rPackages: CRAN and BioC update (#490019)

pkgs/development/r-modules/bioc-annotation-packages.json

@@ -749,8 +749,8 @@
     },
     "CTCF": {
       "name": "CTCF",
-      "version": "0.99.12",
-      "sha256": "0c9s6hb7vac0yirqfyf7k9xnf45qpcj39q37jzsmxdvj2xf7cwd4",
+      "version": "0.99.13",
+      "sha256": "097w2rad5fxyg2dkghz6ws93q1l7hlc6f9dnw1n30gs2bdv5hbyb",
       "depends": []
     },
     "ChemmineDrugs": {
@@ -1521,6 +1521,12 @@
       "sha256": "0bmbp7kydvviczw8axgxq2wdlwq6fdas90jk9bg56avjq5syws2g",
       "depends": ["AnnotationDbi", "GenomicFeatures"]
     },
+    "TxDb_Hsapiens_UCSC_hg19_refGene": {
+      "name": "TxDb.Hsapiens.UCSC.hg19.refGene",
+      "version": "3.22.0",
+      "sha256": "0l2fpmyacyf644pkrrf35gsdpfplk4i9009miqbfg6p09gm5815p",
+      "depends": ["AnnotationDbi", "GenomicFeatures"]
+    },
     "TxDb_Hsapiens_UCSC_hg38_knownGene": {
       "name": "TxDb.Hsapiens.UCSC.hg38.knownGene",
       "version": "3.22.0",
@@ -1563,6 +1569,12 @@
       "sha256": "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9",
       "depends": ["AnnotationDbi", "GenomicFeatures"]
     },
+    "TxDb_Mmusculus_UCSC_mm39_knownGene": {
+      "name": "TxDb.Mmusculus.UCSC.mm39.knownGene",
+      "version": "3.22.0",
+      "sha256": "1apn7prr57njqdc61y1zkw6l4f151dixq1k458gbmgg4pyvlk4jy",
+      "depends": ["AnnotationDbi", "GenomicFeatures"]
+    },
     "TxDb_Mmusculus_UCSC_mm39_refGene": {
       "name": "TxDb.Mmusculus.UCSC.mm39.refGene",
       "version": "3.19.0",
@@ -5099,8 +5111,8 @@
     },
     "reactome_db": {
       "name": "reactome.db",
-      "version": "1.94.0",
-      "sha256": "0a6gx6iss43innhkhydqmv4jpnwkkjfdl32zxr4kjvm57xb2k4p0",
+      "version": "1.95.0",
+      "sha256": "1b87byr45cmqa7jyd5fw3askmrzfhdljjp2d7jcmm88baf45mfg6",
       "depends": ["AnnotationDbi"]
     },
     "rgu34a_db": {
@@ -6399,13 +6411,6 @@
       "depends": ["BiocGenerics", "BSgenome", "GenomeInfoDb", "GenomicRanges", "IRanges", "S4Vectors"],
       "broken": true
     },
-    "TxDb_Mmusculus_UCSC_mm39_knownGene": {
-      "name": "TxDb.Mmusculus.UCSC.mm39.knownGene",
-      "version": "3.21.0",
-      "sha256": "18ckr0sn8ff6ga2rzaxicbbfynvbpx56kl4949fnrgaygxgnlf9p",
-      "depends": ["AnnotationDbi", "GenomicFeatures"],
-      "broken": true
-    },
     "XtraSNPlocs_Hsapiens_dbSNP141_GRCh38": {
       "name": "XtraSNPlocs.Hsapiens.dbSNP141.GRCh38",
       "version": "0.99.12",

pkgs/development/r-modules/default.nix

@@ -431,6 +431,22 @@ let
       cargo
       rustc
     ];
+    b32 = with pkgs; [
+      cargo
+      rustc
+    ];
+    RPesto = with pkgs; [
+      cargo
+      rustc
+    ];
+    fru = with pkgs; [
+      cargo
+      rustc
+    ];
+    fastgeojson = with pkgs; [
+      cargo
+      rustc
+    ];
     audio = [ pkgs.portaudio ];
     BayesChange = [ pkgs.gsl ];
     BayesSAE = [ pkgs.gsl ];
@@ -451,6 +467,7 @@ let
       which
     ];
     bio3d = [ pkgs.zlib ];
+    BigDataStatMeth = [ pkgs.pkg-config ];
     BiocCheck = [ pkgs.which ];
     Biostrings = [ pkgs.zlib ];
     blosc = [ pkgs.pkg-config ];
@@ -568,6 +585,7 @@ let
       cargo
       rustc
     ];
+    harbinger = [ pkgs.glibcLocales ];
     haven = with pkgs; [ zlib.dev ];
     hellorust = [ pkgs.cargo ];
     hgwrr = [ pkgs.gsl ];
@@ -647,6 +665,10 @@ let
       which
       curl.dev
     ];
+    roxigraph = with pkgs; [
+      cargo
+      rustc
+    ];
     rsbml = [ pkgs.pkg-config ];
     rvg = [ pkgs.libpng.dev ];
     MAGEE = [
@@ -838,6 +860,10 @@ let
       cargo
       rustc
     ];
+    caugi = with pkgs; [
+      cargo
+      rustc
+    ];
     sdcTable = with pkgs; [
       gmp
       glpk
@@ -1120,6 +1146,7 @@ let
     nat = [ pkgs.which ];
     nat_templatebrains = [ pkgs.which ];
     pbdZMQ = [ pkgs.zeromq ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.darwin.binutils ];
+    pqsfinder = [ pkgs.boost ];
     bigmemory = lib.optionals stdenv.hostPlatform.isLinux [ pkgs.libuuid.dev ];
     bayesWatch = [ pkgs.boost.dev ];
     clustermq = [ pkgs.pkg-config ];
@@ -1517,12 +1544,18 @@ let
     psbcGroup = [ pkgs.gsl.dev ];
     rrd = [ pkgs.rrdtool ];
     flowWorkspace = [ pkgs.zlib.dev ];
+    MethScope = with pkgs; [
+      ncurses
+      zlib.dev
+    ];
     RITCH = [ pkgs.zlib.dev ];
     RcppMeCab = [ pkgs.mecab ];
     PING = [ pkgs.gsl ];
+    Rwbo = [ pkgs.zlib.dev ];
     PROJ = [ pkgs.proj.dev ];
     RcppAlgos = [ pkgs.gmp.dev ];
     RcppBigIntAlgos = [ pkgs.gmp.dev ];
+    BigDataStatMeth = [ pkgs.zlib ];
     spaMM = [ pkgs.gsl ];
     shrinkTVP = [ pkgs.gsl ];
     sbrl = with pkgs; [
@@ -1543,6 +1576,7 @@ let
         expat
         libxdmcp
       ];
+    XYomics = [ pkgs.boost ];
     HilbertVisGUI = [ pkgs.gtkmm2.dev ];
     textshaping = with pkgs; [
       harfbuzz.dev
@@ -1692,6 +1726,7 @@ let
     "csodata"
     "DiceView"
     "facmodTS"
+    "fwtraits"
     "gasanalyzer"
     "margaret"
     "MSnID"
@@ -1703,6 +1738,7 @@ let
     "PCRA"
     "PSCBS"
     "iemisc"
+    "ready4"
     "red"
     "repmis"
     "R_cache"
@@ -1718,6 +1754,7 @@ let
     "teal_code"
     "TreeTools"
     "TreeSearch"
+    "PKbioanalysis"
     "ACNE"
     "APAlyzer"
     "BAT"
@@ -1894,6 +1931,10 @@ let
       ];
     });
 
+    trajeR = old.trajeR.overrideAttrs (attrs: {
+      patches = [ ./patches/trajeR.patch ];
+    });
+
     arcpbf = old.arcpbf.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1910,6 +1951,18 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    caugi = old.caugi.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+    });
+
+    enderecobr = old.enderecobr.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+      nativeBuildInputs = attrs.nativeBuildInputs ++ [
+        pkgs.cargo
+        pkgs.rustc
+      ];
+    });
+
     h3o = old.h3o.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1918,6 +1971,13 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    roxigraph = old.roxigraph.overrideAttrs (attrs: {
+      env = (attrs.env or { }) // {
+        LIBCLANG_PATH = "${lib.getLib pkgs.libclang}/lib";
+      };
+      postPatch = "patchShebangs configure";
+    });
+
     rshift = old.rshift.overrideAttrs (attrs: {
       postPatch = "patchShebangs configure";
     });
@@ -1930,6 +1990,14 @@ let
       postPatch = "patchShebangs configure";
     });
 
+    yaml12 = old.yaml12.overrideAttrs (attrs: {
+      postPatch = "patchShebangs configure";
+      nativeBuildInputs = attrs.nativeBuildInputs ++ [
+        pkgs.cargo
+        pkgs.rustc
+      ];
+    });
+
     SynExtend = old.SynExtend.overrideAttrs (attrs: {
       # build might fail due to race condition
       enableParallelBuilding = false;
@@ -2259,6 +2327,12 @@ let
       hardeningDisable = [ "format" ];
     });
 
+    harbinger = old.harbinger.overrideAttrs (attrs: {
+      env = (attrs.env or { }) // {
+        LC_ALL = "en_US.UTF-8";
+      };
+    });
+
     HilbertVis = old.HilbertVis.overrideAttrs (attrs: {
       hardeningDisable = [ "format" ];
     });
@@ -2434,7 +2508,6 @@ let
     });
 
     RAppArmor = old.RAppArmor.overrideAttrs (attrs: {
-      patches = [ ./patches/RAppArmor.patch ];
       LIBAPPARMOR_HOME = pkgs.libapparmor;
     });
 
@@ -2907,6 +2980,12 @@ let
       ];
     });
 
+    SAIGEgds = old.SAIGEgds.overrideAttrs (attrs: {
+      env = (attrs.env or { }) // {
+        NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fpermissive";
+      };
+    });
+
     xslt = old.xslt.overrideAttrs (attrs: {
       env = (attrs.env or { }) // {
         NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fpermissive";
@@ -3087,6 +3166,22 @@ let
       '';
     });
 
+    b32 = old.b32.overrideAttrs (_: {
+      preConfigure = "patchShebangs configure";
+    });
+
+    BigDataStatMeth = old.BigDataStatMeth.overrideAttrs (_: {
+      preConfigure = "patchShebangs configure";
+    });
+
+    bigPLSR = old.bigPLSR.overrideAttrs (_: {
+      preConfigure = "patchShebangs configure";
+    });
+
+    RPesto = old.RPesto.overrideAttrs (_: {
+      preConfigure = "patchShebangs configure";
+    });
+
     pkgdepends = old.pkgdepends.overrideAttrs (attrs: {
       postPatch = ''
         patchShebangs configure

pkgs/development/r-modules/patches/RAppArmor.patch

@@ -1,20 +0,0 @@
-diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure
---- RAppArmor_orig/configure	2013-12-17 11:23:00.000000000 +0900
-+++ RAppArmor/configure	2014-10-18 22:22:39.641341244 +0900
-@@ -1,15 +1,2 @@
--if [ ! -e /usr/include/sys/apparmor.h ]
--then
--  echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed."
--  exit 1
--fi
--
--LIBFILE=$(/sbin/ldconfig -p | egrep -oh " [-_a-zA-Z0-9/]*/libapparmor.so(.1)?$")
--
--if [ -z "$LIBFILE" ]
--then
--  echo "libapparmor.so not found. Make sure libapparmor-dev is installed."
--  exit 1
--fi 
--
-+LIBFILE="$LIBAPPARMOR_HOME/lib/libapparmor.so.1"
- echo "PKG_LIBS="$LIBFILE > src/Makevars

pkgs/development/r-modules/patches/trajeR.patch

@@ -0,0 +1,13 @@
+diff --git a/src/Makevars b/src/Makevars
+index d147226..a79380e 100755
+--- a/src/Makevars
++++ b/src/Makevars
+@@ -19,7 +19,7 @@ PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+ 
+ # strip debug symbols for smaller Linux binaries
+ strippedLib: $(SHLIB)
+-		if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; \
++		@if [[ -e "/usr/bin/strip" && -e "/bin/uname" && $(shell uname) == "Linux" ]] ; \
+         then /usr/bin/strip --strip-debug $(SHLIB); fi
+ .phony: strippedLib
+