Update from https://github.com/b-rodrigues/trigger-r-updates/commit/9… #930
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| name: r-daily | |
| on: | |
| push: | |
| branches: | |
| - r-daily-source | |
| jobs: | |
| r-daily-update: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.MY_PAT }} | |
| GITHUB_TOKEN: ${{ secrets.MY_PAT }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| #fetch-depth: 0 | |
| token: ${{ secrets.MY_PAT }} | |
| - name: Configure git | |
| run: | | |
| git config --global user.name "Bruno Rodrigues" | |
| git config --global user.email "bruno@brodrigues.co" | |
| - name: Synching fork | |
| run: | | |
| git remote add upstream https://github.com/NixOS/nixpkgs | |
| git checkout r-daily-source | |
| git fetch upstream | |
| git reset --hard upstream/master | |
| #- name: Fix for S4Vectors (only for darwin, https://github.com/Bioconductor/S4Vectors/commit/31853e4e97ff6bc3a8a2e0fdcc6dde72fb61c045) and sf, terra, vap our | |
| # run: | | |
| # sed -i '/flowClust = old/a \ | |
| # S4Vectors = old.S4Vectors.overrideAttrs (attrs: {\ | |
| # hardeningDisable = [ "format" ];\ | |
| # });\ | |
| # S4Arrays = old.S4Arrays.overrideAttrs (attrs: {\ | |
| # hardeningDisable = [ "format" ];\ | |
| # });\ | |
| # XVector = old.XVector.overrideAttrs (attrs: {\ | |
| # hardeningDisable = [ "format" ];\ | |
| # });\ | |
| # SparseArray = old.SparseArray.overrideAttrs (attrs: {\ | |
| # hardeningDisable = [ "format" ];\ | |
| # });\ | |
| # Rsamtools = old.Rsamtools.overrideAttrs (attrs: {\ | |
| # hardeningDisable = [ "format" ];\ | |
| # });\ | |
| # rtracklayer = old.rtracklayer.overrideAttrs (attrs: {\ | |
| # hardeningDisable = [ "format" ];\ | |
| # });\ | |
| # VariantAnnotation = old.VariantAnnotation.overrideAttrs (attrs: {\ | |
| # hardeningDisable = [ "format" ];\ | |
| # });\ | |
| # ' pkgs/development/r-modules/default.nix | |
| - name: Updating files | |
| run: | | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/.github/workflows/update-cachix.yml -P .github/workflows/ | |
| # start with environments | |
| #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/r-daily.nix | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/cachix.nix | |
| # get updated files from r-daily branch | |
| #cd pkgs/development/r-modules/ | |
| #rm *-packages.json | |
| #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/cran-packages.json | |
| #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-packages.json | |
| #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-annotation-packages.json | |
| #wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-experiment-packages.json | |
| - name: Get patches for Bioc devel | |
| run: | | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/bioc_devel.patch | |
| - name: Update R to 4.4.3 until merged in master | |
| run: | | |
| sed -i 's|sha256 = "sha256-FXjNYD6NhmtYdD5J2L+ZxWnoEHm2pgzzPN973/64F+w=";|sha256 = "sha256-DZPSJEQt6iU8KwhvCI220NPP2bWSzVSW6MshQ+kPyeg=";|' pkgs/applications/science/math/R/default.nix | |
| sed -i 's|version = "4.4.2";|version = "4.4.3";|' pkgs/applications/science/math/R/default.nix | |
| - name: Install Nix | |
| uses: DeterminateSystems/nix-installer-action@main | |
| with: | |
| logger: pretty | |
| log-directives: nix_installer=trace | |
| backtrace: full | |
| - name: Update R packages | |
| run: | | |
| cd pkgs/development/r-modules/ | |
| nix-shell generate-shell.nix --run "Rscript generate-r-packages.R cran > cran-packages.json.new" | |
| nix-shell generate-shell.nix --run "Rscript generate-r-packages.R bioc > bioc-packages.json.new" | |
| nix-shell generate-shell.nix --run "Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.json.new" | |
| nix-shell generate-shell.nix --run "Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.json.new" | |
| - name: Rename files | |
| run: | | |
| cd pkgs/development/r-modules/ | |
| mv cran-packages.json.new cran-packages.json | |
| mv bioc-packages.json.new bioc-packages.json | |
| mv bioc-annotation-packages.json.new bioc-annotation-packages.json | |
| mv bioc-experiment-packages.json.new bioc-experiment-packages.json | |
| - name: Pushing updates | |
| run: | | |
| git checkout -b r-daily | |
| git add . | |
| git commit -m "daily update" || echo "no updated R packages in this period" | |
| git push --force origin r-daily | |
| - name: Get current date | |
| id: date | |
| run: echo "::set-output name=date::$(date +'%Y-%m-%d')" | |
| - name: Pushing updates to dated branch | |
| run: | | |
| git checkout -b ${{ steps.date.outputs.date }} | |
| git add . | |
| git commit -m "R CRAN and Bioc update" || echo "no updated R packages in this period" | |
| git push --force origin ${{ steps.date.outputs.date }} | |
| # now update for bioc devel | |
| - name: Apply patch | |
| run: git apply bioc_devel.patch | |
| - name: Update R packages | |
| run: | | |
| cd pkgs/development/r-modules/ | |
| nix-shell generate-shell.nix --run "Rscript generate-r-packages.R bioc > bioc-packages.json.new" | |
| nix-shell generate-shell.nix --run "Rscript generate-r-packages.R bioc-annotation > bioc-annotation-packages.json.new" | |
| nix-shell generate-shell.nix --run "Rscript generate-r-packages.R bioc-experiment > bioc-experiment-packages.json.new" | |
| - name: Rename files | |
| run: | | |
| cd pkgs/development/r-modules/ | |
| mv bioc-packages.json.new bioc-packages.json | |
| mv bioc-annotation-packages.json.new bioc-annotation-packages.json | |
| mv bioc-experiment-packages.json.new bioc-experiment-packages.json | |
| - name: Pushing updates | |
| run: | | |
| git checkout -b r-bioc-devel | |
| git add . | |
| git commit -m "bioc-devel update" || echo "no updated R packages in this period" | |
| git push --force origin r-bioc-devel | |
| - name: Get sha of r-devel | |
| id: r-devel-sha | |
| run: echo "::set-output name=r-devel-sha::$(nix-prefetch-url https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz)" | |
| - name: Patch for R-devel | |
| run: | | |
| sed -i 's|sha256 = ".*";|sha256 = ${{ steps.r-devel-sha.outputs.r-devel-sha }};|' pkgs/applications/science/math/R/default.nix | |
| sed -i 's|url = "https://cran.r-project.org/src/base/R-.*";|url = "https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz";|' pkgs/applications/science/math/R/default.nix | |
| - name: Pushing updates r-devel-bioc-devel | |
| run: | | |
| git checkout -b r-devel-bioc-devel | |
| git add . | |
| git commit -m "r-devel-bioc-devel update" || echo "no updated R packages in this period" | |
| git push --force origin r-devel-bioc-devel | |
| - name: Pushing updates r-devel | |
| run: | | |
| git checkout r-daily | |
| sed -i 's|sha256 = ".*";|sha256 = "${{ steps.r-devel-sha.outputs.r-devel-sha }}";|' pkgs/applications/science/math/R/default.nix | |
| sed -i 's|url = "https://cran.r-project.org/src/base/R-.*";|url = "https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz";|' pkgs/applications/science/math/R/default.nix | |
| git checkout -b r-devel | |
| git add . | |
| git commit -m "r-devel update" || echo "no updated R packages in this period" | |
| git push --force origin r-devel |