rPackages: fix broken packages

pkgs/development/r-modules/default.nix

···
 
   packagesWithRDepends = {
     # sort -t '=' -k 2
+    FactoMineR = [ self.car ];
   };
 
   packagesWithNativeBuildInputs = {
     # sort -t '=' -k 2
+    graphscan = [ pkgs.gsl ];
     RAppArmor = [ pkgs.apparmor ];
+    BNSP = [ pkgs.gsl ];
     SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
     curl = [ pkgs.curl pkgs.openldap ];
     Rssa = [ pkgs.fftw ];
···
     RCA = [ pkgs.gmp ];
     gmp = [ pkgs.gmp ];
     rcdd = [ pkgs.gmp ];
+    Rlibeemd = [ pkgs.gsl ];
     igraph = [ pkgs.gmp ];
     glpkAPI = [ pkgs.gmp pkgs.glpk ];
     sdcTable = [ pkgs.gmp pkgs.glpk ];
     Rmpfr = [ pkgs.gmp pkgs.mpfr ];
-    BNSP = [ pkgs.gsl ];
+    Formula = [ pkgs.gmp ];
     BayesSAE = [ pkgs.gsl ];
     BayesVarSel = [ pkgs.gsl ];
     HiCseg = [ pkgs.gsl ];
···
     topicmodels = [ pkgs.gsl ];
     RcppGSL = [ pkgs.gsl ];
     bnpmr = [ pkgs.gsl ];
+    V8 = [ pkgs.v8 ];
     geoCount = [ pkgs.gsl ];
+    devEMF = [ pkgs.xlibs.libXft ];
     gsl = [ pkgs.gsl ];
     mvabund = [ pkgs.gsl ];
     diversitree = [ pkgs.gsl pkgs.fftw ];
+    TKF = [ pkgs.gsl ];
     VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
     RGtk2 = [ pkgs.gtk2 ];
     cairoDevice = [ pkgs.gtk2 ];
···
     jpeg = [ pkgs.libjpeg ];
     EMCluster = [ pkgs.liblapack ];
     png = [ pkgs.libpng ];
+    pbdMPI = [ pkgs.openmpi ];
+    bigGP = [ pkgs.openmpi ];
     rtiff = [ pkgs.libtiff ];
     tiff = [ pkgs.libtiff ];
     Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
···
     BayesXsrc = [ pkgs.readline pkgs.ncurses ];
     udunits2 = [ pkgs.udunits pkgs.expat ];
     tkrplot = [ pkgs.xlibs.libX11 ];
-    rzmq = [ pkgs.zeromq2 ];
+    rzmq = [ pkgs.zeromq3 ];
     PopGenome = [ pkgs.zlib ];
     RJaCGH = [ pkgs.zlib ];
     RcppCNPy = [ pkgs.zlib ];
···
     rmatio = [ pkgs.zlib ];
     RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
     seqminer = [ pkgs.zlib pkgs.bzip2 ];
-    rphast = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
-    rtfbs = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
+    seqinr = [ pkgs.zlib ];
+    rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
+    rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
     Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
     SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
     RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
···
 
   packagesWithBuildInputs = {
     # sort -t '=' -k 2
+    svKomodo = [ pkgs.which ];
+    nat = [ pkgs.which ];
+    nat_nblast = [ pkgs.which ];
+    nat_templatebrains = [ pkgs.which ];
+    RMark = [ pkgs.which ];
+    RPushbullet = [ pkgs.which ];
     qtpaint = [ pkgs.cmake ];
     qtbase = [ pkgs.cmake pkgs.perl ];
     gmatrix = [ pkgs.cudatoolkit ];
···
     Cairo = [ pkgs.pkgconfig ];
     Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
     qtutils = [ pkgs.qt4 ];
+    ecoretriever = [ pkgs.which ];
     tcltk2 = [ pkgs.tcl pkgs.tk ];
-    tikzDevice = [ pkgs.texLive ];
+    tikzDevice = [ pkgs.which pkgs.texLive ];
     rPython = [ pkgs.which ];
     CARramps = [ pkgs.which pkgs.cudatoolkit ];
+    gridGraphics = [ pkgs.which ];
     gputools = [ pkgs.which pkgs.cudatoolkit ];
     rpud = [ pkgs.which pkgs.cudatoolkit ];
     adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
···
     "DeducerPlugInScaling"
     "DeducerSpatial"
     "DeducerSurvival"
+    "HomoPolymer"
+    "MetSizeR"
     "DeducerText"
     "Demerelate"
     "DescTools"
···
     "gmatrix" # requires CUDA runtime
     "npRmpi" # tries to run MPI processes
     "sprint" # tries to run MPI processes
+    "pbdMPI" # tries to run MPI processes
   ];
 
   # Packages which cannot be installed due to lack of dependencies or other reasons.
···
     "retistruct" # depends on broken RImageJROI
     "CARrampsOcl" # depends on OpenCL
     "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
-    "alm" # jsonlite.so: undefined symbol: XXX
-    "archivist" # jsonlite.so: undefined symbol: XXX
-    "bold" # jsonlite.so: undefined symbol: XXX
-    "enigma" # jsonlite.so: undefined symbol: XXX
-    "exCon" # jsonlite.so: undefined symbol: XXX
-    "gender" # jsonlite.so: undefined symbol: XXX
-    "jSonarR" # jsonlite.so: undefined symbol: XXX
-    "leafletR" # jsonlite.so: undefined symbol: XXX
-    "opencpu" # jsonlite.so: undefined symbol: XXX
-    "pdfetch" # jsonlite.so: undefined symbol: XXX
-    "polidata" # jsonlite.so: undefined symbol: XXX
-    "pollstR" # jsonlite.so: undefined symbol: XXX
-    "rbison" # jsonlite.so: undefined symbol: XXX
-    "RGA" # jsonlite.so: undefined symbol: XXX
-    "rHealthDataGov" # jsonlite.so: undefined symbol: XXX
-    "rinat" # jsonlite.so: undefined symbol: XXX
-    "rjstat" # jsonlite.so: undefined symbol: XXX
-    "rmongodb" # jsonlite.so: undefined symbol: XXX
-    "rnoaa" # jsonlite.so: undefined symbol: XXX
-    "RSiteCatalyst" # jsonlite.so: undefined symbol: XXX
-    "rsunlight" # jsonlite.so: undefined symbol: XXX
-    "rWBclimate" # jsonlite.so: undefined symbol: XXX
-    "SGP" # jsonlite.so: undefined symbol: XXX
-    "slackr" # jsonlite.so: undefined symbol: XXX
-    "SocialMediaMineR" # jsonlite.so: undefined symbol: XXX
-    "webutils" # jsonlite.so: undefined symbol: XXX
-    "WikipediR" # jsonlite.so: undefined symbol: XXX
     "demi" # requires affy, affxparser, and oligo
     "KANT" # requires affy, and Biobase
     "pathClass" # requires affy, and Biobase
     "msarc" # requires AnnotationDbi
     "ACNE" # requires aroma_affymetrix
+    "Statomica" # requires Biobase, multtest
     "aroma_affymetrix" # requires aroma_core
     "calmate" # requires aroma_core
     "NSA" # requires aroma_core
···
     "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
     "FunctionalNetworks" # requires breastCancerVDX, and Biobase
     "rJPSGCS" # requires chopsticks
-    "OpenCL" # requires CL/opencl.h
+    "OpenCL" # FIXME: requires CL/opencl.h
+    "Rsymphony" # FIXME: requires SYMPHONY
+    "V8" # compilation error
+    "js" # requires broken V8
+    "minimist" # requires broken V8
     "clpAPI" # requires clp
     "pcaL1" # requires clp
     "bmrm" # requires clpAPI
···
     "ParDNAcopy" # requires DNAcopy
     "PSCBS" # requires DNAcopy
     "dcGOR" # requires dnet
-    "bcool" # requires doMPI
     "gitter" # requires EBImage
+    "speaq" # requires MassSpecWavelet
     "Rcell" # requires EBImage
     "RockFab" # requires EBImage
     "babel" # requires edgeR
···
     "QuasiSeq" # requires edgeR
     "SimSeq" # requires edgeR
     "BcDiag" # requires fabia
+    "BACA" # requires RDAVIDWebService
     "superbiclust" # requires fabia
     "curvHDR" # requires flowCore
     "RbioRXN" # requires fmcsR, and KEGGREST
···
     "gridDebug" # requires gridGraphviz
     "RAM" # requires Heatplus
     "RcppRedis" # requires Hiredis
-    "HTSDiff" # requires HTSCluster
     "interval" # requires Icens
     "FAMT" # requires impute
+    "fdrDiscreteNull" # requires edgeR
     "moduleColor" # requires impute
     "PMA" # requires impute
     "samr" # requires impute
···
     "plmDE" # requires limma
     "SQDA" # requires limma
     "PerfMeas" # requires limma, graph, and RBGL
+    "ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
     "rLindo" # requires LINDO API
     "magma" # requires MAGMA
     "HiPLARM" # requires MAGMA or PLASMA
···
     "bigGP" # requires MPI running. HELP WANTED!
     "doMPI" # requires MPI running. HELP WANTED!
     "metaMix" # requires MPI running. HELP WANTED!
-    "pbdMPI" # requires MPI running. HELP WANTED!
     "pmclust" # requires MPI running. HELP WANTED!
     "MSeasyTkGUI" # requires MSeasyTkGUI
     "hddplot" # requires multtest
···
     "taxize" # requres bold
     "cudaBayesreg" # requres Rmath
     "rsprng" # requres sprng
+    "rDEA" # no such file or directory
+    "jomo" # linking errors
+    "mixture" # mixture.so: undefined symbol: dtrmm_
     "evobiR" # requres taxiz
     "bdvis" # requres taxize
     "RNeXML" # requres taxize
···
     "rainfreq" # SDMTools.so: undefined symbol: X
     "MigClim" # SDMTools.So: Undefined Symbol: X
     "PatternClass" # SDMTools.So: Undefined Symbol: X
-    "qtbase" # the smokegen binary cannot find libQtCore.so.4 etc. at runtime
     "jvmr" # tries to download files during its build
     "h2o" # tries to download some h2o.jar during its build
   ];
···
       preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include/curl";
     });
 
+    iFes = old.iFes.overrideDerivation (attrs: {
+      patches = [ ./patches/iFes.patch ];
+      CUDA_HOME = "${pkgs.cudatoolkit}";
+    });
+
     RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
       patchPhase = "patchShebangs configure";
     });
···
     });
 
     RMySQL = old.RMySQL.overrideDerivation (attrs: {
-      configureFlags = [
-        "--with-mysql-dir=${pkgs.mysql}"
-      ];
+      patches = [ ./patches/RMySQL.patch ];
+      MYSQL_DIR="${pkgs.mysql}";
+    });
+
+    devEMF = old.devEMF.overrideDerivation (attrs: {
+      NIX_CFLAGS_LINK = "-L${pkgs.xlibs.libXft}/lib -lXft";
     });
 
     slfm = old.slfm.overrideDerivation (attrs: {
···
     });
 
     openssl = old.openssl.overrideDerivation (attrs: {
-      patches = [ ./patches/openssl.patch ];
-      OPENSSL_HOME = "${pkgs.openssl}";
+      OPENSSL_INCLUDES = "${pkgs.openssl}/include";
     });
 
     Rserve = old.Rserve.overrideDerivation (attrs: {
···
         "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
       ];
     });
-
-    # Depends on broken ecespa package.
-    selectspm = old.selectspm.override { hydraPlatforms = stdenv.lib.platforms.none; };
-
-    # Depends on broken qtbase package.
-    qtutils = old.qtutils.override { hydraPlatforms = stdenv.lib.platforms.none; };
-    qtpaint = old.qtpaint.override { hydraPlatforms = stdenv.lib.platforms.none; };
-    bamboo = old.bamboo.override { hydraPlatforms = stdenv.lib.platforms.none; };
 
   };
 in

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

···
+diff -ru3 RMySQL_orig/configure RMySQL/configure
+--- RMySQL_orig/configure	2015-02-19 22:49:15.812455730 +0300
++++ RMySQL/configure	2015-02-19 22:49:42.066407256 +0300
+@@ -1,7 +1,7 @@
+ # If $MYSQL_DIR is specified, use that
+ if [ "$MYSQL_DIR" ]; then
+-  echo "PKG_CPPFLAGS= -I$MYSQL_DIR/include" > src/Makevars
+-  echo "PKG_LIBS= -L$MYSQL_DIR/lib -lmysqlclient -lz" >> src/Makevars
++  echo "PKG_CPPFLAGS= -I$MYSQL_DIR/include/mysql" > src/Makevars
++  echo "PKG_LIBS= -L$MYSQL_DIR/lib/mysql -lmysqlclient -lz" >> src/Makevars
+   exit 0
+ fi
+ 

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

···
+diff -u3 -r iFes_orig/src/config.mk iFes/src/config.mk
+--- iFes_orig/src/config.mk	2014-12-09 14:19:58.000000000 +0300
++++ iFes/src/config.mk	2015-02-19 22:47:24.426804174 +0300
+@@ -12,7 +12,7 @@
+ endif
+ 
+ # set CUDA_INC to CUDA header dir on your system
+-CUDA_INC := $(CUDA_HOME)/include
++CUDA_INC := $(CUDA_HOME)/usr_include
+ 
+ ARCH := $(shell uname -m)
+ 
+

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

···
-diff -ru -x '*~' openssl_orig/configure openssl/configure
---- openssl_orig/configure	2014-11-08 02:32:33.000000000 +0900
-+++ openssl/configure	2014-11-29 20:57:19.919495325 +0900
-@@ -4,14 +4,15 @@
- # if present, hence this script is not really required. On CRAN, we use
- # the $OPENSSL_INCLUDES variable; elsewhere we assume to the standard
- # linux location: /usr/include/openssl.
--if [ -z "$OPENSSL_INCLUDES" ]; then
--  OPENSSL_INCLUDES="/usr/include"
--else
--  echo "PKG_CPPFLAGS= -I$OPENSSL_INCLUDES" >> src/Makevars
--fi
-+# if [ -z "$OPENSSL_INCLUDES" ]; then
-+#   OPENSSL_INCLUDES="/usr/include"
-+# else
-+#   echo "PKG_CPPFLAGS= -I$OPENSSL_INCLUDES" >> src/Makevars
-+# fi
- 
--# Verify that openssl RNG is present
--if [ ! -e $OPENSSL_INCLUDES/openssl/rand.h ]; then
--  echo "File $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
--  exit 1
--fi
-+# # Verify that openssl RNG is present
-+# if [ ! -e $OPENSSL_INCLUDES/openssl/rand.h ]; then
-+#   echo "File $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
-+#   exit 1
-+# fi
-+echo "PKG_LIBS= -L"${OPENSSL_HOME}/lib" -lssl -lcrypto" > src/Makevars
-\ No newline at end of file