rPackages.RBioFormats: vendor BioFormats from nixpkgs

pkgs/development/r-modules/default.nix

@@ -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
@@ -2021,6 +2020,34 @@ 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";
     });