- Fixed a bug in rix_init() that prevented from writing .Rprofile files.

ropensci · Sep 27, 2024 · cdbef0b · cdbef0b
1 parent 62a9fdf
commit cdbef0b
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Showing 6 changed files with 177 additions and 17 deletions.
diff --git a/R/rix_init.R b/R/rix_init.R
@@ -139,12 +139,24 @@ rix_init <- function(project_path,
   rprofile_quoted <- nix_rprofile()
   rprofile_deparsed <- deparse_chr1(expr = rprofile_quoted, collapse = "\n")
   rprofile_file <- file.path(project_path, ".Rprofile")
-  rprofile_con <- file(rprofile_file, open = "wb", encoding = "native.enc")
 
   rprofile_text <- get_rprofile_text(rprofile_deparsed)
-  on.exit(close(rprofile_con))
-  write_rprofile <- function(rprofile_text, rprofile_file) {
+
+  # This function creates the connection, write the text
+  # and closes the connection
+  # Makes it "as pure as possible"
+  write_rprofile <- function(rprofile_text, rprofile_file, mode) {
+    create_rprofile_con <- function(rprofile_file, mode) {
+      rprofile_con <- file(
+        rprofile_file,
+        open = mode,
+        encoding = "native.enc"
+      )
+    }
+
+    rprofile_con <- create_rprofile_con(rprofile_file, mode)
     writeLines(enc2utf8(rprofile_text), rprofile_con, useBytes = TRUE)
+    on.exit(close(rprofile_con))
   }
 
   is_nix_r <- is_nix_r_session()
@@ -153,7 +165,13 @@ rix_init <- function(project_path,
   # signal message if not quiet
   message_r_session_nix_rstudio(is_nix_r, is_rstudio, message_type)
 
-  rprofile_exists <- file.exists(rprofile_file)
+  # Test for existence and size instead of only existence,
+  # as an active file connection makes the file exist, but is empty
+  # Consider empty files as not existing to avoid not writing
+  # .Rprofile
+  rprofile_exists <- file.exists(rprofile_file) &&
+    `!=`(file.size(rprofile_file), 0L)
+
   timestamp <- format(Sys.time(), "%Y-%m-%dT%H:%M:%S%z")
   rprofile_backup <- paste0(rprofile_file, "_backup_", timestamp)
 
@@ -167,7 +185,7 @@ rix_init <- function(project_path,
           )
         }
       } else {
-        write_rprofile(rprofile_text, rprofile_file = rprofile_con)
+        write_rprofile(rprofile_text, rprofile_file = rprofile_file, mode = "wb")
         if (isFALSE(is_quiet)) {
           message_rprofile(action_string = "Added", project_path = project_path)
         }
@@ -177,7 +195,7 @@ rix_init <- function(project_path,
     create_backup = {
       if (isTRUE(rprofile_exists)) {
         file.copy(from = rprofile_file, to = rprofile_backup)
-        write_rprofile(rprofile_text, rprofile_file = rprofile_con)
+        write_rprofile(rprofile_text, rprofile_file = rprofile_file, mode = "wb")
         if (isFALSE(is_quiet)) {
           cat(
             "\n==> Backed up existing `.Rprofile` in file:\n", rprofile_backup,
@@ -191,13 +209,13 @@ rix_init <- function(project_path,
 
         if (message_type == "verbose") {
           cat("\n* Current lines of local `.Rprofile` are\n:")
-          cat(readLines(con = rprofile_con), sep = "\n")
+          cat(readLines(con = rprofile_file), sep = "\n")
         }
         set_message_session_PATH(message_type = message_type)
       }
     },
     overwrite = {
-      write_rprofile(rprofile_text, rprofile_file = rprofile_con)
+      write_rprofile(rprofile_text, rprofile_file = rprofile_file, mode = "wb")
       if (isTRUE(rprofile_exists)) {
         message_rprofile(
           action_string = "Overwrote", project_path = project_path
@@ -209,7 +227,7 @@ rix_init <- function(project_path,
       }
     },
     append = {
-      cat(paste0(rprofile_text, "\n"), file = rprofile_con, append = TRUE)
+      write_rprofile(rprofile_text, rprofile_file = rprofile_file, mode = "a+")
       message_rprofile(
         action_string = "Appended", project_path = project_path
       )
@@ -218,7 +236,7 @@ rix_init <- function(project_path,
 
   if (message_type == "verbose") {
     cat("\n\n* Current lines of local `.Rprofile` are:\n\n")
-    cat(readLines(con = rprofile_action), sep = "\n")
+    cat(readLines(con = rprofile_file), sep = "\n")
   }
 }
 

diff --git a/README.Rmd b/README.Rmd
@@ -60,7 +60,8 @@ While Nix has a steep learning curve, `{rix}`
    same code in different development environments, and finally to deploy
    software environments in production.
 
-If you want to watch a 5-Minute video introduction click [here](https://www.youtube.com/embed/OOu6gjQ310c?si=tQ-s9ZgEBxak8k8G).
+If you want to watch a 5-Minute video introduction click 
+[here](https://youtu.be/OOu6gjQ310c?si=qQ5lUhAg5U-WT2W1).
 
 Nix includes nearly all CRAN and Bioconductor packages, with the ability to
 install specific package versions or GitHub snapshots. Nix also includes Python,

diff --git a/README.md b/README.md
@@ -55,7 +55,7 @@ While Nix has a steep learning curve, `{rix}`
     finally to deploy software environments in production.
 
 If you want to watch a 5-Minute video introduction click
-[here](https://www.youtube.com/embed/OOu6gjQ310c?si=tQ-s9ZgEBxak8k8G).
+[here](https://youtu.be/OOu6gjQ310c?si=qQ5lUhAg5U-WT2W1).
 
 Nix includes nearly all CRAN and Bioconductor packages, with the ability
 to install specific package versions or GitHub snapshots. Nix also

diff --git a/inst/extdata/default.nix b/inst/extdata/default.nix
@@ -1,9 +1,9 @@
-# This file was generated by the {rix} R package v0.12.2 on 2024-09-26
+# This file was generated by the {rix} R package v0.12.3 on 2024-09-27
 # with following call:
 # >rix(r_ver = "976fa3369d722e76f37c77493d99829540d43845",
 #  > git_pkgs = list(package_name = "rix",
 #  > repo_url = "https://github.com/ropensci/rix/",
-#  > commit = "d576259a2601dd6036dc85d110581784d753e622"),
+#  > commit = "f69c72dc7d27d12ab65ce1a7c48e541d3097bf69"),
 #  > ide = "other",
 #  > project_path = "inst/extdata",
 #  > overwrite = TRUE)
@@ -18,8 +18,8 @@ let
       name = "rix";
       src = pkgs.fetchgit {
         url = "https://github.com/ropensci/rix/";
-        rev = "d576259a2601dd6036dc85d110581784d753e622";
-        sha256 = "sha256-Tb/4qNwKYoMnd3KZ/Y4rXKKtmeF6n92JBy9ztXAG1pY=";
+        rev = "f69c72dc7d27d12ab65ce1a7c48e541d3097bf69";
+        sha256 = "sha256-PIY5z3/GmXMIpwRNfvooyxih0/hTbYPL5Q1cD2U/og0=";
       };
       propagatedBuildInputs = builtins.attrValues {
         inherit (pkgs.rPackages) 

diff --git a/tests/testthat/_snaps/rix_init/append_Rprofile.txt b/tests/testthat/_snaps/rix_init/append_Rprofile.txt
@@ -0,0 +1,42 @@
+This is in the original Rprofile
+### File generated by `rix::rix_init()` ###
+# 1. Currently, system RStudio does not inherit environmental variables
+#   defined in `$HOME/.zshrc`, `$HOME/.bashrc` and alike. This is workaround to
+#   make the path of the nix store and hence basic nix commands available
+#   in an RStudio session
+# 2. For nix-R session, remove `R_LIBS_USER`, system's R user library.`.
+#   This guarantees no user libraries from the system are loaded and only
+#   R packages in the Nix store are used. This makes Nix-R behave in pure manner
+#   at run-time.
+{
+    is_rstudio <- Sys.getenv("RSTUDIO") == "1"
+    is_nix_r <- nzchar(Sys.getenv("NIX_STORE"))
+    if (isFALSE(is_nix_r) && isTRUE(is_rstudio)) {
+        cat("{rix} detected RStudio R session")
+        old_path <- Sys.getenv("PATH")
+        nix_path <- "/nix/var/nix/profiles/default/bin"
+        has_nix_path <- any(grepl(nix_path, old_path))
+        if (isFALSE(has_nix_path)) {
+            Sys.setenv(PATH = paste(old_path, nix_path, sep = ":"))
+        }
+        rm(old_path, nix_path)
+    }
+    if (isTRUE(is_nix_r)) {
+        install.packages <- function(...) {
+            stop("You are currently in an R session running from Nix.\n", "Don't install packages using install.packages(),\nadd them to ", "the default.nix file instead.")
+        }
+        update.packages <- function(...) {
+            stop("You are currently in an R session running from Nix.\n", "Don't update packages using update.packages(),\n", "generate a new default.nix with a more recent version of R. ", "If you need bleeding edge packages, read the", "'Understanding the rPackages set release cycle and using ", "bleeding edge packages' vignette.")
+        }
+        remove.packages <- function(...) {
+            stop("You are currently in an R session running from Nix.\n", "Don't remove packages using `remove.packages()``,\ndelete them ", "from 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)
+        new_paths <- current_paths[-user_dir]
+        .libPaths(new_paths)
+        rm(current_paths, userlib_paths, user_dir, new_paths)
+    }
+    rm(is_rstudio, is_nix_r)
+}
diff --git a/tests/testthat/test-rix_init.R b/tests/testthat/test-rix_init.R
@@ -1,6 +1,9 @@
-testthat::test_that("Snapshot test of rix_init()", {
+testthat::test_that("Snapshot test of rix_init(), overwrite", {
   path_env_nix <- tempdir()
 
+  # Create an empty file, and overwrite it
+  rprofile_file <- paste0(path_env_nix, "/.Rprofile")
+
   save_rix_init_test <- function(path_env_nix) {
     rix_init(
       project_path = path_env_nix,
@@ -11,8 +14,69 @@ testthat::test_that("Snapshot test of rix_init()", {
     paste0(path_env_nix, "/.Rprofile")
   }
 
+  rprofile_con <- file(rprofile_file, open = "wb", encoding = "native.enc")
+  on.exit(close(rprofile_con), add = TRUE)
+
+  testthat::expect_snapshot_file(
+    path = save_rix_init_test(path_env_nix),
+    name = "golden_Rprofile.txt",
+  )
+
+  on.exit(
+    unlink(path_env_nix, recursive = TRUE, force = TRUE),
+    add = TRUE
+  )
+})
+
+
+testthat::test_that("Snapshot test of rix_init(), create_missing, no file", {
+  path_env_nix <- tempdir()
+
+  save_rix_init_test <- function(path_env_nix) {
+    rix_init(
+      project_path = path_env_nix,
+      rprofile_action = "create_missing",
+      message_type = "simple"
+    )
+
+    paste0(path_env_nix, "/.Rprofile")
+  }
+
+  testthat::expect_snapshot_file(
+    path = save_rix_init_test(path_env_nix),
+    name = "golden_Rprofile.txt",
+  )
+
+  on.exit(
+    unlink(path_env_nix, recursive = TRUE, force = TRUE),
+    add = TRUE
+  )
+})
+
+testthat::test_that("Snapshot test of rix_init(), create_missing, empty file", {
+  # Empty should be considered as missing
+  # We're creating an empty .Rprofile by opening a file connection
+  # and then rix_init() should consider it missing and write
+
+  path_env_nix <- tempdir()
+
+  rprofile_file <- paste0(path_env_nix, "/.Rprofile")
+
+  save_rix_init_test <- function(path_env_nix) {
+    rix_init(
+      project_path = path_env_nix,
+      rprofile_action = "create_missing",
+      message_type = "simple"
+    )
+
+    rprofile_file
+  }
+
   testthat::announce_snapshot_file("find_rev/golden_Rprofile.txt")
 
+  rprofile_con <- file(rprofile_file, open = "wb", encoding = "native.enc")
+  on.exit(close(rprofile_con), add = TRUE)
+
   testthat::expect_snapshot_file(
     path = save_rix_init_test(path_env_nix),
     name = "golden_Rprofile.txt",
@@ -23,3 +87,38 @@ testthat::test_that("Snapshot test of rix_init()", {
     add = TRUE
   )
 })
+
+
+testthat::test_that("Snapshot test of rix_init(), append", {
+  path_env_nix <- tempdir()
+
+  save_rix_init_test <- function(path_env_nix) {
+    rix_init(
+      project_path = path_env_nix,
+      rprofile_action = "append",
+      message_type = "simple"
+    )
+
+    paste0(path_env_nix, "/.Rprofile")
+  }
+
+  rprofile_file <- paste0(path_env_nix, "/.Rprofile")
+  rprofile_con <- file(rprofile_file, open = "a+", encoding = "native.enc")
+
+  writeLines(enc2utf8("This is in the original Rprofile"),
+    rprofile_con,
+    useBytes = TRUE
+  )
+
+  close(rprofile_con)
+
+  testthat::expect_snapshot_file(
+    path = save_rix_init_test(path_env_nix),
+    name = "append_Rprofile.txt",
+  )
+
+  on.exit(
+    unlink(path_env_nix, recursive = TRUE, force = TRUE),
+    add = TRUE
+  )
+})