diff options
Diffstat (limited to 'pkgs/development/r-modules/default.nix')
| -rw-r--r-- | pkgs/development/r-modules/default.nix | 36 |
1 files changed, 27 insertions, 9 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index cb5cc5220dfe8..d22504e71a479 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -1,4 +1,13 @@ -/* This file defines the composition for CRAN (R) packages. */ +/* This file defines the composition for R packages. */ + +let + importJSON = f: builtins.fromJSON (builtins.readFile f); + + biocPackagesGenerated = importJSON ./bioc-packages.json; + biocAnnotationPackagesGenerated = importJSON ./bioc-annotation-packages.json; + biocExperimentPackagesGenerated = importJSON ./bioc-experiment-packages.json; + cranPackagesGenerated = importJSON ./cran-packages.json; +in { R, pkgs, overrides }: @@ -46,7 +55,7 @@ let # from the name, version, sha256, and optional per-package arguments above # deriveBioc = mkDerive { - mkHomepage = {name, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html"; + mkHomepage = {name, biocVersion}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html"; mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz" "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz" @@ -68,7 +77,7 @@ let hydraPlatforms = []; }; deriveCran = mkDerive { - mkHomepage = {name, ...}: "https://cran.r-project.org/web/packages/${name}/"; + mkHomepage = {name}: "https://cran.r-project.org/web/packages/${name}/"; mkUrls = {name, version}: [ "mirror://cran/${name}_${version}.tar.gz" "mirror://cran/Archive/${name}/${name}_${version}.tar.gz" @@ -287,10 +296,18 @@ let # packages in `_self` may depends on overridden packages. self = (defaultOverrides _self self) // overrides; _self = { inherit buildRPackage; } // - import ./bioc-packages.nix { inherit self; derive = deriveBioc; } // - import ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } // - import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } // - import ./cran-packages.nix { inherit self; derive = deriveCran; }; + mkPackageSet deriveBioc biocPackagesGenerated // + mkPackageSet deriveBiocAnn biocAnnotationPackagesGenerated // + mkPackageSet deriveBiocExp biocExperimentPackagesGenerated // + mkPackageSet deriveCran cranPackagesGenerated; + + # Takes in a generated JSON file's imported contents + # and transforms it by swapping each element of the depends array with the dependency's derivation + # and passing this new object to the provided derive function + mkPackageSet = derive: packagesJSON: lib.mapAttrs ( + k: v: derive packagesJSON.extraArgs (v // { depends = lib.map (name: builtins.getAttr name self) v.depends; }) + ) packagesJSON.packages; + # tweaks for the individual packages and "in self" follow @@ -608,7 +625,7 @@ let RCurl = [ pkgs.curl.dev ]; R2SWF = [ pkgs.pkg-config ]; rDEA = [ pkgs.glpk ]; - rgl = with pkgs; [ libGLU libGLU.dev libGL xorg.libX11.dev freetype.dev libpng.dev ]; + rgl = with pkgs; [ libGLU libGL xorg.libX11.dev freetype.dev libpng.dev ]; RGtk2 = [ pkgs.pkg-config ]; RProtoBuf = [ pkgs.pkg-config ]; Rpoppler = [ pkgs.pkg-config ]; @@ -782,6 +799,7 @@ let vapour = with pkgs; [ proj.dev gdal ]; MedianaDesigner = [ pkgs.zlib.dev ]; ChemmineOB = [ pkgs.eigen ]; + DGP4LCF = [ pkgs.lapack pkgs.blas ]; }; packagesRequiringX = [ @@ -1256,7 +1274,7 @@ let pbdZMQ = old.pbdZMQ.overrideAttrs (attrs: { postPatch = lib.optionalString stdenv.isDarwin '' for file in R/*.{r,r.in}; do - sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file + sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.cctools}/bin/\1"#g' $file done ''; }); |