Update r-daily.yml #220
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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: Change Bioconductor mirror | |
| run: sed -i 's|http://bioconductor\.statistik\.tu-dortmund\.de/packages/|http://bioconductor.org/packages/|g' pkgs/development/r-modules/generate-r-packages.R | |
| # - name: Remove escapeName | |
| # run: sed -i 's|escapeName(name)|name|g' pkgs/development/r-modules/generate-r-packages.R | |
| - name: Update R | |
| run: | | |
| sed -i 's|version = "4.3.3"|version = "4.4.0"|g' pkgs/applications/science/math/R/default.nix | |
| sed -i 's|sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA="|sha256 = "sha256-rOQSX5uXbSxTvMX8owx14w1O3EAVhIWcutsIDnK18DA="|g' pkgs/applications/science/math/R/default.nix | |
| - name: Fix for rJava | |
| run: sed -i 's|rJava = with pkgs; \[ zlib bzip2\.dev icu xz\.dev pcre\.dev jdk libzip \];|rJava = with pkgs; \[ zlib bzip2\.dev icu xz\.dev pcre\.dev jdk libzip libdeflate \];|g' pkgs/development/r-modules/default.nix | |
| - name: Fix for S4Vectors (https://github.com/Bioconductor/S4Vectors/commit/31853e4e97ff6bc3a8a2e0fdcc6dde72fb61c045) and sf, terra, vapour | |
| 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" ];\ | |
| });\ | |
| terra = old.terra.overrideAttrs (attrs: {\ | |
| configureFlags = [\ | |
| "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"\ | |
| ];\ | |
| });\ | |
| sf = old.sf.overrideAttrs (attrs: {\ | |
| configureFlags = [\ | |
| "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"\ | |
| ];\ | |
| });\ | |
| vapour = old.vapour.overrideAttrs (attrs: {\ | |
| configureFlags = [\ | |
| "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib"\ | |
| ];\ | |
| });\ | |
| ' pkgs/development/r-modules/default.nix | |
| - name: Updating files | |
| run: | | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily-source/.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.nix | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/cran-packages.nix | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-packages.nix | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-annotation-packages.nix | |
| wget https://raw.githubusercontent.com/rstats-on-nix/nixpkgs/r-daily/pkgs/development/r-modules/bioc-experiment-packages.nix | |
| - name: Install Nix | |
| uses: DeterminateSystems/nix-installer-action@main | |
| with: | |
| logger: pretty | |
| log-directives: nix_installer=trace | |
| backtrace: full | |
| - name: Nix cache | |
| uses: DeterminateSystems/magic-nix-cache-action@main | |
| - name: Build development environment | |
| run: | | |
| nix-build r-daily.nix | |
| - name: Update R packages | |
| run: | | |
| nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R cran > cran-packages.nix.new" | |
| nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R bioc > bioc-packages.nix.new" | |
| nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R 'bioc-annotation' > bioc-annotation-packages.nix.new" | |
| nix-shell r-daily.nix --run "cd pkgs/development/r-modules/ && Rscript generate-r-packages.R 'bioc-experiment' > bioc-experiment-packages.nix.new" | |
| - name: Rename files | |
| run: | | |
| cd pkgs/development/r-modules/ | |
| mv cran-packages.nix.new cran-packages.nix | |
| mv bioc-packages.nix.new bioc-packages.nix | |
| mv bioc-annotation-packages.nix.new bioc-annotation-packages.nix | |
| mv bioc-experiment-packages.nix.new bioc-experiment-packages.nix | |
| - 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 |