update for addressing errors for BiocCheck::BiocCheck('new-package'=T…

…RUE)
JEFworks-Lab · May 29, 2024 · 3747b8f · 3747b8f
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commit 3747b8f
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -7,4 +7,4 @@
 ^data-raw$
 ^.github$
 ^vignettes/merfish_mousePOA_raw.RDS$
-^vignettes/formatting-SpatialExperiment-for-SEraster.Rmd$
+^vignettes/formatting-SpatialExperiment-for-SEraster.Rmd$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -42,7 +42,7 @@ Suggests:
     testthat (>= 3.0.0),    
     knitr,
     rmarkdown
-VignetteBuilder: knitr, rmarkdown
+VignetteBuilder: knitr
 Config/testthat/edition: 3
 RoxygenNote: 7.3.1
 Depends: 

diff --git a/R/main.R b/R/main.R
@@ -645,7 +645,7 @@ permutateByRotation <- function(input, n_perm = 1, verbose = FALSE) {
 
       ## get original x,y coordinates
       pos_orig <- data.frame(spatialCoords(spe))
-      stopifnot("Column 1 and 2 of the spatialCoords slot should be named x and y, respectively. Please change column names accordingly."=colnames(pos_orig)[1:2] == c("x", "y"))
+      stopifnot("Column 1 and 2 of the spatialCoords slot should be named x and y, respectively. Please change column names accordingly."=colnames(pos_orig)[seq_along(c("x", "y"))] == c("x", "y"))
 
       output2 <- lapply(angles, function(angle) {
         ## rotate around the midrange point
@@ -679,7 +679,7 @@ permutateByRotation <- function(input, n_perm = 1, verbose = FALSE) {
 
     ## get original x,y coordinates
     pos_orig <- data.frame(spatialCoords(input))
-    stopifnot("Column 1 and 2 of the spatialCoords slot should be named x and y, respectively. Please change column names accordingly."=colnames(pos_orig)[1:2] == c("x", "y"))
+    stopifnot("Column 1 and 2 of the spatialCoords slot should be named x and y, respectively. Please change column names accordingly."=colnames(pos_orig)[seq_along(c("x", "y"))] == c("x", "y"))
 
     output  <- lapply(angles, function(angle) {
       ## rotate around the midrange point