again fix remaing lint errors

R/make_nixpkgs_url.R

@@ -1,5 +1,6 @@
 #' make_nixpkgs_url Find the right Nix revision
-#' @param r_version Character. R version to look for, for example, "4.2.0". If a nixpkgs revision is provided instead, this gets returned.
+#' @param r_version Character. R version to look for, for example, "4.2.0". If a
+#' nixpkgs revision is provided instead, this gets returned.
 #' @return A character. The url to use
 #'
 #' @examples

R/rix_helpers.R

@@ -1,6 +1,9 @@
-#' generate_header Internal function used to generate the header of the `default.nix` file.
-#' @param nix_repo Character. nixpkgs reop to use (upstream or rstats-on-nix fork) with latest commit hash.
-#' @param r_version Character. R version to look for, for example, "4.2.0". If a nixpkgs revision is provided instead, this gets returned.
+#' generate_header Internal function used to generate the header of the
+#' `default.nix` file.
+#' @param nix_repo Character. nixpkgs reop to use (upstream or rstats-on-nix
+#' fork) with latest commit hash.
+#' @param r_version Character. R version to look for, for example, "4.2.0". If a
+#' nixpkgs revision is provided instead, this gets returned.
 #' @param rix_call Character, call to rix().
 #' @noRd
 generate_header <- function(nix_repo,
@@ -70,9 +73,11 @@ let
   }
 }
 
-#' generate_rix_call Internal function used to generate the call to `rix()` as shown in `default.nix`
+#' generate_rix_call Internal function used to generate the call to `rix()` as
+#' shown in `default.nix`
 #' @param rix_call Character, call to rix().
-#' @param nix_repo Character. nixpkgs reop to use (upstream or rstats-on-nix fork) with latest commit hash.
+#' @param nix_repo Character. nixpkgs reop to use (upstream or rstats-on-nix
+#' fork) with latest commit hash.
 #' @noRd
 generate_rix_call <- function(rix_call, nix_repo) {
   if (grepl("NixOS", nix_repo$url)) {
@@ -108,20 +113,24 @@ get_rpkgs <- function(r_pkgs, ide) {
     r_pkgs
   }
 
+  # nolint start: object_name_linter
   rPackages <- paste(c("", r_pkgs), collapse = "\n      ")
 
   rPackages <- gsub("\\.", "_", rPackages)
+  # nolint end
 
   list(
     "rPackages" = rPackages,
     "archive_pkgs" = archive_pkgs
   )
 }
 
-#' generate_rpkgs Internal function that generates the string containing the correct Nix expression to get R packages.
+#' generate_rpkgs Internal function that generates the string containing the
+#' correct Nix expression to get R packages.
 #' @param rPackages Character, list of R packages to install.
 #' @param flag_rpkgs Character, are there any R packages at all?
 #' @noRd
+#' # nolint start: object_name_linter
 generate_rpkgs <- function(rPackages, flag_rpkgs) {
   if (flag_rpkgs == "") {
     NULL
@@ -136,8 +145,10 @@ generate_rpkgs <- function(rPackages, flag_rpkgs) {
     )
   }
 }
+# nolint end: object_name_linter
 
-#' generate_local_r_pkgs Internal function that generates the string containing the correct Nix expression for installing local packages
+#' 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
@@ -156,7 +167,8 @@ generate_local_r_pkgs <- function(local_r_pkgs, flag_local_r_pkgs) {
   }
 }
 
-#' generate_tex_pkgs Internal function that generates the string containing the correct Nix expression to get LaTeX packages.
+#' generate_tex_pkgs Internal function that generates the string containing the
+#' correct Nix expression to get LaTeX packages.
 #' @param tex_pkgs Character, list of LaTeX packages to install.
 #' @noRd
 generate_tex_pkgs <- function(tex_pkgs) {
@@ -176,15 +188,17 @@ generate_tex_pkgs <- function(tex_pkgs) {
   }
 }
 
-#' generate_system_pkgs Internal function that formats the system package names correctly for Nix.
+#' generate_system_pkgs Internal function that formats the system package names
+#' correctly for Nix.
 #' @param system_pkgs Character, list of LaTeX packages to install.
 #' @param r_pkgs Character, list of LaTeX packages to install.
 #' @noRd
 get_system_pkgs <- function(system_pkgs, r_pkgs) {
   # We always need these packages
   system_pkgs <- c(system_pkgs, "R", "glibcLocales", "nix")
 
-  # If the user wants the R {quarto} package, then the quarto software needs to be installed
+  # If the user wants the R {quarto} package, then the quarto software needs to
+  # be installed
   system_pkgs <- if (any(grepl("quarto", r_pkgs))) {
     unique(c(system_pkgs, "quarto"))
   } else {
@@ -194,7 +208,8 @@ get_system_pkgs <- function(system_pkgs, r_pkgs) {
 }
 
 
-#' generate_system_pkgs Internal function that generates the string containing the correct Nix expression to get system packages.
+#' generate_system_pkgs Internal function that generates the string containing
+#' the correct Nix expression to get system packages.
 #' @param system_pkgs Character, list of LaTeX packages to install.
 #' @param r_pkgs Character, list of LaTeX packages to install.
 #' @noRd
@@ -210,12 +225,16 @@ generate_system_pkgs <- function(system_pkgs, r_pkgs) {
 }
 
 
-#' generate_git_archived_pkgs Internal function that generates the string containing the correct Nix expression to get system packages.
+#' generate_git_archived_pkgs Internal function that generates the string
+#' containing the correct Nix expression to get system packages.
 #' @param git_pkgs Character, list of R packages to install from Github.
-#' @param archive_pkgs Character, list of R packages to install from the CRAN archives.
+#' @param archive_pkgs Character, list of R packages to install from the CRAN
+#' archives.
 #' @param flag_git_archive Character, are there R packages from Github at all?
 #' @noRd
-generate_git_archived_pkgs <- function(git_pkgs, archive_pkgs, flag_git_archive) {
+generate_git_archived_pkgs <- function(git_pkgs,
+                                       archive_pkgs,
+                                       flag_git_archive) {
   if (flag_git_archive == "") {
     NULL
   } else {
@@ -225,7 +244,8 @@ generate_git_archived_pkgs <- function(git_pkgs, archive_pkgs, flag_git_archive)
 }
 
 
-#' generate_locale_variables Internal function that generates the string containing the correct Nix expression to set locales.
+#' generate_locale_variables Internal function that generates the string
+#' containing the correct Nix expression to set locales.
 #' @noRd
 generate_locale_variables <- function() {
   locale_defaults <- list(

R/rix_init.R

@@ -1,13 +1,13 @@
 #' Initiate and maintain an isolated, project-specific, and runtime-pure R
 #' setup via Nix.
 #'
-#' Creates an isolated project folder for a Nix-R configuration. `rix::rix_init()`
-#' also adds, appends, or updates with or without backup a custom `.Rprofile`
-#' file with code that initializes a startup R environment without system's user
-#' libraries within a Nix software environment. Instead, it restricts search
-#' paths to load R packages exclusively from the Nix store. Additionally, it
-#' makes Nix utilities like `nix-shell` available to run system commands from
-#' the system's RStudio R session, for both Linux and macOS.
+#' Creates an isolated project folder for a Nix-R configuration.
+#' `rix::rix_init()` also adds, appends, or updates with or without backup a
+#' custom `.Rprofile` file with code that initializes a startup R environment
+#' without system's user libraries within a Nix software environment. Instead,
+#' it restricts search paths to load R packages exclusively from the Nix store.
+#' Additionally, it makes Nix utilities like `nix-shell` available to run system
+#' commands from the system's RStudio R session, for both Linux and macOS.
 #'
 #' **Enhancement of computational reproducibility for Nix-R environments:**
 #'
@@ -75,12 +75,14 @@
 #'   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
@@ -272,6 +274,7 @@ message_rprofile <- function(action_string = "Added",
 #' @return Character vector that lists `PATH` entries after modification, which
 #' are separated by `":"`.
 #' @noRd
+# nolint start: object_name_linter
 set_message_session_PATH <- function(message_type =
                                        c("simple", "quiet", "verbose")) {
   message_type <- match.arg(message_type,
@@ -293,6 +296,7 @@ set_message_session_PATH <- function(message_type =
     cat("\n\n* Updated `PATH` variable is:\n\n", PATH)
   }
 }
+# nolint end: object_name_linter
 
 
 #' Report whether the current R session is running in Nix and RStudio, or not.
@@ -392,6 +396,7 @@ set_nix_path <- function() {
 #' @return language object with parsed expression
 #' @noRd
 nix_rprofile <- function() {
+  # nolint start: object_name_linter
   quote({
     is_rstudio <- Sys.getenv("RSTUDIO") == "1"
     is_nix_r <- nzchar(Sys.getenv("NIX_STORE"))
@@ -417,19 +422,37 @@ 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.")
+        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.\nDon't update packages using update.packages(),\ngenerate 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.")
+        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.\nDon't remove packages using remove.packages(),\ndelete them from the default.nix file instead.")
+        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)
+      user_dir <- grep(
+        paste(userlib_paths, collapse = "|"),
+        current_paths,
+        fixed = TRUE
+      )
       new_paths <- current_paths[-user_dir]
       # sets new library path without user library, making nix-R pure at
       # run-time
@@ -439,4 +462,5 @@ nix_rprofile <- function() {
 
     rm(is_rstudio, is_nix_r)
   })
+  # nolint end: object_name
 }