#changed github workflow to R-4.3

kullrich · Dec 22, 2023 · 88163b8 · 88163b8
1 parent 2f12c74
commit 88163b8
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git 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
@@ -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')"