Update r-daily.yml #224
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |