From 59996ef21968650513708d03f8fa086bfeaee302 Mon Sep 17 00:00:00 2001 From: Artur-man Date: Thu, 28 May 2026 14:07:52 +0200 Subject: [PATCH 1/4] new r-universe bioc workflow --- .github/workflows/check.yml | 304 +++++++++++++++---------------- .github/workflows/r-universe.yml | 14 ++ 2 files changed, 166 insertions(+), 152 deletions(-) create mode 100644 .github/workflows/r-universe.yml diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml index 8ac46c6..1a5bba5 100644 --- a/.github/workflows/check.yml +++ b/.github/workflows/check.yml @@ -1,152 +1,152 @@ -on: - push: - pull_request: - -name: R-CMD-check - -jobs: - check: - runs-on: ${{ matrix.config.os }} - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - _R_CHECK_TESTS_NLINES_: 0 - NOT_CRAN: true - HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: true - _R_CHECK_FORCE_SUGGESTS_: false #TODO: drop this for now! - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - strategy: - fail-fast: false - matrix: - config: - - {os: macos-latest, r: 'devel'} - - {os: windows-latest, r: 'devel', rtools-version: '45'} - - {os: ubuntu-latest, r: 'devel'} - - {os: ubuntu-24.04, r: 'devel'} - - steps: - - ## Most of these steps are the same as the ones in - ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml - ## If they update their steps, we will also need to update ours. - - name: Checkout Repository - uses: actions/checkout@v3 - - ## pandoc - - name: Setup pandoc from r-lib - uses: r-lib/actions/setup-pandoc@v2 - - ## R is already included in the Bioconductor docker images - - name: Setup R from r-lib - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - rtools-version: ${{ matrix.config.rtools-version }} - - ## Windows dependencies - - name: Install Windows system dependencies - if: runner.os == 'Windows' - run: | - ## Edit below if you have any Windows system dependencies - shell: Rscript {0} - - ## linux dependencies - - name: Install linux system dependencies - if: runner.os == 'Linux' - run: | - sudo apt-get install -y libgdal-dev - sudo apt-get install -y libfftw3-dev - sudo apt-get install -y libmagick++-dev - sudo apt-get install -y cmake - sudo apt-get install -y libhdf5-dev - sudo apt-get install -y git - sudo apt-get install -y libssl-dev - sudo apt-get install -y libcurl4-openssl-dev - sudo apt-get install -y libgit2-dev - sudo apt-get install -y libxml2-dev - sudo apt-get install -y libfontconfig1-dev - sudo apt-get install -y libharfbuzz-dev - sudo apt-get install -y libfribidi-dev - sudo apt-get install -y libfreetype6-dev - sudo apt-get install -y libpng-dev - sudo apt-get install -y libtiff5-dev - sudo apt-get install -y libjpeg-dev - sudo apt-get install -y libz-dev - # install jdk - sudo apt-get install -y libz-dev - sudo apt upgrade -y - sudo apt-get install -y openjdk-21-jdk - export JAVA_HOME=/usr/lib/jvm/java-21-openjdk-arm64/ - R CMD javareconf -e - - ## macOS dependencies - - name: Install macOS system dependencies - if: runner.os == 'macOS' - run: | - ## Enable installing XML from source if needed - brew install libxml2 - echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV - - ## Required to install magick as noted at - ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 - brew install imagemagick@6 - - ## For textshaping, required by ragg, and required by pkgdown - brew install harfbuzz fribidi - - ## For installing usethis's dependency gert - brew install libgit2 - - ## hdf5 - brew install hdf5 - - ## Required for tcltk - brew install xquartz --cask - - ## remotes, devtools - - name: Query dependencies - run: | - install.packages('remotes') - install.packages('devtools') - shell: Rscript {0} - - ## BiocManager - - name: Install BiocManager - run: | - remotes::install_cran("BiocManager") - shell: Rscript {0} - - # All Other dependencies - - name: Install dependencies - run: | - ## Try installing the package dependencies in steps. First the local - ## dependencies, then any remaining dependencies to avoid the - ## issues described at - ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html - ## https://github.com/r-lib/remotes/issues/296 - ## Ideally, all dependencies should get installed in the first pass. - install.packages(c("rcmdcheck", "BiocCheck", "remotes"), repos = BiocManager::repositories()) - remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) - shell: Rscript {0} - - # All Other dependencies - - name: Install Suggested dependencies - run: | - BiocManager::install('RBioFormats') - shell: Rscript {0} - - ## R CMD Check - - name: Run CMD check - env: - _R_CHECK_CRAN_INCOMING_: false - DISPLAY: 99.0 - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck( - args = c("--no-manual", "--no-vignettes", "--timings"), - build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), - error_on = "error", - check_dir = "check" - ) - shell: Rscript {0} \ No newline at end of file +# on: +# push: +# pull_request: +# +# name: R-CMD-check +# +# jobs: +# check: +# runs-on: ${{ matrix.config.os }} +# env: +# R_REMOTES_NO_ERRORS_FROM_WARNINGS: true +# _R_CHECK_TESTS_NLINES_: 0 +# NOT_CRAN: true +# HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: true +# _R_CHECK_FORCE_SUGGESTS_: false #TODO: drop this for now! +# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# +# strategy: +# fail-fast: false +# matrix: +# config: +# - {os: macos-latest, r: 'devel'} +# - {os: windows-latest, r: 'devel', rtools-version: '45'} +# - {os: ubuntu-latest, r: 'devel'} +# - {os: ubuntu-24.04, r: 'devel'} +# +# steps: +# +# ## Most of these steps are the same as the ones in +# ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml +# ## If they update their steps, we will also need to update ours. +# - name: Checkout Repository +# uses: actions/checkout@v3 +# +# ## pandoc +# - name: Setup pandoc from r-lib +# uses: r-lib/actions/setup-pandoc@v2 +# +# ## R is already included in the Bioconductor docker images +# - name: Setup R from r-lib +# uses: r-lib/actions/setup-r@v2 +# with: +# r-version: ${{ matrix.config.r }} +# rtools-version: ${{ matrix.config.rtools-version }} +# +# ## Windows dependencies +# - name: Install Windows system dependencies +# if: runner.os == 'Windows' +# run: | +# ## Edit below if you have any Windows system dependencies +# shell: Rscript {0} +# +# ## linux dependencies +# - name: Install linux system dependencies +# if: runner.os == 'Linux' +# run: | +# sudo apt-get install -y libgdal-dev +# sudo apt-get install -y libfftw3-dev +# sudo apt-get install -y libmagick++-dev +# sudo apt-get install -y cmake +# sudo apt-get install -y libhdf5-dev +# sudo apt-get install -y git +# sudo apt-get install -y libssl-dev +# sudo apt-get install -y libcurl4-openssl-dev +# sudo apt-get install -y libgit2-dev +# sudo apt-get install -y libxml2-dev +# sudo apt-get install -y libfontconfig1-dev +# sudo apt-get install -y libharfbuzz-dev +# sudo apt-get install -y libfribidi-dev +# sudo apt-get install -y libfreetype6-dev +# sudo apt-get install -y libpng-dev +# sudo apt-get install -y libtiff5-dev +# sudo apt-get install -y libjpeg-dev +# sudo apt-get install -y libz-dev +# # install jdk +# sudo apt-get install -y libz-dev +# sudo apt upgrade -y +# sudo apt-get install -y openjdk-21-jdk +# export JAVA_HOME=/usr/lib/jvm/java-21-openjdk-arm64/ +# R CMD javareconf -e +# +# ## macOS dependencies +# - name: Install macOS system dependencies +# if: runner.os == 'macOS' +# run: | +# ## Enable installing XML from source if needed +# brew install libxml2 +# echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV +# +# ## Required to install magick as noted at +# ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 +# brew install imagemagick@6 +# +# ## For textshaping, required by ragg, and required by pkgdown +# brew install harfbuzz fribidi +# +# ## For installing usethis's dependency gert +# brew install libgit2 +# +# ## hdf5 +# brew install hdf5 +# +# ## Required for tcltk +# brew install xquartz --cask +# +# ## remotes, devtools +# - name: Query dependencies +# run: | +# install.packages('remotes') +# install.packages('devtools') +# shell: Rscript {0} +# +# ## BiocManager +# - name: Install BiocManager +# run: | +# remotes::install_cran("BiocManager") +# shell: Rscript {0} +# +# # All Other dependencies +# - name: Install dependencies +# run: | +# ## Try installing the package dependencies in steps. First the local +# ## dependencies, then any remaining dependencies to avoid the +# ## issues described at +# ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html +# ## https://github.com/r-lib/remotes/issues/296 +# ## Ideally, all dependencies should get installed in the first pass. +# install.packages(c("rcmdcheck", "BiocCheck", "remotes"), repos = BiocManager::repositories()) +# remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) +# shell: Rscript {0} +# +# # All Other dependencies +# - name: Install Suggested dependencies +# run: | +# BiocManager::install('RBioFormats') +# shell: Rscript {0} +# +# ## R CMD Check +# - name: Run CMD check +# env: +# _R_CHECK_CRAN_INCOMING_: false +# DISPLAY: 99.0 +# run: | +# options(crayon.enabled = TRUE) +# rcmdcheck::rcmdcheck( +# args = c("--no-manual", "--no-vignettes", "--timings"), +# build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), +# error_on = "error", +# check_dir = "check" +# ) +# shell: Rscript {0} \ No newline at end of file diff --git a/.github/workflows/r-universe.yml b/.github/workflows/r-universe.yml new file mode 100644 index 0000000..34e58ae --- /dev/null +++ b/.github/workflows/r-universe.yml @@ -0,0 +1,14 @@ +name: Test R-universe + +on: + push: + branches: [devel] +pull_request: + + jobs: + build: + name: R-universe testing +uses: r-universe-org/workflows/.github/workflows/build.yml@v3 +with: + universe: bioc +organization: bioconductor \ No newline at end of file From 463a86c0037600491c3b8ef76120dff865ad1484 Mon Sep 17 00:00:00 2001 From: Artur-man Date: Thu, 28 May 2026 14:09:29 +0200 Subject: [PATCH 2/4] update gha --- .github/workflows/r-universe.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/r-universe.yml b/.github/workflows/r-universe.yml index 34e58ae..2ccd1f5 100644 --- a/.github/workflows/r-universe.yml +++ b/.github/workflows/r-universe.yml @@ -2,13 +2,13 @@ name: Test R-universe on: push: - branches: [devel] -pull_request: - - jobs: + branches: [main] + pull_request: + +jobs: build: - name: R-universe testing -uses: r-universe-org/workflows/.github/workflows/build.yml@v3 -with: - universe: bioc -organization: bioconductor \ No newline at end of file + name: R-universe testing + uses: r-universe-org/workflows/.github/workflows/build.yml@v3 + with: + universe: bioc + organization: bioconductor \ No newline at end of file From 6f8d7f2434b10204ea2cccac6d4f89a3b8eea2b1 Mon Sep 17 00:00:00 2001 From: Artur-man Date: Thu, 28 May 2026 14:10:41 +0200 Subject: [PATCH 3/4] delete old gha --- .github/workflows/check.yml | 152 ------------------------------------ 1 file changed, 152 deletions(-) delete mode 100644 .github/workflows/check.yml diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml deleted file mode 100644 index 1a5bba5..0000000 --- a/.github/workflows/check.yml +++ /dev/null @@ -1,152 +0,0 @@ -# on: -# push: -# pull_request: -# -# name: R-CMD-check -# -# jobs: -# check: -# runs-on: ${{ matrix.config.os }} -# env: -# R_REMOTES_NO_ERRORS_FROM_WARNINGS: true -# _R_CHECK_TESTS_NLINES_: 0 -# NOT_CRAN: true -# HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: true -# _R_CHECK_FORCE_SUGGESTS_: false #TODO: drop this for now! -# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} -# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} -# -# strategy: -# fail-fast: false -# matrix: -# config: -# - {os: macos-latest, r: 'devel'} -# - {os: windows-latest, r: 'devel', rtools-version: '45'} -# - {os: ubuntu-latest, r: 'devel'} -# - {os: ubuntu-24.04, r: 'devel'} -# -# steps: -# -# ## Most of these steps are the same as the ones in -# ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml -# ## If they update their steps, we will also need to update ours. -# - name: Checkout Repository -# uses: actions/checkout@v3 -# -# ## pandoc -# - name: Setup pandoc from r-lib -# uses: r-lib/actions/setup-pandoc@v2 -# -# ## R is already included in the Bioconductor docker images -# - name: Setup R from r-lib -# uses: r-lib/actions/setup-r@v2 -# with: -# r-version: ${{ matrix.config.r }} -# rtools-version: ${{ matrix.config.rtools-version }} -# -# ## Windows dependencies -# - name: Install Windows system dependencies -# if: runner.os == 'Windows' -# run: | -# ## Edit below if you have any Windows system dependencies -# shell: Rscript {0} -# -# ## linux dependencies -# - name: Install linux system dependencies -# if: runner.os == 'Linux' -# run: | -# sudo apt-get install -y libgdal-dev -# sudo apt-get install -y libfftw3-dev -# sudo apt-get install -y libmagick++-dev -# sudo apt-get install -y cmake -# sudo apt-get install -y libhdf5-dev -# sudo apt-get install -y git -# sudo apt-get install -y libssl-dev -# sudo apt-get install -y libcurl4-openssl-dev -# sudo apt-get install -y libgit2-dev -# sudo apt-get install -y libxml2-dev -# sudo apt-get install -y libfontconfig1-dev -# sudo apt-get install -y libharfbuzz-dev -# sudo apt-get install -y libfribidi-dev -# sudo apt-get install -y libfreetype6-dev -# sudo apt-get install -y libpng-dev -# sudo apt-get install -y libtiff5-dev -# sudo apt-get install -y libjpeg-dev -# sudo apt-get install -y libz-dev -# # install jdk -# sudo apt-get install -y libz-dev -# sudo apt upgrade -y -# sudo apt-get install -y openjdk-21-jdk -# export JAVA_HOME=/usr/lib/jvm/java-21-openjdk-arm64/ -# R CMD javareconf -e -# -# ## macOS dependencies -# - name: Install macOS system dependencies -# if: runner.os == 'macOS' -# run: | -# ## Enable installing XML from source if needed -# brew install libxml2 -# echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV -# -# ## Required to install magick as noted at -# ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 -# brew install imagemagick@6 -# -# ## For textshaping, required by ragg, and required by pkgdown -# brew install harfbuzz fribidi -# -# ## For installing usethis's dependency gert -# brew install libgit2 -# -# ## hdf5 -# brew install hdf5 -# -# ## Required for tcltk -# brew install xquartz --cask -# -# ## remotes, devtools -# - name: Query dependencies -# run: | -# install.packages('remotes') -# install.packages('devtools') -# shell: Rscript {0} -# -# ## BiocManager -# - name: Install BiocManager -# run: | -# remotes::install_cran("BiocManager") -# shell: Rscript {0} -# -# # All Other dependencies -# - name: Install dependencies -# run: | -# ## Try installing the package dependencies in steps. First the local -# ## dependencies, then any remaining dependencies to avoid the -# ## issues described at -# ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html -# ## https://github.com/r-lib/remotes/issues/296 -# ## Ideally, all dependencies should get installed in the first pass. -# install.packages(c("rcmdcheck", "BiocCheck", "remotes"), repos = BiocManager::repositories()) -# remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) -# shell: Rscript {0} -# -# # All Other dependencies -# - name: Install Suggested dependencies -# run: | -# BiocManager::install('RBioFormats') -# shell: Rscript {0} -# -# ## R CMD Check -# - name: Run CMD check -# env: -# _R_CHECK_CRAN_INCOMING_: false -# DISPLAY: 99.0 -# run: | -# options(crayon.enabled = TRUE) -# rcmdcheck::rcmdcheck( -# args = c("--no-manual", "--no-vignettes", "--timings"), -# build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), -# error_on = "error", -# check_dir = "check" -# ) -# shell: Rscript {0} \ No newline at end of file From 1a0bbb857415b52fd6e99665b837ff060c4f5aba Mon Sep 17 00:00:00 2001 From: Artur-man Date: Thu, 28 May 2026 14:11:01 +0200 Subject: [PATCH 4/4] update gha --- .github/workflows/r-universe.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/r-universe.yml b/.github/workflows/r-universe.yml index 2ccd1f5..09cacec 100644 --- a/.github/workflows/r-universe.yml +++ b/.github/workflows/r-universe.yml @@ -2,7 +2,7 @@ name: Test R-universe on: push: - branches: [main] + branches: [devel] pull_request: jobs: