Merge pull request #316 from mixOmicsTeam/github-actions-fix

GitHub actions fix: r-cmd-check

.github/workflows/actions.yml

@@ -76,8 +76,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # - { os: windows-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
-          # - { os: macOS-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
+          - { os: windows-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
+          - { os: macOS-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}'}
           - { os: ubuntu-latest, r: '${{ needs.versions.outputs.r }}', bioc: '${{ needs.versions.outputs.bioc }}', image: 'bioconductor/bioconductor_docker:${{ needs.versions.outputs.bioc }}'}
 
     env:
@@ -124,17 +124,38 @@ jobs:
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
           restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-
 
-      - name: Install system dependencies 🔧
+## the below step doesn't work anymore because 'sysreqs' API is archived
+      # - name: Install system dependencies 🔧
+      #   if: runner.os == 'Linux'
+      #   env:
+      #     RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+      #   run: |
+      #     Rscript -e "remotes::install_github('r-hub/sysreqs')"
+      #     sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+      #     sudo -s eval "$sysreqs"
+      #     sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev
+
+      - name: Install system and package dependencies using github action 🔧
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-repositories: 'https://cloud.r-project.org'
+
+      - name: Install extra dependencies for macOS
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          brew install gcc
+
+      - name: Install extra dependencies for linux
         if: runner.os == 'Linux'
         env:
           RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-          sudo apt-get update && sudo apt-get -y install libcurl4-openssl-dev
+          sudo apt-get update
+          sudo apt-get install -y pandoc-citeproc
+          sudo apt-get install -y qpdf
 
-      - name: Install dependencies 🔨
+      - name: Install R dependencies 🔨
         run: |
           options(repos = c(CRAN = "https://cran.r-project.org"))
           remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpus=2)
@@ -149,17 +170,24 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
+        # runs rmdcheck, first runs 'devtools::install to make sure there is a copy of mixOmics the parallel workers can access'
       - name: Check ✅ 
         if: (!contains(github.event.head_commit.message, 'skip-check'))
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        run: |
+          remotes::install_cran("devtools", Ncpus=2)
+          devtools::install()
+          devtools::check(args = c("--no-manual"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Check --as-cran ✅ ✅ 
         if: github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics'
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), error_on = "never", check_dir = "check/asCRAN", build_args = c("--no-build-vignettes"))
+        run: |
+          options(devtools.check.dir = "check/asCRAN", devtools.check.warning = "never")
+          devtools::check(args = c("--no-manual", "--as-cran", "--ignore-vignettes", "--run-dontrun"), build_args = c("--no-build-vignettes"))
         shell: Rscript {0}
+
 #       - name: BiocCheck 🧬 ✅
 #         if: github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics'
 #         run: |
@@ -190,17 +218,17 @@ jobs:
           build_args: BIOC_VERSION=${{ needs.versions.outputs.bioc }} 
 
       - name: Test coverage 🔍
-        # if: (matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release')
+        if: github.event_name == 'schedule' && github.repository == 'mixOmicsTeam/mixOmics'
         # the commands between 'set +e' and 'set -e' are run without throwing any error
         run: |
           set +e
           Rscript -e "covr::codecov(type = c('tests', 'examples'))"
           set -e
 
-      - name: Notify Slack 📣
-        uses: 8398a7/action-slack@v3
-        with:
-          status: ${{ job.status }}
-          fields: repo,message,commit,author,action,eventName,ref,workflow,job,took # selectable (default: repo,message)
-        env:
-          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # set in rep's setting >> secrets
+      # - name: Notify Slack 📣
+      #   uses: 8398a7/action-slack@v3
+      #   with:
+      #     status: ${{ job.status }}
+      #     fields: repo,message,commit,author,action,eventName,ref,workflow,job,took # selectable (default: repo,message)
+      #   env:
+      #     SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # set in rep's setting >> secrets

DESCRIPTION

@@ -6,29 +6,34 @@ Depends: R (>= 3.5.0),
          MASS, 
          lattice, 
          ggplot2
-Imports: igraph,
-         ellipse,
-         corpcor,
-         RColorBrewer,
-         parallel,
-         dplyr,
-         tidyr,
-         reshape2,
-         methods,
-         matrixStats,
-         rARPACK,
-         gridExtra,
-         grDevices,
-         graphics,
-         stats,
-         ggrepel,
-         BiocParallel,
-         utils
-Suggests: BiocStyle, 
-          knitr, 
-          rmarkdown, 
-          testthat, 
-          rgl
+Imports: 
+    igraph,
+    ellipse,
+    corpcor,
+    RColorBrewer,
+    parallel,
+    dplyr,
+    tidyr,
+    reshape2,
+    methods,
+    matrixStats,
+    rARPACK,
+    gridExtra,
+    grDevices,
+    graphics,
+    stats,
+    ggrepel,
+    BiocParallel,
+    utils,
+    gsignal
+Suggests: 
+    BiocStyle,
+    knitr,
+    rmarkdown,
+    testthat,
+    rgl,
+    microbenchmark,
+    magick
 Authors@R: 
     c(person("Kim-Anh", "Le Cao", role = "aut", email = "[email protected]"), 
       person("Florian", "Rohart", role = "aut"), 
@@ -64,5 +69,5 @@ biocViews: ImmunoOncology,
            MultipleComparison, 
            Classification, 
            Regression
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8

NAMESPACE

@@ -108,6 +108,7 @@ S3method(summary,mixo_pls)
 S3method(summary,mixo_spls)
 S3method(summary,pca)
 S3method(summary,rcc)
+export("%fp%")
 export(auroc)
 export(background.predict)
 export(block.pls)
@@ -121,15 +122,21 @@ export(color.GreenRed)
 export(color.jet)
 export(color.mixo)
 export(color.spectral)
+export(dctii_m_transforms)
 export(explained_variance)
+export(facewise_product)
+export(facewise_transpose)
+export(ft)
 export(get.BER)
 export(get.confusion_matrix)
 export(imgCor)
 export(impute.nipals)
 export(ipca)
 export(logratio.transfo)
+export(m_product)
 export(map)
 export(mat.rank)
+export(matrix_to_m_transforms)
 export(mint.block.pls)
 export(mint.block.plsda)
 export(mint.block.spls)
@@ -160,6 +167,10 @@ export(spca)
 export(spls)
 export(splsda)
 export(study_split)
+export(tpca)
+export(tpls)
+export(tplsda)
+export(tsvdm)
 export(tune)
 export(tune.block.splsda)
 export(tune.mint.splsda)