From c88c282d5c90bb82d7fffa77436cdd2c4f681b01 Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Wed, 17 Aug 2022 11:33:15 +0200 Subject: [PATCH 1/2] Split release and devel BiocManager installation --- .github/workflows/build.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index f0d9722..ffb00e0 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -72,13 +72,21 @@ jobs: done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') # Installing package dependencies ------------------------ # - - name: Installing package dependencies + - name: Installing package dependencies (release) + if: ${{ matrix.config.r == 'release' }} run: | remotes::install_cran(c("rcmdcheck", "BiocManager")) BiocManager::install("GenomicRanges") BiocManager::install("Rsamtools") remotes::install_deps(dependencies = TRUE) shell: Rscript {0} + - name: Installing package dependencies (devel) + if: ${{ matrix.config.r == 'devel' }} + run: | + remotes::install_cran(c("rcmdcheck", "BiocManager")) + remotes::install_deps(dependencies = TRUE) + BiocManager::install(version = "devel") + shell: Rscript {0} # Checking package --------------------------------------- # - name: Checking package From dab9845338116996679a192ba0b3f48037745957 Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Wed, 17 Aug 2022 13:43:53 +0200 Subject: [PATCH 2/2] Skipping test against R-devel in certain months According to , Bioconductor relies on R-release during the April-October release cycle, which makes it challenging to do a CI check on R-devel. So we skip the check against R-devel during these months (until a better solution comes around). --- .github/workflows/build.yml | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index ffb00e0..194dbd4 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -30,6 +30,9 @@ jobs: - {os: ubuntu-latest, r: 'release'} - {os: ubuntu-latest, r: 'devel'} steps: + - name: Retrieving current month + if: runner.os == 'Linux' + run: echo "CURRENT_MONTH=$(date +%m)" >> $GITHUB_ENV # Checking out code -------------------------------------- # - name: Checking out the repository @@ -72,24 +75,18 @@ jobs: done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') # Installing package dependencies ------------------------ # - - name: Installing package dependencies (release) - if: ${{ matrix.config.r == 'release' }} + - name: Installing package dependencies + if: ${{ env.CURRENT_MONTH < 4 || env.CURRENT_MONTH > 10 }} run: | remotes::install_cran(c("rcmdcheck", "BiocManager")) BiocManager::install("GenomicRanges") BiocManager::install("Rsamtools") remotes::install_deps(dependencies = TRUE) shell: Rscript {0} - - name: Installing package dependencies (devel) - if: ${{ matrix.config.r == 'devel' }} - run: | - remotes::install_cran(c("rcmdcheck", "BiocManager")) - remotes::install_deps(dependencies = TRUE) - BiocManager::install(version = "devel") - shell: Rscript {0} # Checking package --------------------------------------- # - name: Checking package + if: ${{ env.CURRENT_MONTH < 4 || env.CURRENT_MONTH > 10 }} env: _R_CHECK_CRAN_INCOMING_REMOTE_: false run: |