points, with horizontal text +#| fig.alt: "A 3-by-3 grid of text on top of points, with horizontal text #| justification increasing from 0 to 1 on the x-axis and vertical #| justification increasing from 0 to 1 on the y-axis. The points make it #| easier to see the relative placement of text." diff --git a/vignettes/ggplot2.Rmd b/vignettes/ggplot2.Rmd index f82f092df8..36193b65a4 100644 --- a/vignettes/ggplot2.Rmd +++ b/vignettes/ggplot2.Rmd @@ -23,7 +23,7 @@ This allows you to 'speak' a graph from composable elements, instead of being li More complete information about how to use ggplot2 can be found in the [book](https://ggplot2-book.org/), but here you'll find a brief overview of the plot components and some terse examples to build a plot like this: ```{r cake, echo = FALSE} -#| fig.alt = "Scatterplot of city versus highway miles per gallon, for many cars +#| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars #| coloured by engine displacement. The plot has six panels in a 2-row, #| 3-column layout, showing the combinations of three types of drive train and #| year of manifacture. Every panel has an individual trendline." @@ -41,7 +41,7 @@ ggplot(mpg, aes(cty, hwy)) + For structure, we go over the 7 composable parts that come together as a set of instructions on how to draw a chart. ```{r overview_graphic, echo=FALSE} -#| fig.alt = "A schematic displaying seven overlaying rhombuses indicating the +#| fig.alt: "A schematic displaying seven overlaying rhombuses indicating the #| different composable parts. From bottom to top, the labels read 'Data', #| 'Mapping', 'Layers', 'Scales', 'Facets', 'Coordinates' and 'Theme'." n <- 7 @@ -108,7 +108,7 @@ Every layer consists of three important parts: A layer can be constructed using the `geom_*()` and `stat_*()` functions. These functions often determine one of the three parts of a layer, while the other two can still be specified. Here is how we can use two layers to display the `cty` and `hwy` columns of the `mpg` dataset as points and stack a trend line on top. ```{r example_layer, fig.show='hold'} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The plot has a blue trendline with a positive slope." ggplot(mpg, aes(cty, hwy)) + # to create a scatterplot @@ -125,7 +125,7 @@ Scales are responsible for updating the limits of a plot, setting the breaks, fo To use scales, one can use one of the scale functions that are patterned as `scale_{aesthetic}_{type}()` functions, where `{aesthetic}` is one of the pairings made in the mapping part of a plot. To map the `class` column in the `mpg` dataset to the viridis colour palette, we can write the following: ```{r example_scales} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The points are coloured according to seven classes of cars." ggplot(mpg, aes(cty, hwy, colour = class)) + geom_point() + @@ -141,7 +141,7 @@ The facets have their own mapping that can be given as a formula. To plot subsets of the `mpg` dataset based on levels of the `drv` and `year` variables, we can use `facet_grid()` as follows: ```{r example_facets} -#| fig.alt = "Scatterplot of city versus highway miles per gallon, for many cars. +#| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars. #| The plot has six panels in a 2-row, 3-column layout, showing the #| combinations of three types of drive train and year of manifacture." ggplot(mpg, aes(cty, hwy)) + @@ -157,7 +157,7 @@ While typically Cartesian coordinates are used, the coordinate system powers the We can also use coordinates to display a plot with a fixed aspect ratio so that one unit has the same length in both the x and y directions. The `coord_fixed()` function sets this ratio automatically. ```{r example_coords} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The aspect ratio of the plot is such that units on the x-axis #| have the same length as units on the y-axis." ggplot(mpg, aes(cty, hwy)) + @@ -172,7 +172,7 @@ The [theme](https://ggplot2-book.org/themes) system controls almost any visuals To tweak the look of the plot, one can use many of the built-in `theme_*()` functions and/or detail specific aspects with the `theme()` function. The `element_*()` functions control the graphical attributes of theme components. ```{r example_theme} -#| fig.alt = "A scatterplot showing city versus highway miles per gallon for +#| fig.alt: "A scatterplot showing city versus highway miles per gallon for #| many cars. The points are coloured according to seven classes of cars. The #| legend of the colour is displayed on top of the plot. The plot has thick #| axis lines and the bottom axis line is blue." @@ -191,7 +191,7 @@ ggplot(mpg, aes(cty, hwy, colour = class)) + As mentioned at the start, you can layer all of the pieces to build a customized plot of your data, like the one shown at the beginning of this vignette: ```{r outro} -#| fig.alt = "Scatterplot of city versus highway miles per gallon, for many cars +#| fig.alt: "Scatterplot of city versus highway miles per gallon, for many cars #| coloured by engine displacement. The plot has six panels in a 2-row, #| 3-column layout, showing the combinations of three types of drive train and #| year of manifacture. Every panel has an individual trendline."