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Merge pull request #7 from rformassspectrometry/jomain
Suggested updates and fixes for PlainTextParam
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| ## Read more about GitHub actions the features of this GitHub Actions workflow | ||
| ## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action | ||
| ## | ||
| ## For more details, check the biocthis developer notes vignette at | ||
| ## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html | ||
| ## | ||
| ## You can add this workflow to other packages using: | ||
| ## > biocthis::use_bioc_github_action() | ||
| ## | ||
| ## Using GitHub Actions exposes you to many details about how R packages are | ||
| ## compiled and installed in several operating system.s | ||
| ### If you need help, please follow the steps listed at | ||
| ## https://github.com/r-lib/actions#where-to-find-help | ||
| ## | ||
| ## If you found an issue specific to biocthis's GHA workflow, please report it | ||
| ## with the information that will make it easier for others to help you. | ||
| ## Thank you! | ||
|
|
||
| ## Acronyms: | ||
| ## * GHA: GitHub Action | ||
| ## * OS: operating system | ||
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| on: | ||
| push: | ||
| pull_request: | ||
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| name: R-CMD-check-bioc | ||
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| ## These environment variables control whether to run GHA code later on that is | ||
| ## specific to testthat, covr, and pkgdown. | ||
| ## | ||
| ## If you need to clear the cache of packages, update the number inside | ||
| ## cache-version as discussed at https://github.com/r-lib/actions/issues/86. | ||
| ## Note that you can always run a GHA test without the cache by using the word | ||
| ## "/nocache" in the commit message. | ||
| env: | ||
| has_testthat: 'true' | ||
| run_covr: 'true' | ||
| run_pkgdown: 'true' | ||
| has_RUnit: 'false' | ||
| has_BiocCheck: 'false' | ||
| cache-version: 'cache-v1' | ||
|
|
||
| jobs: | ||
| build-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
| container: ${{ matrix.config.cont }} | ||
| ## Environment variables unique to this job. | ||
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| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
| - { os: macOS-latest, r: 'devel', bioc: '3.20'} | ||
| - { os: windows-latest, r: 'devel', bioc: '3.20'} | ||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| NOT_CRAN: true | ||
| TZ: UTC | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
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||
| steps: | ||
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| ## Set the R library to the directory matching the | ||
| ## R packages cache step further below when running on Docker (Linux). | ||
| - name: Set R Library home on Linux | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| mkdir /__w/_temp/Library | ||
| echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile | ||
| ## 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@v2 | ||
|
|
||
| ## R is already included in the Bioconductor docker images | ||
| - name: Setup R from r-lib | ||
| if: runner.os != 'Linux' | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
|
|
||
| ## pandoc is already included in the Bioconductor docker images | ||
| - name: Setup pandoc from r-lib | ||
| if: runner.os != 'Linux' | ||
| uses: r-lib/actions/setup-pandoc@v2 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- | ||
|
|
||
| - name: Cache R packages on Linux | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: /home/runner/work/_temp/Library | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- | ||
|
|
||
| - name: Install Linux system dependencies | ||
| if: runner.os == 'Linux' | ||
| 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 macOS system dependencies | ||
| if: matrix.config.os == 'macOS-latest' | ||
| run: | | ||
| ## Enable installing XML from source if needed | ||
| brew install libxml2 | ||
| echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | ||
| ## Required to install magick as noted at | ||
| ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | ||
| brew install imagemagick@6 | ||
| ## For textshaping, required by ragg, and required by pkgdown | ||
| brew install harfbuzz fribidi | ||
| ## For installing usethis's dependency gert | ||
| brew install libgit2 | ||
| ## required for ncdf4 - can not use the homebrew one because that uses GCC | ||
| ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/ | ||
| curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz | ||
| tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C / | ||
| rm netcdf-4.7.4-darwin.17-x86_64.tar.gz | ||
| curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz | ||
| tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C / | ||
| rm hdf5-1.12.0-darwin.17-x86_64.tar.gz | ||
| curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz | ||
| tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C / | ||
| rm szip-2.1.1-darwin.17-x86_64.tar.gz | ||
| - name: Install Windows system dependencies | ||
| if: runner.os == 'Windows' | ||
| run: | | ||
| ## Edit below if you have any Windows system dependencies | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install BiocManager | ||
| run: | | ||
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | ||
| remotes::install_cran("BiocManager") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Set BiocVersion | ||
| run: | | ||
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install dependencies pass 1 | ||
| 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. | ||
| ## Pass #1 at installing dependencies | ||
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | ||
| continue-on-error: true | ||
| shell: Rscript {0} | ||
|
|
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| - name: Install dependencies pass 2 | ||
| run: | | ||
| ## Pass #2 at installing dependencies | ||
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | ||
| ## Manually install required packages | ||
| BiocManager::install('rhdf5', dependencies = TRUE, ask = FALSE, update = FALSE, INSTALL_opts = '--force-biarch') | ||
| BiocManager::install("mzR", dependencies = TRUE, ask = FALSE, update = FALSE) | ||
| BiocManager::install("msdata") | ||
| message(paste('****', Sys.time(), 'force installation of selected packages ****')) | ||
| BiocManager::install(c("BiocStyle", "rmarkdown", "magick", "Spectra")) | ||
| ## For running the checks | ||
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | ||
| remotes::install_cran("rcmdcheck") | ||
| BiocManager::install("BiocCheck") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install BiocGenerics | ||
| if: env.has_RUnit == 'true' | ||
| run: | | ||
| ## Install BiocGenerics | ||
| BiocManager::install("BiocGenerics") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install covr | ||
| if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| remotes::install_cran("covr") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install pkgdown | ||
| if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| remotes::install_github("r-lib/pkgdown") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Session info | ||
| run: | | ||
| options(width = 100) | ||
| pkgs <- installed.packages()[, "Package"] | ||
| sessioninfo::session_info(pkgs, include_base = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Run CMD check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_: false | ||
| run: | | ||
| rcmdcheck::rcmdcheck( | ||
| args = c("--no-build-vignettes", "--no-manual", "--timings"), | ||
| build_args = c("--no-manual", "--no-resave-data"), | ||
| error_on = "warning", | ||
| check_dir = "check" | ||
| ) | ||
| shell: Rscript {0} | ||
|
|
||
| ## Might need an to add this to the if: && runner.os == 'Linux' | ||
| - name: Reveal testthat details | ||
| if: env.has_testthat == 'true' | ||
| run: find . -name testthat.Rout -exec cat '{}' ';' | ||
|
|
||
| - name: Run RUnit tests | ||
| if: env.has_RUnit == 'true' | ||
| run: | | ||
| BiocGenerics:::testPackage() | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Run BiocCheck | ||
| if: env.has_BiocCheck == 'true' | ||
| run: | | ||
| BiocCheck::BiocCheck( | ||
| dir('check', 'tar.gz$', full.names = TRUE), | ||
| `quit-with-status` = TRUE, | ||
| `no-check-R-ver` = TRUE, | ||
| `no-check-bioc-help` = TRUE | ||
| ) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Test coverage | ||
| if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| covr::codecov() | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install package | ||
| if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: R CMD INSTALL . | ||
|
|
||
| - name: Deploy package | ||
| if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| git config --global user.email "actions@github.com" | ||
| git config --global user.name "GitHub Actions" | ||
| git config --global --add safe.directory /__w/MsIO/MsIO | ||
| Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" | ||
| shell: bash {0} | ||
| ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) | ||
| ## at least one locally before this will work. This creates the gh-pages | ||
| ## branch (erasing anything you haven't version controlled!) and | ||
| ## makes the git history recognizable by pkgdown. | ||
|
|
||
| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@master | ||
| with: | ||
| name: ${{ runner.os }}-biocversion-devel-r-devel-results | ||
| path: check |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,5 @@ | ||
| # Version 0.0 | ||
|
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| ## Changes in 0.0.2 | ||
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| - Refactor code for text-based import and export of MS data objects. |
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