Unverified Commit 284add3b authored by Justin Bedő's avatar Justin Bedő Committed by GitHub
Browse files

rPackages.RBioFormats: fix build and revdeps properly (#472944)

parents 78ee285a 6772a554

pkgs/by-name/bf/bftools/package.nix

+3 −2
Original line number Diff line number Diff line
@@ -8,11 +8,11 @@ 


stdenv.mkDerivation rec {

  pname = "bftools";

  version = "6.3.0";

  version = "7.3.0";



  src = fetchzip {

    url = "http://downloads.openmicroscopy.org/bio-formats/${version}/artifacts/bftools.zip";

    sha256 = "02nvvmpfglpah1ihd08aw65g1794w588c988cdar1hfl4s80qwhb";

    hash = "sha256-EQ7P07d53e6Q/9Wt2Pa1h0TfuYblOZeByGW30oE3i6M=";

  };



  installPhase = ''
@@ -39,6 +39,7 @@ stdenv.mkDerivation rec { 


  meta = {

    description = "Bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included";

    mainProgram = "showinf";

    sourceProvenance = with lib.sourceTypes; [ binaryBytecode ];

    license = lib.licenses.gpl2;

    platforms = lib.platforms.all;

pkgs/development/r-modules/default.nix

+28 −1
Original line number Diff line number Diff line
@@ -1758,7 +1758,6 @@ let 
    "Rmpi" # tries to run MPI processes

    "ReactomeContentService4R" # tries to connect to Reactome

    "PhIPData" # tries to download something from a DB

    "RBioFormats" # tries to download jar during load test

    "pbdMPI" # tries to run MPI processes

    "CTdata" # tries to connect to ExperimentHub

    "rfaRm" # tries to connect to Ebi
@@ -2030,6 +2029,34 @@ let 
      '';

    });



    RBioFormats = old.RBioFormats.overrideAttrs (attrs: {

      # 1. Never download the jar file

      # 2. Use jar from pkgs.bftools instead

      # 3. Break the build if versions don't match

      propagatedBuildInputs = (attrs.propagatedBuildInputs or [ ]) ++ [ pkgs.bftools ];



      postPatch = ''

        substituteInPlace "R/zzz.R" \

          --replace-fail '!file.exists(bf_jar)' 'FALSE' \

          --replace-fail \

          '.jpackage(pkg, lib.loc = lib, morePaths = c(jars, bf_jar))' \

          '.jpackage(pkg, lib.loc = lib, morePaths = union(jars, "${lib.getBin pkgs.bftools}/share/java/bioformats_package.jar"))' \

          --replace-fail 'bf_jar <-' 'stopifnot(bf_ver == "${pkgs.bftools.version}");bf_jar <-'

      '';



      # Ensure that bftools version matches that in the package DESCRIPTION

      preInstall = ''

        rbf_version="$(sed  -n 's/^BioFormats: //p' DESCRIPTION)"

        bf_version="${pkgs.bftools.version}"

        if [ "$rbf_version" != "$bf_version" ]; then

           echo "BioFormats version mismatch detected!"

           echo "RBioformats needs: $rbf_version"

           echo "bftools provides: $bf_version"

           exit 1

        fi

      '';

    });



    rbm25 = old.rbm25.overrideAttrs (attrs: {

      postPatch = "patchShebangs configure";

    });