ci: use pinned package versions via pak

Author: kelly-sovacool

.github/actions/install-r-pak/action.yml

@@ -0,0 +1,56 @@
+name: Install R + pak
+description: |
+  Install R and dependencies with pak
+inputs:
+  r-version:
+    description: "The version of R to install"
+    default: "release"
+  http-user-agent:
+    default: ""
+  use-public-rspm:
+    default: true
+  versions-file:
+    default: ""
+    description: "File with content to pass to the extra-packages argument of setup-r-dependencies"
+  extra-packages:
+    default: ""
+    description: "More packages to install in addition to those specified in versions-file"
+  needs:
+    default: ""
+    description: "Config/Needs field from DESCRIPTION to pass along to setup-r-dependencies"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: r-lib/actions/setup-pandoc@v2
+
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ inputs.r-version }}
+        http-user-agent: ${{ inputs.http-user-agent }}
+        use-public-rspm: ${{ inputs.use-public-rspm }}
+
+
+    - name: Set package versions
+      shell: bash
+      run: |
+        # get package versions from file
+        if [ -f ${{ inputs.versions-file }} ]; then
+          PKG_VERSIONS=$(cat ${{ inputs.versions-file }})
+        fi
+
+        # get additional package versions from input
+        if [ "${{ inputs.extra-packages }}" ]; then
+          if [ "$PKG_VERSIONS" ]; then
+            PKG_VERSIONS="${PKG_VERSIONS}, ${{ inputs.extra-packages }}"
+          else
+            PKG_VERSIONS="${{ inputs.extra-packages }}"
+          fi
+        fi
+
+        echo "PKG_VERSIONS=${PKG_VERSIONS}" >> "$GITHUB_ENV"
+
+    - uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        extra-packages: "${{ env.PKG_VERSIONS }}"
+        needs: ${{ inputs.needs }}

.github/install-pak.R

@@ -0,0 +1,23 @@
+#!/usr/bin/env Rscript --vanilla
+# Usage:
+#   Rscript .github/install-pak.R [path/to/versions_file]
+
+clargs <- commandArgs(trailingOnly = TRUE)
+versions_file <- if (!is.na(clargs[1])) {
+  clargs[1]
+} else{
+  '.github/package-versions.txt'
+}
+message(cat("versions_file:", versions_file, "\n"))
+
+if (!require('pak', quietly = TRUE)) {
+  install.packages('pak', repos = 'https://packagemanager.posit.co/cran/latest')
+}
+
+
+pkgs <- strsplit(readChar(versions_file, file.info(versions_file)$size) |> trimws(),
+                 "[[:space:],]+")[[1]]
+
+pak::pkg_install(c(pkgs, "deps::.", "local::."),
+                 upgrade = FALSE,
+                 dependencies = "all")

.github/package-versions.txt

@@ -0,0 +1 @@
+any::[email protected], any::[email protected], any::[email protected], any::[email protected]

.github/workflows/pkgdown.yaml

@@ -33,10 +33,11 @@ jobs:
           use-public-rspm: true
           r-version: 4.3
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: ./.github/actions/install-r-pak
         with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
+          versions-file: .github/package-versions.txt
+          extra-packages: local::.
+          needs: dev
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

DESCRIPTION

@@ -49,6 +49,7 @@ Imports:
     gdata,
     ggExtra,
     ggplot2 (>= 3.3.6),
+    ggplot2 (< 4.0.0),
     ggpubr (>= 0.4.0),
     ggrepel,
     globals (>= 0.16.1),
@@ -67,7 +68,7 @@ Imports:
     magrittr (>= 2.0.3),
     markdown (>= 1.1),
     MAST (>= 1.20.0),
-    Matrix (== 1.6.1),
+    Matrix (>= 1.6.1),
     methods (>= 4.1.3),
     pheatmap,
     plotly (>= 4.10.0),
@@ -100,6 +101,7 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0)
 biocViews:
+Config/Needs/dev: pkgdown, rcmdcheck
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

Dockerfile

@@ -123,9 +123,9 @@ RUN apt-get update && apt-get upgrade -y && \
 
 # install R package
 COPY . /opt2/SCWorkflow
-RUN R -e 'remotes::install_version("Seurat", version="4.3.0", upgrade="never"); remotes::install_version("SeuratObject", version="4.1.3", upgrade="never"); remotes::install_version("Matrix", version="1.6.1", upgrade="never")' && \
-  R -e "remotes::install_local('/opt2/SCWorkflow', dependencies = TRUE, upgrade='never', repos='http://cran.rstudio.com'); library(SCWorkflow)" && \
-  R -s -e "readr::write_tsv(tibble::as_tibble(installed.packages()), '/mnt/r-packages.tsv')"
+RUN Rscript /opt2/SCWorkflow/.github/install-pak.R /opt2/SCWorkflow/.github/package-versions.txt && \
+	R -e "library(SCWorkflow)" && \
+	R -s -e "readr::write_tsv(tibble::as_tibble(installed.packages()), '/mnt/r-packages.tsv')"
 
 # add scworkflow exec to the path
 RUN chmod -R +x /usr/local/lib/R/site-library/SCWorkflow/exec