diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 1936945..b43d794 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -54,9 +54,9 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } - - { os: macOS-latest, r: '4.2', bioc: '3.16'} - #- { os: windows-latest, r: '4.2', bioc: '3.16'} + - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } + - { os: macOS-latest, r: '4.3', bioc: '3.18'} + #- { os: windows-latest, r: '4.3', bioc: '3.16'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: @@ -107,16 +107,16 @@ jobs: uses: actions/cache@v3 with: path: ${{ env.R_LIBS_USER }} - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3- - name: Cache R packages on Linux if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " uses: actions/cache@v3 with: path: /home/runner/work/_temp/Library - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2- + key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3- - name: Install Linux system dependencies if: runner.os == 'Linux' @@ -305,7 +305,7 @@ jobs: if: failure() uses: actions/upload-artifact@master with: - name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results + name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results path: check diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ca44ed3..3b55d0c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -4,7 +4,7 @@ before_script: - apt-get update - apt-get -y install libcurl4-openssl-dev libssl-dev libxml2-dev libglu1-mesa-dev libssh2-1-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libgit2-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev pandoc r-cran-devtools r-cran-testthat r-cran-curl r-bioc-biostrings - R -e "dir(); getwd(); sessionInfo(); install.packages('pkgdown'); devtools::install()" - - R -e "setwd(paste0(find.package('CRBHits'), '/extdata/')); system(paste0('unzip last-1453.zip')); setwd(paste0(find.package('CRBHits'), '/extdata/last-1453/')); system('make')" + - R -e "setwd(paste0(find.package('CRBHits'), '/extdata/')); system(paste0('unzip last-1521.zip')); setwd(paste0(find.package('CRBHits'), '/extdata/last-1521/')); system('make')" - R -e "setwd(paste0(find.package('CRBHits'), '/extdata/')); system(paste0('tar -xvf KaKs_Calculator2.0_src.tar.gz')); setwd(paste0(find.package('CRBHits'), '/extdata/KaKs_Calculator2.0_src/src/')); system('make clean'); system('make')" - R -e "setwd(paste0(find.package('CRBHits'), '/extdata/')); system(paste0('unzip dagchainer.zip')); setwd(paste0(find.package('CRBHits'), '/extdata/dagchainer/')); system('make')"