cran-packages: marks broken packages broken instead of removeing them

pkgs/development/r-modules/broken-packages.nix

@@ -38,9 +38,6 @@
   "rsunlight" # jsonlite.so: undefined symbol: XXX
   "slackr" # jsonlite.so: undefined symbol: XXX
   "webutils" # jsonlite.so: undefined symbol: XXX
-  "HPO" # requires AnnotationDbi
-  "HPO.db" # requires AnnotationDbi
-  "HPO_db" # requires AnnotationDbi
   "msarc" # requires AnnotationDbi
   "ppiPre" # requires AnnotationDbi
   "RobLox" # requires Biobase
@@ -69,7 +66,6 @@
   "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
   "PubMedWordcloud" # requires GOsummaries
   "ExomeDepth" # requires GenomicRanges, and Rsamtools
-  "HPOSim" # requires HPO_db
   "HTSDiff" # requires HTSCluster
   "RAM" # requires Heatplus
   "RcppRedis" # requires Hiredis
@@ -125,7 +121,6 @@
   "calmate" # requires aroma_core
   "beadarrayFilter" # requires beadarray
   "PepPrep" # requires biomaRt
-  "oposSOM" # requires biomaRt
   "snplist" # requires biomaRt
   "FunctionalNetworks" # requires breastCancerVDX, and Biobase
   "rJPSGCS" # requires chopsticks
@@ -187,7 +182,6 @@
   "CORM" # requires limma
   "DAAGbio" # requires limma
   "DCGL" # requires limma
-  "GOsummaries" # requires limma
   "SQDA" # requires limma
   "metaMA" # requires limma
   "plmDE" # requires limma
@@ -216,7 +210,6 @@
   "qtlnet" # requires pcalg
   "SigTree" # requires phyloseq
   "saps" # requires piano, and survcomp
-  "sgof" # requires plot2D
   "surveillance" # requires polyCub
   "aLFQ" # requires protiq
   "NLPutils" # requires qdap

pkgs/development/r-modules/cran-packages.nix

@@ -11,7 +11,14 @@ let
   #
   # some packages, e.g. cncaGUI, require X running while installation,
   # so that we use xvfb-run if requireX is true.
-  derive = lib.makeOverridable ({ name, version, sha256, depends ? [], doCheck ? true, requireX ? false, hydraPlatforms ? R.meta.hydraPlatforms  }: buildRPackage {
+  derive = lib.makeOverridable ({
+        name, version, sha256,
+        depends ? [],
+        doCheck ? true,
+        requireX ? false,
+        broken ? false,
+        hydraPlatforms ? R.meta.hydraPlatforms
+      }: buildRPackage {
     name = "${name}-${version}";
     src = fetchurl {
       urls = [
@@ -25,6 +32,7 @@ let
     nativeBuildInputs = depends;
     meta.homepage = "http://cran.r-project.org/web/packages/${name}/";
     meta.hydraPlatforms = hydraPlatforms;
+    meta.broken = broken;
   });
 
   # Overrides package definitions with nativeBuildInputs.
@@ -131,10 +139,36 @@ let
     in
       builtins.listToAttrs nameValuePairs;
 
+  # Overrides package definition to mark it broken.
+  # For example,
+  #
+  # overrideBroken [
+  #   "foo"
+  # ] old
+  #
+  # results in
+  #
+  # {
+  #   foo = old.foo.override {
+  #     broken = true;
+  #   };
+  # }
+  overrideBroken = packageNames: old:
+    let
+      nameValuePairs = map (name: {
+        inherit name;
+        value = (builtins.getAttr name old).override {
+          broken = true;
+        };
+      }) packageNames;
+    in
+      builtins.listToAttrs nameValuePairs;
+
   packagesWithNativeBuildInputs = import ./packages-with-native-build-inputs.nix pkgs;
   packagesWithBuildInputs = import ./packages-with-build-inputs.nix pkgs;
   packagesRequireingX = import ./packages-requireing-x.nix;
   packagesToSkipCheck = import ./packages-to-skip-check.nix;
+  brokenPackages = import ./broken-packages.nix;
 
   defaultOverrides = old: new:
     let old0 = old; in
@@ -143,7 +177,8 @@ let
       old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
       old3 = old2 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old2);
       old4 = old3 // (overrideBuildInputs packagesWithBuildInputs old3);
-      old = old4;
+      old5 = old4 // (overrideBroken brokenPackages old4);
+      old = old5;
     in old // (import ./default-overrides.nix stdenv pkgs old new);
 
 
@@ -151,12 +186,7 @@ let
   # `_self` is a collection of packages;
   # `self` is `_self` with overridden packages;
   # packages in `_self` may depends on overridden packages.
-  overridden = (defaultOverrides _self self) // overrides;
-
-  maskedPackages = import ./masked-packages.nix;
-  masked = removeAttrs overridden maskedPackages;
-
-  self = masked;
+  self = (defaultOverrides _self self) // overrides;
   _self = import ./sources.nix { inherit self derive; };
 in
   self