rPackages.RBioFormats: vendor BioFormats from nixpkgs

    "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

      '';

    });

    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";

    });