fix: update Dockerfile

.github/package-versions.txt

@@ -0,0 +1 @@
+any::Seurat@4.1.1, any::Matrix@1.5.1

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, dev, DEV]
+    branches: [ main, master, dev, DEV ]
   pull_request:
-    branches: [main, master, dev, DEV]
+    branches: [ main, master, dev, DEV ]
   workflow_dispatch:
 
 name: R-CMD-check
@@ -19,35 +19,40 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.1.3' }
+          - { os: ubuntu-latest, r: "4.1.3" }
           #- { os: ubuntu-latest, r: 'oldrel-1' }
           #- { os: macos-latest, r: 'release' }
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-    container:
-      image: nciccbr/scworkflow:v1.0.2_79e5d37
     steps:
       - uses: actions/checkout@v4
-      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - uses: CCBR/actions/install-r-pak@main
         with:
+          versions-file: .github/package-versions.txt
           extra-packages: local::.
           needs: dev
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
 
   lint:
     runs-on: ubuntu-latest
-    container:
-      image: nciccbr/scworkflow:v1.0.2_79e5d37
     steps:
       - uses: actions/checkout@v4
-      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - uses: CCBR/actions/install-r-pak@main
         with:
+          r-version: 4.1.3
+          versions-file: .github/package-versions.txt
           needs: dev
+
       - name: Good Practice checks
         shell: Rscript {0}
         run: |
@@ -103,11 +108,12 @@ jobs:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
 
-  check: # make sure all check jobs pass. https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+  check:
+    # make sure all check jobs pass. https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
     runs-on: ubuntu-latest
     container:
       image: nciccbr/scworkflow:v1.0.2_79e5d37
-    needs: [R-CMD-check, lint, test-coverage]
+    needs: [ R-CMD-check, lint, test-coverage ]
     if: always()
     steps:
       - name: Successful build

.github/workflows/docker.yml

@@ -56,4 +56,4 @@ jobs:
             BUILD_DATE=${{ steps.vars.outputs.DATE }}
             BUILD_TAG=${{ steps.vars.outputs.VERSION_TAG }}
             REPONAME=${{ env.IMAGE_NAME }}
-            R_VERSION=4.3.2
+            R_VERSION=4.1.3

.github/workflows/pkgdown.yaml

@@ -2,11 +2,11 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [ main, master ]
   pull_request:
-    branches: [main, master]
+    branches: [ main, master ]
   release:
-    types: [published]
+    types: [ published ]
   workflow_dispatch:
 
 name: pkgdown
@@ -27,9 +27,10 @@ jobs:
       image: nciccbr/scworkflow:v1.0.2_79e5d37
     steps:
       - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: CCBR/actions/install-r-pak@main
         with:
+          r-version: 4.1.3
+          versions-file: .github/package-versions.txt
           extra-packages: local::.
           needs: dev
 

.github/workflows/test-coverage.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, dev, DEV]
+  pull_request:
+    branches: [main, master, dev, DEV]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: CCBR/actions/install-r-pak@main
+        with:
+          r-version: 4.1.3
+          versions-file: .github/package-versions.txt
+          needs: dev
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -9,10 +9,10 @@ tests/testthat/fixtures/
 tests/testthat/output/
 
 .Rproj.user
-
 inst/doc
 /doc/
 /Meta/
 
 .github.zip
 decision_log.md
+

DESCRIPTION

@@ -34,7 +34,6 @@ Imports:
     callr (>= 3.7.1),
     celldex,
     colorspace,
-    colorspace,
     ComplexHeatmap (>= 2.10.0),
     cowplot (>= 1.1.1),
     data.table (>= 1.14.2),
@@ -52,23 +51,45 @@ Imports:
     ggplot2 (>= 3.3.6),
     ggpubr (>= 0.4.0),
     ggrepel,
+    globals (>= 0.16.1),
     gridBase (>= 0.4-7),
     gridExtra (>= 2.3),
     gtable (>= 0.3.1),
+    harmony (>= 0.1.1),
+    hdf5r (>= 1.3.5),
     htmlwidgets,
+    httpuv (>= 1.6.5),
     httr,
     jsonlite,
+    leiden (>= 0.4.2),
+    limma (>= 3.50.3),
+    magrittr (>= 2.0.3),
+    markdown (>= 1.1),
     MAST (>= 1.20.0),
-    patchwork,
+    methods (>= 4.1.3),
     pheatmap,
+    plotly (>= 4.10.0),
     plyr,
     png,
+    progressr (>= 0.10.1),
+    purrr (>= 0.3.4),
+    quantmod (>= 0.4.20),
     RColorBrewer (>= 1.1-3),
+    reshape2 (>= 1.4.4),
+    reticulate (>= 1.25),
+    rlang (>= 1.0.6),
     scales,
     scDblFinder,
     Seurat (>= 4.1.1),
     SingleR (>= 1.8.1),
+    statmod (>= 1.4.37),
+    stringr (>= 1.4.1),
+    svglite (>= 2.1.0),
+    tibble (>= 3.1.8),
     tidyr,
+    tidyverse (>= 1.3.2),
+    viridisLite (>= 0.4.0),
+    xfun (>= 0.32),
     zip (>= 2.2.0)
 Suggests:
     knitr,

Dockerfile

@@ -26,39 +26,139 @@ RUN conda config --add channels conda-forge \
  && conda config --set channel_priority strict
 
 # install conda packages
-RUN mamba install -y -c conda-forge \
+# Note: Most version pins removed to allow conda to resolve compatible versions with R 4.1.3
+# Only R version is pinned per requirement
+RUN mamba install -y \
     r-base=${R_VERSION} \
-    r-devtools \
+    r-anndata \
+    r-biocmanager \
+    r-callr \
+    bioconductor-celldex \
+    r-colorspace \
+    bioconductor-complexheatmap \
+    r-cowplot \
+    r-data.table \
+    r-dendextend \
+    r-dendsort \
+    r-digest \
+    r-dplyr \
+    bioconductor-edger \
+    r-future \
+    r-future.apply \
+    r-gargle \
+    r-gdata \
+    r-ggextra \
     r-ggplot2 \
-    r-ggrepel r-viridis r-upsetr r-patchwork r-plotly \
-    r-matrix r-mgcv r-survival \
-    bioconductor-genomicranges \
-    bioconductor-summarizedexperiment \
-    bioconductor-delayedarray \
-    bioconductor-s4arrays \
-    bioconductor-annotationdbi \
-    bioconductor-annotate \
-    bioconductor-keggrest \
+    r-ggpubr \
+    r-ggrepel \
+    r-globals \
+    r-gridbase \
+    r-gridextra \
+    r-gtable \
+    r-harmony \
+    r-hdf5r \
+    r-htmlwidgets \
+    r-httpuv \
+    r-httr \
+    r-jsonlite \
+    r-leiden \
+    bioconductor-limma \
+    r-magrittr \
+    r-markdown \
+    bioconductor-mast \
+    r-pheatmap \
+    r-plotly \
+    r-plyr \
+    r-png \
+    r-progressr \
+    r-purrr \
+    r-quantmod \
+    r-rcolorbrewer \
+    r-reshape2 \
+    r-reticulate \
+    r-rlang \
+    r-scales \
+    bioconductor-scdblfinder \
+    r-seurat=4.1.1 \
+    bioconductor-singler \
+    r-statmod \
+    r-stringr \
+    r-svglite \
+    r-tibble \
+    r-tidyr \
+    r-tidyverse \
+    r-viridislite \
+    r-xfun \
+    r-zip \
+    r-knitr \
+    r-rmarkdown \
+    r-roxygen2 \
+    r-testthat \
+    r-usethis \
+    r-cffr \
+    r-covr \
+    r-goodpractice \
+    r-here \
+    r-lintr \
+    r-pkgdown \
+    r-rcmdcheck \
   && conda clean -afy
 
 # install R package
 COPY . /opt2/SCWorkflow
-RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, repos='http://cran.rstudio.com')"
+RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, upgrade = 'never', repos='http://cran.rstudio.com')"
 
 # add scworkflow exec to the path
 # RUN chmod -R +x /opt2/conda/lib/R/library/SCWorkflow/exec
 # ENV PATH="$PATH:/opt2/conda/lib/R/library/SCWorkflow/exec"
 # RUN scworkflow --help
 
 # copy example script & json to data
-COPY ./inst/extdata/example_script.sh /data2/
-COPY ./inst/extdata/json_args/ /data2/json_args/
+# COPY ./inst/extdata/example_script.sh /data2/
+# COPY ./inst/extdata/json_args/ /data2/json_args/
 
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 
+# Verify all dependencies from DESCRIPTION are installed
+RUN cat > /tmp/check_description_deps.R << 'EOF'
+# Parse DESCRIPTION file and check if all dependencies are installed
+desc_file <- "/opt2/SCWorkflow/DESCRIPTION"
+if (!file.exists(desc_file)) {
+  stop("DESCRIPTION file not found at ", desc_file)
+}
+# Read and parse DESCRIPTION
+desc <- read.dcf(desc_file)
+# Extract dependencies
+extract_packages <- function(str) {
+  if (is.na(str) || str == "") return(character(0))
+  # Split by comma and clean up whitespace and version specs
+  pkgs <- strsplit(str, ",")[[1]]
+  pkgs <- trimws(pkgs)
+  pkgs <- gsub("\\s*\\(.*\\)$", "", pkgs)  # Remove version specs
+  pkgs <- pkgs[pkgs != ""]
+  pkgs
+}
+deps <- unique(c(
+  extract_packages(desc[1, "Depends"]),
+  extract_packages(desc[1, "Imports"]),
+  extract_packages(desc[1, "Suggests"]),
+  extract_packages(desc[1, "Config/Needs/dev"])
+))
+# Remove base R
+deps <- deps[!grepl("^R$", deps)]
+# Check if each dependency is installed
+missing <- deps[!vapply(deps, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1))]
+if (length(missing) > 0) {
+  stop("The following dependencies are missing: ", paste(missing, collapse = ", "))
+} else {
+  message("All dependencies are installed.")
+}
+EOF
+RUN R --vanilla --slave --file=/tmp/check_description_deps.R
+
 # cleanup
 WORKDIR /data2
 RUN apt-get clean && apt-get purge \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*