Merge pull request #231 from b-rodrigues/rix_init_after_rix

- rix() now runs rix_init() to ensure runtime purity

.Rbuildignore

@@ -22,3 +22,5 @@ create_dev_env.R
 ^.*.tar.gz
 ^\.pre-commit-config\.yaml$
 ^data-raw$
+.envrc
+.direnv

.github/workflows/test-fetchlocal.yml

@@ -35,14 +35,14 @@ jobs:
 
       - name: Build default.nix with 2 local packages
         run: |
-          nix-shell ./inst/extdata/default.nix --run "Rscript -e \"library(rix);rix('4.3.1', local_pkgs = c('chronicler_0.2.1.tar.gz', 'knitr_1.43.tar.gz'), overwrite = TRUE)\""
+          nix-shell ./inst/extdata/default.nix --run "Rscript -e \"library(rix);rix('4.3.1', local_r_pkgs = c('chronicler_0.2.1.tar.gz', 'knitr_1.43.tar.gz'), overwrite = TRUE)\""
 
       - name: Build default.nix
         run: nix-build
 
       - name: Build default.nix with 1 local package
         run: |
-          nix-shell ./inst/extdata/default.nix --run "Rscript -e \"library(rix);rix('4.3.1', local_pkgs = 'chronicler_0.2.1.tar.gz', overwrite = TRUE)\""
+          nix-shell ./inst/extdata/default.nix --run "Rscript -e \"library(rix);rix('4.3.1', local_r_pkgs = 'chronicler_0.2.1.tar.gz', overwrite = TRUE)\""
 
       - name: Build default.nix
         run: nix-build

R/fetchers.R

@@ -118,6 +118,10 @@ remove_base <- function(list_imports) {
 get_imports <- function(path) {
   tmp_dir <- tempdir()
 
+  # Some packages have a Description file in the testthat folder
+  # (see jimhester/lookup) so we need to get rid of that
+  path <- Filter(function(x)!grepl("testthat", x), path)
+
   # Is the path pointing to a tar.gz archive
   # or directly to a DESCRIPTION file?
   if (grepl("\\.tar\\.gz", path)) {
@@ -189,25 +193,25 @@ fetchlocal <- function(local_pkg) {
 }
 
 #' fetchlocals Installs a local R package
-#' @param local_pkgs Either a list of paths to local packages, or a path to a
+#' @param local_r_pkgs Either a list of paths to local packages, or a path to a
 #' single package
 #' @return A character. The Nix definition to build the local R packages from
 #' local sources.
 #' @noRd
-fetchlocals <- function(local_pkgs) {
-  paths_exist <- file.exists(local_pkgs)
+fetchlocals <- function(local_r_pkgs) {
+  paths_exist <- file.exists(local_r_pkgs)
 
   if (!all(paths_exist)) {
     stop(
       paste0(
-        "local_pkgs: The following paths are incorrect:\n",
-        paste(local_pkgs[!paths_exist], collapse = "\n")
+        "local_r_pkgs: The following paths are incorrect:\n",
+        paste(local_r_pkgs[!paths_exist], collapse = "\n")
       )
     )
-  } else if (length(local_pkgs) == 1) {
-    fetchlocal(local_pkgs)
+  } else if (length(local_r_pkgs) == 1) {
+    fetchlocal(local_r_pkgs)
   } else {
-    paste(lapply(local_pkgs, fetchlocal), collapse = "\n")
+    paste(lapply(local_r_pkgs, fetchlocal), collapse = "\n")
   }
 }
 

R/rix_helpers.R

@@ -137,21 +137,21 @@ generate_rpkgs <- function(rPackages, flag_rpkgs) {
   }
 }
 
-#' generate_local_pkgs Internal function that generates the string containing the correct Nix expression for installing local packages
-#' @param local_pkgs Character, list of local R packages to install.
-#' @param flag_local_pkgs Character, are there any local R packages at all?
+#' generate_local_r_pkgs Internal function that generates the string containing the correct Nix expression for installing local packages
+#' @param local_r_pkgs Character, list of local R packages to install.
+#' @param flag_local_r_pkgs Character, are there any local R packages at all?
 #' @noRd
-generate_local_pkgs <- function(local_pkgs, flag_local_pkgs) {
-  if (flag_local_pkgs == "") {
+generate_local_r_pkgs <- function(local_r_pkgs, flag_local_r_pkgs) {
+  if (flag_local_r_pkgs == "") {
     NULL
   } else {
     sprintf(
       "
-  local_pkgs = [
+  local_r_pkgs = [
     %s
   ];
 ",
-      fetchlocals(local_pkgs)
+      fetchlocals(local_r_pkgs)
     )
   }
 }
@@ -272,13 +272,13 @@ generate_locale_variables <- function() {
 #' @param attrib Character, set the correct wrapper for the Nix expression.
 #' @param flag_git_archive Character, are there R packages from Github at all?
 #' @param flag_rpkgs Character, are there any R packages at all?
-#' @param flag_local_pkgs Character, are there any local R packages at all?
+#' @param flag_local_r_pkgs Character, are there any local R packages at all?
 #' @noRd
 generate_wrapped_pkgs <- function(ide,
                                   attrib,
                                   flag_git_archive,
                                   flag_rpkgs,
-                                  flag_local_pkgs) {
+                                  flag_local_r_pkgs) {
   if (flag_rpkgs == "") {
     return(NULL)
   } else if (ide %in% names(attrib)) {
@@ -291,7 +291,7 @@ generate_wrapped_pkgs <- function(ide,
       attrib[ide],
       flag_git_archive,
       flag_rpkgs,
-      flag_local_pkgs
+      flag_local_r_pkgs
     )
   } else {
     NULL
@@ -303,14 +303,14 @@ generate_wrapped_pkgs <- function(ide,
 #' @param flag_git_archive Character, are there R packages from Github at all?
 #' @param flag_rpkgs Character, are there any R packages at all?
 #' @param flag_tex_pkgs Character, are there any LaTex packages at all?
-#' @param flag_local_pkgs Character, are there any wrapped packages at all?
+#' @param flag_local_r_pkgs Character, are there any wrapped packages at all?
 #' @param flag_wrapper Character, are there any wrapped packages at all?
 #' @param shell_hook Character, the mkShell's shellHook.
 #' @noRd
 generate_shell <- function(flag_git_archive,
                            flag_rpkgs,
                            flag_tex_pkgs,
-                           flag_local_pkgs,
+                           flag_local_r_pkgs,
                            flag_wrapper,
                            shell_hook) {
   sprintf(
@@ -328,7 +328,7 @@ pkgs.mkShell {
     flag_git_archive,
     flag_rpkgs,
     flag_tex_pkgs,
-    flag_local_pkgs,
+    flag_local_r_pkgs,
     flag_wrapper,
     shell_hook
   )

R/rix_init.R

@@ -15,13 +15,13 @@
 #' reproducibility of Nix-R environments during runtime. Concretely, if you
 #' already have a system or user library of R packages (if you have R installed
 #' through the usual means for your operating system), using `rix::rix_init()`
-#' will prevent Nix-R environments to load packages from the user library
-#' which would cause issues. 
-#' Notably, no restart is required as environmental variables are set in the current session, in
-#' addition to writing an `.Rprofile` file. This is particularly useful to make
-#' [rix::with_nix()] evaluate custom R functions from any "Nix-to-Nix" or
-#' "System-to-Nix" R setups. It introduces two side-effects that
-#' take effect both in a current or later R session setup:
+#' will prevent Nix-R environments to load packages from the user library which
+#' would cause issues. Notably, no restart is required as environmental
+#' variables are set in the current session, in addition to writing an
+#' `.Rprofile` file. This is particularly useful to make [rix::with_nix()]
+#' evaluate custom R functions from any "Nix-to-Nix" or "System-to-Nix" R
+#' setups. It introduces two side-effects that take effect both in a current or
+#' later R session setup:
 #'
 #' 1. **Adjusting `R_LIBS_USER` path:**
 #'    By default, the first path of `R_LIBS_USER` points to the user library
@@ -41,9 +41,9 @@
 #'    In a host RStudio session not launched via Nix (`nix-shell`), the
 #'    environmental variables from `~/.zshrc` or `~/.bashrc` may not be
 #'    inherited. Consequently, Nix command line interfaces like `nix-shell`
-#'    might not be found. The `.Rprofile` code written by `rix::rix_init()` ensures
-#'    that Nix command line programs are accessible by adding the path of the
-#'    "bin" directory of the default Nix profile,
+#'    might not be found. The `.Rprofile` code written by `rix::rix_init()`
+#'    ensures that Nix command line programs are accessible by adding the path
+#'    of the "bin" directory of the default Nix profile,
 #'    `"/nix/var/nix/profiles/default/bin"`, to the `PATH` variable in an
 #'    RStudio R session.
 #'
@@ -55,28 +55,32 @@
 #' packaged for macOS. We recommend calling `rix::rix_init()` prior to comparing R
 #' code ran between two software environments with `rix::with_nix()`.
 #'
-#' @param project_path Character with the folder path to the isolated nix-R project.
-#' Defaults to `"."`, which is the current working directory path. If the folder
-#' does not exist yet, it will be created.
+#' `rix::rix_init()` is called automatically by `rix::rix()` when generating a
+#' `default.nix` file, and when called by `rix::rix()` will only add the `.Rprofile`
+#' if none exists. In case you have a custom `.Rprofile` that you wish to keep
+#' using, but also want to benefit from what `rix_init()` offers, manually call
+#' it and set the `rprofile_action` to `"append"`.
+#'
+#' @param project_path Character with the folder path to the isolated nix-R
+#'   project. Defaults to `"."`, which is the current working directory path. If
+#'   the folder does not exist yet, it will be created.
 #' @param rprofile_action Character. Action to take with `.Rprofile` file
-#' destined for `project_path` folder. Possible values include
-#' `"create_missing"`, which only writes `.Rprofile` if it
-#' does not yet exist (otherwise does nothing); `"create_backup"`, which copies
-#' the existing `.Rprofile` to a new backup file, generating names with
-#' POSIXct-derived strings that include the time zone information. A new
-#' `.Rprofile` file will be written with default code from `rix::rix_init()`;
-#' `"overwrite"` overwrites the `.Rprofile` file if it does exist; `"append"`
-#' appends the existing file with code that is tailored to an isolated Nix-R
-#' project setup.
+#'   destined for `project_path` folder. Possible values include
+#'   `"create_missing"`, which only writes `.Rprofile` if it does not yet exist
+#'   (otherwise does nothing) - this is the action set when using `rix()` - ;
+#'   `"create_backup"`, which copies the existing `.Rprofile` to a new backup
+#'   file, generating names with POSIXct-derived strings that include the time
+#'   zone information. A new `.Rprofile` file will be written with default code
+#'   from `rix::rix_init()`; `"overwrite"` overwrites the `.Rprofile` file if it
+#'   does exist; `"append"` appends the existing file with code that is tailored
+#'   to an isolated Nix-R project setup.
 #' @param message_type Character. Message type, defaults to `"simple"`, which
-#' gives minimal but sufficient feedback. Other values are currently
-#' `"quiet`, which writes `.Rprofile` without message, and
-#' `"verbose"`, which displays the mechanisms implemented to achieve fully
-#' controlled R project environments in Nix.
+#'   gives minimal but sufficient feedback. Other values are currently
+#'   `"quiet`, which writes `.Rprofile` without message, and `"verbose"`,
+#'   which displays the mechanisms implemented to achieve fully controlled R project environments in Nix.
 #' @export
 #' @seealso [with_nix()]
-#' @return Nothing, this function only has the side-effect of writing a file
-#'   called ".Rprofile" to the specified path.
+#' @return Nothing, this function only has the side-effect of writing a file called ".Rprofile" to the specified path.
 #' @examples
 #' \dontrun{
 #' # create an isolated, runtime-pure R setup via Nix
@@ -412,6 +416,9 @@ nix_rprofile <- function() {
     }
 
     if (isTRUE(is_nix_r)) {
+      install.packages <- function(...){
+          stop("You are currently in an R session running from Nix.\nDon't install packages using install.packages(),\nadd them to the default.nix file instead.")
+        }
       current_paths <- .libPaths()
       userlib_paths <- Sys.getenv("R_LIBS_USER")
       user_dir <- grep(paste(userlib_paths, collapse = "|"), current_paths, fixed = TRUE)

R/with_nix.R

@@ -38,12 +38,11 @@
 #' can easily do so by providing Nix expressions in custom `.nix` or
 #' `default.nix` files in different subfolders of the project.
 #'
-#' It is recommended that you use `rix_init()` to generate a custom `.Rprofile`
+#' `rix_init()` is run automatically to generate a custom `.Rprofile`
 #' file for the subshell in `project_dir`. The defaults in that file ensure
 #' that only R packages from the Nix store, that are defined in the subshell
 #' `.nix` file are loaded and system's libraries are excluded.
 #'
-#'
 #' To do its job, `with_nix()` heavily relies on patterns that manipulate
 #' language expressions (aka computing on the language) offered in base R as
 #' well as the \{codetools\} package by Luke Tierney.

inst/extdata/default.nix

@@ -1,6 +1,6 @@
-# This file was generated by the {rix} R package v0.7.1 on 2024-06-28
+# This file was generated by the {rix} R package v0.7.1 on 2024-07-02
 # with following call:
-# >rix(r_ver = "1e3deb3d8a86a870d925760db1a5adecc64d329d",
+# >rix(r_ver = "b9014df496d5b68bf7c0145d0e9b0f529ce4f2a8",
 #  > r_pkgs = NULL,
 #  > system_pkgs = NULL,
 #  > git_pkgs = list(package_name = "rix",
@@ -11,20 +11,20 @@
 #  > project_path = "../inst/extdata",
 #  > overwrite = TRUE,
 #  > shell_hook = NULL)
-# It uses nixpkgs' revision 1e3deb3d8a86a870d925760db1a5adecc64d329d for reproducibility purposes
+# It uses nixpkgs' revision b9014df496d5b68bf7c0145d0e9b0f529ce4f2a8 for reproducibility purposes
 # which will install R version latest.
 # Report any issues to https://github.com/b-rodrigues/rix
 let
- pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/1e3deb3d8a86a870d925760db1a5adecc64d329d.tar.gz") {};
+ pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/b9014df496d5b68bf7c0145d0e9b0f529ce4f2a8.tar.gz") {};
 
   git_archive_pkgs = [
     (pkgs.rPackages.buildRPackage {
       name = "rix";
       src = pkgs.fetchgit {
         url = "https://github.com/b-rodrigues/rix/";
         branchName = "master";
-        rev = "1a9680f892024ca08d2b5af737baba0a9a042339";
-        sha256 = "sha256-HkNE+4VrtqEOOMxyxqz6jnSMg/1SOppdTyKif/yR0ss=";
+        rev = "ad53dccd9f87e56a5c9e486b11e5c8f659fcb162";
+        sha256 = "sha256-spwHEm6ohT5p2Ef8GNbsMjyL3FgMoAvCn7mQjZ2ruQs=";
       };
       propagatedBuildInputs = builtins.attrValues {
         inherit (pkgs.rPackages)