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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| name: "Update cachix cache for bleeding edge" | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - r-daily | ||
|
|
||
| jobs: | ||
| r-update-cachix: | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| matrix: | ||
| os: [ubuntu-latest, macos-latest] | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: cachix/install-nix-action@v27 | ||
| with: | ||
| nix_path: nixpkgs=channel:nixos-unstable | ||
|
|
||
| - uses: cachix/cachix-action@v15 | ||
| with: | ||
| name: rstats-on-nix | ||
| # If you chose signing key for write access | ||
| # signingKey: '${{ secrets.CACHIX_SIGNING_KEY }}' | ||
| # If you chose API tokens for write access OR if you have a private cache | ||
| authToken: '${{ secrets.CACHIX_AUTH }}' | ||
|
|
||
| - run: | | ||
| if [ "$RUNNER_OS" == "Linux" ]; then | ||
| nix-build --keep-going --max-jobs 1 --cores 2 --argstr system x86_64-linux cachix.nix | ||
| nix-build --keep-going --max-jobs 1 --cores 2 --argstr system aarch64-linux cachix.nix | ||
| else | ||
| nix-build --keep-going --max-jobs 1 --cores 2 cachix.nix | ||
| fi | ||
| - run: nix-store -qR --include-outputs $(nix-instantiate cachix.nix) | cachix push rstats-on-nix | ||
| - run: nix-shell cachix.nix --run "echo OK" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R | ||
| index 57f55a6eb65b..10905dd10d4b 100755 | ||
| --- a/pkgs/development/r-modules/generate-r-packages.R | ||
| +++ b/pkgs/development/r-modules/generate-r-packages.R | ||
| @@ -14,12 +14,8 @@ library(jsonlite) | ||
| locale <- Sys.setlocale(locale = "C") | ||
|
|
||
| biocVersion <- BiocManager:::.version_map() | ||
| -biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")] | ||
| -if ("release" %in% biocVersion$BiocStatus) { | ||
| - biocVersion <- as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"]) | ||
| -} else { | ||
| - biocVersion <- max(as.character(biocVersion$Bioc)) | ||
| -} | ||
| + | ||
| +biocVersion <- subset(biocVersion, BiocStatus == "devel")$Bioc | ||
|
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||
| mirrorUrls <- list( bioc=paste0("http://bioconductor.org/packages/", biocVersion, "/bioc/src/contrib/") | ||
| , "bioc-annotation"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/annotation/src/contrib/") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| let | ||
| pkgs = import (fetchTarball "https://github.com/rstats-on-nix/nixpkgs/archive/refs/heads/r-daily.tar.gz") {}; | ||
| system_packages = builtins.attrValues { | ||
| inherit (pkgs) R quarto glibcLocalesUtf8 nix; | ||
| }; | ||
| r_packages = builtins.attrValues { | ||
| inherit (pkgs.rPackages) | ||
| ALDEx2 | ||
| Boom | ||
| cubature | ||
| FlexReg | ||
| OpenMx | ||
| VariantAnnotation | ||
| arrow | ||
| cbq | ||
| data_table | ||
| duckdb | ||
| glmmrBase | ||
| mlpack | ||
| multinma | ||
| networkscaleup | ||
| pema | ||
| psBayesborrow | ||
| qeML | ||
| rJava | ||
| readxl | ||
| rts2 | ||
| s2 | ||
| seqtrie | ||
| tidyverse | ||
| Rcpp | ||
| blavaan | ||
| codetools | ||
| collapse | ||
| devtools | ||
| fixest | ||
| fledge | ||
| geos | ||
| gpboost | ||
| httr | ||
| igraph | ||
| jsonlite | ||
| knitr | ||
| mikropml | ||
| quarto | ||
| rmarkdown | ||
| rstanarm | ||
| sf | ||
| stars | ||
| stringi | ||
| sys | ||
| terra | ||
| testthat | ||
| vapour; | ||
| }; | ||
| wrapped_pkgs = pkgs.rstudioWrapper.override { | ||
| packages = [ r_packages ]; | ||
| }; | ||
| in | ||
| pkgs.mkShell { | ||
| LOCALE_ARCHIVE = if pkgs.system == "x86_64-linux" then "${pkgs.glibcLocalesUtf8}/lib/locale/locale-archive" else ""; | ||
| LANG = "en_US.UTF-8"; | ||
| LC_ALL = "en_US.UTF-8"; | ||
| LC_TIME = "en_US.UTF-8"; | ||
| LC_MONETARY = "en_US.UTF-8"; | ||
| LC_PAPER = "en_US.UTF-8"; | ||
| LC_MEASUREMENT = "en_US.UTF-8"; | ||
|
|
||
| buildInputs = [ system_packages r_packages wrapped_pkgs ]; | ||
|
|
||
| } |
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