Version up #120
Workflow file for this run
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| name: Basic checks | |
| on: [push] | |
| env: | |
| cache-version: v1 | |
| repo-name: tidyomics/tidyomicsBlog | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| define-docker-info: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| outputs: | |
| imagename: ${{ steps.findinfo.outputs.imagename }} | |
| steps: | |
| - id: findinfo | |
| name: Find Bioc release version to select Docker | |
| run: | | |
| ## Define the Bioconductor release version RELEASE_x_y | |
| biocrelease=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == 'release')[, 'Bioc']; res <- gsub('.', '_', res, fixed=TRUE); res <- gsub('^', 'RELEASE_', res); cat(as.character(res))") | |
| ## Print the results | |
| echo $biocrelease | |
| ## Define the image name and print the information | |
| imagename="bioconductor/bioconductor_docker:${biocrelease}" | |
| echo $imagename | |
| ## Save the info for the next job | |
| echo "::set-output name=imagename::${imagename}" | |
| shell: | |
| bash {0} | |
| install-packages: | |
| runs-on: ubuntu-latest | |
| needs: define-docker-info | |
| ## The docker container to use. Note that we link a directory on the GHA | |
| ## runner to a docker directory, such that we can then cache the linked | |
| ## directory. This directory will contain the R packages used. | |
| container: | |
| image: ${{ needs.define-docker-info.outputs.imagename }} | |
| volumes: | |
| - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| submodules: true # Fetch Hugo themes (true OR recursive) | |
| fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod | |
| - name: Query dependencies and update old packages | |
| run: | | |
| BiocManager::install(ask=FALSE) | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v1 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- | |
| # This lets us augment with additional dependencies | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') | |
| echo $sysreqs | |
| sudo -s eval "$sysreqs" | |
| - name: Install dependencies | |
| run: | | |
| options(repos = c(CRAN = "https://cran.r-project.org")) | |
| BiocManager::repositories() | |
| ## To fix preprocessCore error https://github.com/stemangiola/tidybulk/issues/145 | |
| BiocManager::install("preprocessCore", configure.args="--disable-threading") | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |