Adapt to upcoming changes in rbinom in R devel

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

@@ -0,0 +1,154 @@
+on:
+  workflow_dispatch: # enable "run workflow" button
+  # pull_request:
+  #   branches:
+  #     - devel
+
+name: R-CMD-check-devel
+
+jobs:
+  R-CMD-check-devel:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }} - ${{ matrix.config.bioc }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: windows-latest, r: 'devel', bioc: 'devel'}
+          - { os: macOS-latest, r: 'devel', bioc: 'devel', curlConfigPath: '/usr/bin/'}
+          - { os: ubuntu-latest, r: 'devel', bioc: 'devel'}
+          - { os: windows-latest, r: 'release', bioc: 'devel'}
+          # - { os: ubuntu-16.04, r: 'devel', bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest", deploy = 'no'}
+          # - { os: ubuntu-latest, r: 'devel', image: 'bioconductor/bioconductor_docker:devel', deploy: 'no'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config
+      cache-version: v2
+
+    steps:
+      - name: checkout branch
+        uses: actions/checkout@v3
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        if: matrix.config.image == null
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - name: R version
+        run: Rscript -e 'R.version'
+
+      - name: Set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+        if: matrix.config.image == null
+
+      - name: Install BiocManager, remotes and RCurl
+        run: |
+          install.packages(c('BiocManager', 'remotes', 'RCurl'))
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, update = FALSE)
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        run: |
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows' && matrix.config.image == null
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          pak-version: devel
+
+      # - name: Install Linux system dependencies
+      #   if: runner.os == 'Linux'
+      #   env:
+      #     RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+      #   run: |
+      #     sudo apt-get update && sudo apt-get -y install libharfbuzz-dev libfribidi-dev
+      #     Rscript -e "remotes::install_github('r-hub/sysreqs')"
+      #     sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+      #     sudo -s eval "$sysreqs"
+
+      - name: Install macOS system dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install harfbuzz
+          brew install fribidi
+          brew install jpeg fftw
+          mkdir -p /Users/runner/.R
+          touch /Users/runner/.R/Makevars
+          echo 'export CPPFLAGS="-I/opt/homebrew/opt/jpeg/include"' >> /Users/runner/.R/Makevars
+          echo 'export LDFLAGS="-L/opt/homebrew/opt/jpeg/lib"' >> /Users/runner/.R/Makevars
+          echo 'export PKG_CONFIG_PATH="/opt/homebrew/opt/jpeg/lib/pkgconfig"' >> /Users/runner/.R/Makevars
+          Rscript -e 'BiocManager::install(c("GenomeInfoDbData"), type = "source")'
+          Rscript -e 'BiocManager::install(c("GenomicFeatures"), type = "source")'
+
+
+      - name: Install R package dependencies
+        run: |
+          local_deps <- remotes::local_package_deps(dependencies = TRUE)
+          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
+          print(deps)
+          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L, ask = FALSE, update = FALSE)
+          remotes::install_cran('rcmdcheck', Ncpu = 2L)
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Build, Install, Check
+        id: build-install-check
+        uses: grimbough/bioc-actions/build-install-check@v1
+
+      - name: Upload install log if the build/install/check step fails
+        if: always() && (steps.build-install-check.outcome == 'failure')
+        uses: actions/upload-artifact@v4
+        with:
+          name: install-log
+          path: |
+            ${{ steps.build-install-check.outputs.install-log }}
+
+      - name: Show testthat output (windows)
+        if: always() && runner.os == 'Windows'
+        run: |
+            type ${{ steps.build-install-check.outputs.check-dir }}\tests\testthat.Rout
+        shell: cmd
+
+      - name: Show testthat output (non-windows)
+        if: always() && runner.os != 'Windows'
+        run: |
+            cat ${{ steps.build-install-check.outputs.check-dir }}/tests/testthat.Rout
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-results
+          path: ${{ steps.build-install-check.outputs.check-dir }}
+
+
+
+
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: eisaR
 Title: Exon-Intron Split Analysis (EISA) in R
-Version: 1.25.2
+Version: 1.25.3
 Authors@R: c(person("Michael", "Stadler", email = "michael.stadler@fmi.ch", role = c("aut", "cre")),
              person("Dimos", "Gaidatzis", email = "dimosthenis.gaidatzis@fmi.ch", role = "aut"),
              person("Lukas", "Burger", email = "lukas.burger@fmi.ch", role = "aut"),

tests/testthat/test_runEISA.R

@@ -65,6 +65,10 @@ test_that("runEISA() runs", {
 
 context("runEISA gives expected results")
 test_that("runEISA() gives expected results", {
+    # rbinom was fixed in R 4.7 - fix to 4.6 behavior to get reproducible
+    # simulated data across R versions
+    suppressWarnings(RNGversion("4.6"))
+
     # construct artificial example
     fracIntron <- 0.2
     ngenes <- 3000L