Use pak instead of remotes

.github/workflows/test-action.yaml

@@ -50,7 +50,7 @@ jobs:
         uses: ./
         with:
           path: stageddeps.elecinfra
-          version: v0.2.7
+          version: v0.3.1
           enable-bioc-repos: true
           enable-check: false
         env:

README.md

@@ -83,14 +83,13 @@ The following options are available are available for this action:
 
 <!-- BEGIN_ACTION_DOC -->
 ### Inputs
-
 * `run-system-dependencies`:
 
   _Description_: Check for and install system dependencies
 
   _Required_: `false`
 
-  _Default_: `false`
+  _Default_: `False`
 
 * `git-user-name`:
 
@@ -126,11 +125,11 @@ The following options are available are available for this action:
 
 * `threads`:
 
-  *Description*: Number of threads to use. Set to 'auto' to use max available threads
+  _Description_: Number of threads to use. Set to 'auto' to use max available threads
 
   _Required_: `false`
 
-  _Default_: `1`
+  _Default_: `auto`
 
 * `cran-repos`:
 
@@ -146,12 +145,13 @@ The following options are available are available for this action:
 
   _Required_: `false`
 
-  _Default_: `false`
+  _Default_: `False`
 
 * `token-mapping`:
 
   _Description_: Token mapping that is used in `staged.dependencies.token_mapping` delimited by comma. Note that you will need to set these tokens with their respective values as environment variables while using this action.
 
+
   _Required_: `false`
 
   _Default_: `https://github.com=GITHUB_PAT,https://gitlab.com=GITLAB_PAT`
@@ -162,7 +162,7 @@ The following options are available are available for this action:
 
   _Required_: `false`
 
-  _Default_: `false`
+  _Default_: `False`
 
 * `git-ref`:
 
@@ -178,34 +178,25 @@ The following options are available are available for this action:
 
   _Required_: `false`
 
-  _Default_: `true`
+  _Default_: `True`
 
 * `quiet`:
 
   _Description_: If TRUE, suppress output
 
   _Required_: `false`
 
-  _Default_: `true`
-
-* `upgrade-remotes`:
-
-    _Description_: If TRUE, upgrades the 'remotes' R package to the edge version
-
-    _Required_: `false`
-
-    _Default_: `false`
+  _Default_: `True`
 
 * `direction`:
 
-    _Description_: The direction to use to install dependencies. Choose between 'upstream', 'downstream' and 'all'
+  _Description_: The direction to use to install dependencies. Choose between 'upstream', 'downstream' and 'all'
 
-    _Required_: `false`
+  _Required_: `false`
 
-    _Default_: `all`
+  _Default_: `all`
 
 ### Outputs
-
 None
 <!-- END_ACTION_DOC -->
 

action.yml

@@ -56,10 +56,6 @@ inputs:
     description: If TRUE, suppress output
     required: false
     default: true
-  upgrade-remotes:
-    description: If TRUE, upgrades the 'remotes' R package to the edge version
-    required: false
-    default: false
   direction:
     description: The direction to use to install dependencies. Choose between 'upstream', 'downstream' and 'all'
     required: false
@@ -81,7 +77,6 @@ runs:
       shell: bash
       env:
         SD_REPO_PATH: "${{ inputs.path }}"
-        SD_UPGRADE_REMOTES: "${{ inputs.upgrade-remotes }}"
 
     - name: Run staged dependencies
       run: ${GITHUB_ACTION_PATH}/staged-dependencies.R
@@ -99,5 +94,4 @@ runs:
         SD_RENV_RESTORE: "${{ inputs.renv-restore }}"
         SD_GIT_REF: "${{ inputs.git-ref }}"
         SD_QUIET: "${{ inputs.quiet }}"
-        SD_UPGRADE_REMOTES: "${{ inputs.upgrade-remotes }}"
         SD_DIRECTION: "${{ inputs.direction }}"

staged-dependencies.R

@@ -31,7 +31,6 @@ token_mapping <- Sys.getenv(
 check <- Sys.getenv("SD_ENABLE_CHECK", "false")
 renv_restore <- Sys.getenv("SD_RENV_RESTORE", "true")
 sd_quiet <- isTRUE(as.logical(Sys.getenv("SD_QUIET", "true")))
-upgrade_remotes <- isTRUE(as.logical(Sys.getenv("SD_UPGRADE_REMOTES", "false")))
 
 cat("\n==================================\n")
 cat("Running staged dependencies installer\n")
@@ -47,7 +46,6 @@ cat(paste("git_user_name: \"", git_user_name, "\"\n", sep = ""))
 cat(paste("git_user_email: \"", git_user_email, "\"\n", sep = ""))
 cat(paste("renv_restore: \"", renv_restore, "\"\n", sep = ""))
 cat(paste("sd_quiet: \"", sd_quiet, "\"\n", sep = ""))
-cat(paste("upgrade_remotes: \"", upgrade_remotes, "\"\n", sep = ""))
 cat(paste("direction: \"", direction, "\"\n", sep = ""))
 cat("==================================\n")
 
@@ -68,22 +66,15 @@ options(
   staged.dependencies.token_mapping = split_to_map(token_mapping)
 )
 
-# Install the remotes package
-if (!require("remotes", quietly = sd_quiet)) {
+# Install the pak package
+if (!require("pak", quietly = sd_quiet)) {
   install.packages(
-    "remotes",
+    "pak",
     upgrade = "never",
     Ncpus = threads
   )
 }
 
-# Upgrade the remotes package to get the latest bugfixes
-if (upgrade_remotes == "true") {
-  remotes::install_github("r-lib/remotes@main")
-  # Reload remotes
-  require(remotes)
-}
-
 # Install dependencies from renv
 if (file.exists("renv.lock") && renv_restore == "true") {
   if (!require("renv", quietly = sd_quiet)) {
@@ -109,13 +100,9 @@ if (file.exists("staged_dependencies.yaml")) {
   }
   if (install_sd) {
     cat("Installing Staged Dependencies\n\n")
-    remotes::install_github(
-      "openpharma/staged.dependencies",
-      ref = sd_version,
-      Ncpus = threads,
-      upgrade = "never",
-      force = TRUE,
-      quiet = sd_quiet
+    pak::pkg_install(
+      paste0("openpharma/staged.dependencies@", sd_version),
+      upgrade = FALSE,
     )
   }
 
@@ -133,7 +120,10 @@ if (file.exists("staged_dependencies.yaml")) {
   if (git_ref != "" &&
     !startsWith(git_ref, "refs/pull") &&
     !startsWith(git_ref, "refs/head")) {
-    x <- staged.dependencies::dependency_table(ref = git_ref, direction = direction)
+    x <- staged.dependencies::dependency_table(
+      ref = git_ref,
+      direction = direction
+    )
   } else {
     x <- staged.dependencies::dependency_table(direction = direction)
   }
@@ -156,13 +146,3 @@ if (file.exists("staged_dependencies.yaml")) {
     quiet = sd_quiet
   )
 }
-
-# Install any remaining dependencies
-if (!file.exists("renv.lock") || renv_restore != "true") {
-  remotes::install_deps(
-    dependencies = TRUE,
-    upgrade = "never",
-    Ncpus = threads,
-    quiet = sd_quiet
-  )
-}

system-dependencies.R

@@ -1,60 +1,80 @@
 #!/usr/bin/env Rscript
 
 repo_path <- Sys.getenv("SD_REPO_PATH", ".")
-upgrade_remotes <- Sys.getenv("SD_UPGRADE_REMOTES", "")
-
-# temporary fix for remotes : 
-Sys.setenv(RSPM_ROOT = "https://packagemanager.posit.co")
 
 cat("\n==================================\n")
 cat("Running system dependencies installer\n")
 cat(paste("repo_path: \"", repo_path, "\"\n", sep = ""))
 cat("==================================\n")
 
-# Install the remotes package
-if (!require("remotes")) {
+# Install the pak package
+if (!require("pak")) {
   install.packages(
-    "remotes",
+    "pak",
+    upgrade = "never",
     repos = "https://cloud.r-project.org/"
   )
 }
 
-# Upgrade the remotes package to get the latest bugfixes
-if (upgrade_remotes == "true") {
-  remotes::install_github("r-lib/remotes@main")
-  # Reload remotes
-  require(remotes)
-}
-
 os_info <- read.csv("/etc/os-release", sep = "=", header = FALSE)
 v_os_info <- setNames(os_info$V2, os_info$V1)
 
 if (v_os_info[["NAME"]] == "Ubuntu") {
   ubuntu_version <- as.character(v_os_info[["VERSION_ID"]])
   cat(paste("Ubuntu version: \"", ubuntu_version, "\"\n", sep = ""))
-  sys_deps_for_pkg <- remotes::system_requirements(
-    os = "ubuntu",
-    os_release = ubuntu_version,
-    path = repo_path
-  )
-  sys_pgks <- gsub("^apt-get install -y ", "", sys_deps_for_pkg)
-  sys_pgks <- c("libgit2-dev", sys_pgks) # For installing staged.dependencies
-  has_pkgs <- vapply(
-    sys_pgks,
-    function(pkg) {
-      system2(
-        "sudo",
-        c("dpkg", "-l", pkg),
-        stdout = NULL,
-        stderr = NULL
-      ) == 0
+  tryCatch(
+    {
+      sys_reqs <- pak::pkg_sysreqs(
+        read.dcf(file.path(repo_path, "DESCRIPTION"))[,"Package"]
+      )
+      sys_pkgs <- c(unlist(strsplit(
+        gsub("^apt-get -y install ", "", sys_reqs["install_scripts"]), "\\s"
+      )))
+      if (length(sys_pkgs) > 0) {
+        # For installing staged.dependencies
+        sys_pkgs <- c("libgit2-dev", sys_pkgs)
+      } else {
+        sys_pkgs <- c("libgit2-dev")
+      }
+      cat("\nChecking if the following dependencies are installed:\n")
+      cat(sys_pkgs)
+      has_pkgs <- vapply(
+        sys_pkgs,
+        function(pkg) {
+          system2(
+            "sudo",
+            c("dpkg", "-l", pkg),
+            stdout = NULL,
+            stderr = NULL
+          ) == 0
+        },
+        logical(1)
+      )
+      if (any(!has_pkgs)) {
+        cat("\nThe following system dependencies will be installed:\n")
+        cat(sys_pkgs[!has_pkgs])
+        system2("sudo", c("apt-get", "update"))
+        system2("sudo", c("apt-get", "install", "-y", sys_pkgs[!has_pkgs]))
+      } else {
+        cat(
+          "\nLooks like all the required system dependencies are installed.\n"
+        )
+      }
+    },
+    # This error handling is with pak::pkg_sysreqs() in mind.
+    # If a package is missing from pak database
+    # (e.g. because it's not publicly available),
+    # pak will fail to determine system dependencies.
+    error = function(x) {
+      cat("An error occurred while installing system dependencies:\n")
+      message(conditionMessage(x))
     },
-    logical(1)
+    warning = function(x) {
+      cat("A warning occurred while installing system dependencies:\n")
+      message(conditionMessage(x))
+    }
   )
-  if (any(!has_pkgs)) {
-    system2("sudo", c("apt-get", "update"))
-    system2("sudo", c("apt-get", "install", "-y", sys_pgks[!has_pkgs]))
-  }
+
 } else {
   cat(paste(
     "System dependencies not implemented for os:",