cran-packages: restructured

2024-11-16 06:45:16 +01:00 · 2014-11-21 22:23:36 +09:00 · 2014-11-21 22:23:36 +09:00 · 2a1d9ddbf2
commit 2a1d9ddbf2
parent e125997df6
28 changed files with 7317 additions and 6034 deletions
--- a/pkgs/development/r-modules/cran-packages.nix
+++ b/pkgs/development/r-modules/cran-packages.nix
--- a/pkgs/development/r-modules/defaultOverrides.nix
+++ b/pkgs/development/r-modules/defaultOverrides.nix
@ -0,0 +1,148 @@
+overrideDerivation: pkgs: old: new: {
+  RcppArmadillo = overrideDerivation old.RcppArmadillo (attrs: {
+    patchPhase = "patchShebangs configure";
+  });
+
+  rpf = overrideDerivation old.rpf (attrs: {
+    patchPhase = "patchShebangs configure";
+  });
+
+  BayesXsrc = overrideDerivation old.BayesXsrc (attrs: {
+    patches = [ ./patches/BayesXsrc.patch ];
+  });
+
+  rJava = overrideDerivation old.rJava (attrs: {
+    preConfigure = ''
+      export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
+      export JAVA_HOME=${pkgs.jdk}
+    '';
+  });
+
+  JavaGD = overrideDerivation old.JavaGD (attrs: {
+    preConfigure = ''
+      export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
+      export JAVA_HOME=${pkgs.jdk}
+    '';
+  });
+
+  Mposterior = overrideDerivation old.Mposterior (attrs: {
+    PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
+  });
+
+  qtbase = overrideDerivation old.qtbase (attrs: {
+    patches = [ ./patches/qtbase.patch ];
+  });
+
+  Rmpi = overrideDerivation old.Rmpi (attrs: {
+    configureFlags = [
+      "--with-Rmpi-type=OPENMPI"
+    ];
+  });
+
+  npRmpi = overrideDerivation old.npRmpi (attrs: {
+    configureFlags = [
+      "--with-Rmpi-type=OPENMPI"
+    ];
+  });
+
+  Rmpfr = overrideDerivation old.Rmpfr (attrs: {
+    configureFlags = [
+      "--with-mpfr-include=${pkgs.mpfr}/include"
+    ];
+  });
+
+  RVowpalWabbit = overrideDerivation old.RVowpalWabbit (attrs: {
+    configureFlags = [
+      "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
+    ];
+  });
+
+  RAppArmor = overrideDerivation old.RAppArmor (attrs: {
+    patches = [ ./patches/RAppArmor.patch ];
+    LIBAPPARMOR_HOME = "${pkgs.apparmor}";
+  });
+
+  RMySQL = overrideDerivation old.RMySQL (attrs: {
+    configureFlags = [
+      "--with-mysql-dir=${pkgs.mysql}"
+    ];
+  });
+
+  slfm = overrideDerivation old.slfm (attrs: {
+    PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
+  });
+
+  SamplerCompare = overrideDerivation old.SamplerCompare (attrs: {
+    PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
+  });
+
+  gputools = overrideDerivation old.gputools (attrs: {
+    patches = [ ./patches/gputools.patch ];
+    CUDA_HOME = "${pkgs.cudatoolkit}";
+  });
+
+  CARramps = overrideDerivation old.CARramps (attrs: {
+    patches = [ ./patches/CARramps.patch ];
+    configureFlags = [
+      "--with-cuda-home=${pkgs.cudatoolkit}"
+    ];
+  });
+
+  gmatrix = overrideDerivation old.gmatrix (attrs: {
+    patches = [ ./patches/gmatrix.patch ];
+    CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
+    R_INC_PATH = "${pkgs.R}/lib/R/include";
+    CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include";
+  });
+
+  rpud = overrideDerivation old.rpud (attrs: {
+    patches = [ ./patches/rpud.patch ];
+    CUDA_HOME = "${pkgs.cudatoolkit}";
+  });
+
+  WideLM = overrideDerivation old.WideLM (attrs: {
+    patches = [ ./patches/WideLM.patch ];
+    configureFlags = [
+      "--with-cuda-home=${pkgs.cudatoolkit}"
+    ];
+  });
+
+  EMCluster = overrideDerivation old.EMCluster (attrs: {
+    patches = [ ./patches/EMCluster.patch ];
+  });
+
+  spMC = overrideDerivation old.spMC (attrs: {
+    patches = [ ./patches/spMC.patch ];
+  });
+
+  BayesLogit = overrideDerivation old.BayesLogit (attrs: {
+    patches = [ ./patches/BayesLogit.patch ];
+  });
+
+  BayesBridge = overrideDerivation old.BayesBridge (attrs: {
+    patches = [ ./patches/BayesBridge.patch ];
+  });
+
+  dbarts = overrideDerivation old.dbarts (attrs: {
+    patches = [ ./patches/dbarts.patch ];
+  });
+
+  openssl = overrideDerivation old.openssl (attrs: {
+    patches = [ ./patches/openssl.patch ];
+    OPENSSL_HOME = "${pkgs.openssl}";
+  });
+
+  Rserve = overrideDerivation old.Rserve (attrs: {
+    patches = [ ./patches/Rserve.patch ];
+    configureFlags = [
+      "--with-server" "--with-client"
+    ];
+  });
+
+  nloptr = overrideDerivation old.nloptr (attrs: {
+    configureFlags = [
+      "--with-nlopt-cflags=-I${pkgs.nlopt}/include"
+      "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
+    ];
+  });
+}
--- a/pkgs/development/r-modules/generate_sources.R
+++ b/pkgs/development/r-modules/generate_sources.R
@ -0,0 +1,43 @@
+library(data.table)
+library(parallel)
+cl <- makeCluster(10)
+options(repos=structure(c(CRAN="http://cran.rstudio.com/")))
+
+nixPrefetch <- function(name, version) {
+    system(paste0("nix-prefetch-url --type sha256 http://cran.rstudio.com/src/contrib/", name, "_", version, ".tar.gz"), intern=TRUE)
+    # system(paste0("nix-hash --flat --base32 --type sha256 /nix/store/*", name, "_", version, ".tar.gz", "| head -n 1"), intern=TRUE)
+}
+
+formatPackage <- function(name, version, sha256, depends, imports, linkingTo, knownPackages) {
+    attr <- gsub(".", "_", name, fixed=TRUE)
+    if (is.na(depends)) depends <- "";
+    depends <- unlist(strsplit(depends, split="[ \t\n]*,[ \t\n]*", fixed=FALSE))
+    depends <- c(depends, unlist(strsplit(imports, split="[ \t\n]*,[ \t\n]*", fixed=FALSE)))
+    depends <- c(depends, unlist(strsplit(linkingTo, split="[ \t\n]*,[ \t\n]*", fixed=FALSE)))
+    depends <- sapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1")
+    depends <- depends[depends %in% knownPackages]
+    depends <- sapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
+    depends <- paste(depends, collapse=" ")
+    paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
+}
+
+clusterExport(cl, c("nixPrefetch"))
+
+pkgs <- as.data.table(available.packages(filters=c("R_version", "OS_type", "CRAN", "duplicates")))
+pkgs <- subset(pkgs, Repository=="http://cran.rstudio.com/src/contrib")
+pkgs <- pkgs[order(Package)]
+pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
+knownPackages <- unique(pkgs$Package)
+
+nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6], knownPackages))
+
+cat("# This file is generated from generate_sources.R. DO NOT EDIT.\n")
+cat("# Execute the following command to update the file.\n")
+cat("#\n")
+cat("# Rscript generate_sources.R > sources.nix\n")
+cat("\n")
+cat("{ self, derive }: with self; {\n")
+cat(paste(nix, collapse="\n"), "\n")
+cat("}\n")
+
+stopCluster(cl)
--- a/pkgs/development/r-modules/generic-builder.nix
+++ b/pkgs/development/r-modules/generic-builder.nix
@ -1,9 +1,9 @@
-R:
+{ R, xvfb_run, utillinux }:

 { name, buildInputs ? [], ... } @ attrs:

 R.stdenv.mkDerivation ({
-  buildInputs = buildInputs ++ [R];
+  buildInputs = buildInputs ++ [R xvfb_run utillinux];

  configurePhase = ''
    runHook preConfigure
@ -16,10 +16,22 @@ R.stdenv.mkDerivation ({
    runHook postBuild
  '';

+  installOptions = if attrs.skipTest or false then
+    "--no-test-load "
+  else
+    "";
+
+  rCommand = if attrs.requireX or false then
+    # Unfortunately, xvfb-run has a race condition even with -a option, so that
+    # we acquire a lock explicitly.
+    "flock ${xvfb_run} xvfb-run -a -e xvfb-error R"
+  else
+    "R";
+
  installPhase = ''
    runHook preInstall
    mkdir -p $out/library
-    R CMD INSTALL -l $out/library .
+    $rCommand CMD INSTALL $installOptions --configure-args="$configureFlags" -l $out/library .
    runHook postInstall
  '';

--- a/pkgs/development/r-modules/maskedPackages.nix
+++ b/pkgs/development/r-modules/maskedPackages.nix
@ -0,0 +1,290 @@
+# Packages which cannot be installed due to lack of dependencies or other reasons.
+[
+  # sort -t '#' -k 2
+
+  "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
+  "Actigraphy" # SDMTools.so: undefined symbol: X
+  "MigClim" # SDMTools.So: Undefined Symbol: X
+  "PatternClass" # SDMTools.So: Undefined Symbol: X
+  "lefse" # SDMTools.so: undefined symbol: X
+  "raincpc" # SDMTools.so: undefined symbol: X
+  "rainfreq" # SDMTools.so: undefined symbol: X
+  "CARrampsOcl" # depends on OpenCL
+  "RGA" # jsonlite.so: undefined symbol: XXX
+  "RSiteCatalyst" # jsonlite.so: undefined symbol: XXX
+  "RSocrata" # jsonlite.so: undefined symbol: XXX
+  "SGP" # jsonlite.so: undefined symbol: XXX
+  "SocialMediaMineR" # jsonlite.so: undefined symbol: XXX
+  "WikipediR" # jsonlite.so: undefined symbol: XXX
+  "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
+  "rHealthDataGov" # jsonlite.so: undefined symbol: XXX
+  "rWBclimate" # jsonlite.so: undefined symbol: XXX
+  "rbison" # 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
+  "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
+  "RobLoxBioC" # requires Biobase
+  "compendiumdb" # requires Biobase
+  "ktspair" # requires Biobase
+  "permGPU" # requires Biobase
+  "propOverlap" # requires Biobase
+  "GExMap" # requires Biobase and multtest
+  "IsoGene" # requires Biobase, and affy
+  "mGSZ" # requires Biobase, and limma
+  "NCmisc" # requires BiocInstaller
+  "RADami" # requires Biostrings
+  "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
+  "SimRAD" # requires Biostrings, and ShortRead
+  "SeqFeatR" # requires Biostrings, qvalue, and widgetTools
+  "OpenCL" # requires CL/opencl.h
+  "cplexAPI" # requires CPLEX
+  "CHAT" # requires DNAcopy
+  "PSCBS" # requires DNAcopy
+  "ParDNAcopy" # requires DNAcopy
+  "Rcell" # requires EBImage
+  "RockFab" # requires EBImage
+  "gitter" # requires EBImage
+  "rggobi" # requires GGobi
+  "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
+  "MSIseq" # requires IRanges
+  "SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
+  "interval" # requires Icens
+  "PhViD" # requires LBE
+  "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
+  "bigpca" # requires NCmisc
+  "reader" # requires NCmisc
+  "ROracle" # requires OCI
+  "BRugs" # requires OpenBUGS
+  "smart" # requires PMA
+  "aroma_cn" # requires PSCBS
+  "aroma_core" # requires PSCBS
+  "RQuantLib" # requires QuantLib
+  "RSeed" # requires RBGL, and graph
+  "gRbase" # requires RBGL, and graph
+  "ora" # requires ROracle
+  "semiArtificial" # requires RSNNS
+  "branchLars" # requires Rgraphviz
+  "gcExplorer" # requires Rgraphviz
+  "hasseDiagram" # requires Rgraphviz
+  "hpoPlot" # requires Rgraphviz
+  "strum" # requires Rgraphviz
+  "dagbag" # requires Rlapack
+  "ltsk" # requires Rlapack and Rblas
+  "REBayes" # requires Rmosek
+  "LinRegInteractive" # requires Rpanel
+  "RVideoPoker" # requires Rpanel
+  "ArrayBin" # requires SAGx
+  "RSAP" # requires SAPNWRFCSDK
+  "DBKGrad" # requires SDD
+  "pubmed_mineR" # requires SSOAP
+  "ENA" # requires WGCNA
+  "GOGANPA" # requires WGCNA
+  "nettools" # requires WGCNA
+  "rneos" # requires XMLRPC
+  "demi" # requires affy, affxparser, and oligo
+  "KANT" # requires affy, and Biobase
+  "pathClass" # requires affy, and Biobase
+  "ACNE" # requires aroma_affymetrix
+  "NSA" # requires aroma_core
+  "aroma_affymetrix" # requires aroma_core
+  "calmate" # requires aroma_core
+  "beadarrayFilter" # requires beadarray
+  "PepPrep" # requires biomaRt
+  "oposSOM" # requires biomaRt
+  "snplist" # requires biomaRt
+  "FunctionalNetworks" # requires breastCancerVDX, and Biobase
+  "rJPSGCS" # requires chopsticks
+  "clpAPI" # requires clp
+  "pcaL1" # requires clp
+  "bmrm" # requires clpAPI
+  "sequenza" # requires copynumber
+  "Rcplex" # requires cplexAPI
+  "dcGOR" # requires dnet
+  "bcool" # requires doMPI
+  "GSAgm" # requires edgeR
+  "HTSCluster" # requires edgeR
+  "QuasiSeq" # requires edgeR
+  "SimSeq" # requires edgeR
+  "babel" # requires edgeR
+  "edgeRun" # requires edgeR
+  "BcDiag" # requires fabia
+  "superbiclust" # requires fabia
+  "curvHDR" # requires flowCore
+  "RbioRXN" # requires fmcsR, and KEGGREST
+  "LogisticDx" # requires gRbase
+  "gRain" # requires gRbase
+  "gRbase" # requires gRbase
+  "gRc" # requires gRbase
+  "gRim" # requires gRbase
+  "topologyGSA" # requires gRbase
+  "qdap" # requires gender
+  "orQA" # requires genefilter
+  "apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
+  "miRtest" # requires globaltest, GlobalAncova, and limma
+  "PairViz" # requires graph
+  "eulerian" # requires graph
+  "gRapHD" # requires graph
+  "msSurv" # requires graph
+  "RnavGraph" # requires graph, and RBGL
+  "iRefR" # requires graph, and RBGL
+  "pcalg" # requires graph, and RBGL
+  "protiq" # requires graph, and RBGL
+  "classGraph" # requires graph, and Rgraphviz
+  "epoc" # requires graph, and Rgraphviz
+  "gridGraphviz" # requires graph, and Rgraphviz
+  "ddepn" # requires graph, and genefilter
+  "gridDebug" # requires gridGraphviz
+  "DRI" # requires impute
+  "FAMT" # requires impute
+  "PMA" # requires impute
+  "WGCNA" # requires impute
+  "moduleColor" # requires impute
+  "samr" # requires impute
+  "swamp" # requires impute
+  "MetaDE" # requires impute, and Biobase
+  "FHtest" # requires interval
+  "RefFreeEWAS" # requires isva
+  "AntWeb" # requires leafletR
+  "ecoengine" # requires leafletR
+  "spocc" # requires leafletR
+  "sybilSBML" # requires libSBML
+  "RDieHarder" # requires libdieharder
+  "CORM" # requires limma
+  "DAAGbio" # requires limma
+  "DCGL" # requires limma
+  "GOsummaries" # requires limma
+  "SQDA" # requires limma
+  "metaMA" # requires limma
+  "plmDE" # requires limma
+  "RPPanalyzer" # requires limma, and Biobase
+  "PerfMeas" # requires limma, graph, and RBGL
+  "MAMA" # requires metaMA
+  "Rmosek" # requires mosek
+  "PCS" # requires multtest
+  "TcGSA" # requires multtest
+  "hddplot" # requires multtest
+  "mutoss" # requires multtest
+  "structSSI" # requires multtest
+  "mutossGUI" # requires mutoss
+  "Biograph" # requires mvna
+  "MSeasy" # requires mzR, and xcms
+  "x_ent" # requires opencpu
+  "pbdBASE" # requires pbdMPI
+  "pbdDEMO" # requires pbdMPI
+  "pbdDMAT" # requires pbdMPI
+  "pbdSLAP" # requires pbdMPI
+  "LOST" # requires pcaMethods
+  "multiDimBio" # requires pcaMethods
+  "crmn" # requires pcaMethods, and Biobase
+  "imputeLCMD" # requires pcaMethods, and impute
+  "MEET" # requires pcaMethods, and seqLogo
+  "qtlnet" # requires pcalg
+  "SigTree" # requires phyloseq
+  "saps" # requires piano, and survcomp
+  "sgof" # requires plot2D
+  "surveillance" # requires polyCub
+  "aLFQ" # requires protiq
+  "NLPutils" # requires qdap
+  "NBPSeq" # requires qvalue
+  "RSNPset" # requires qvalue
+  "evora" # requires qvalue
+  "isva" # requires qvalue
+  "pi0" # requires qvalue
+  "CrypticIBDcheck" # requires rJPSGCS
+  "PKgraph" # requires rggobi
+  "SeqGrapheR" # requires rggobi
+  "beadarrayMSV" # requires rggobi
+  "clusterfly" # requires rggobi
+  "HierO" # requires rneos
+  "fPortfolio" # requires rneos
+  "GUIDE" # requires rpanel
+  "SDD" # requires rpanel
+  "biotools" # requires rpanel
+  "erpR" # requires rpanel
+  "gamlss_demo" # requires rpanel
+  "lgcp" # requires rpanel
+  "optBiomarker" # requires rpanel
+  "soilphysics" # requires rpanel
+  "vows" # requires rpanel
+  "PCGSE" # requires safe
+  "DepthProc" # requires samr
+  "netClass" # requires samr
+  "RcmdrPlugin_seeg" # requires seeg
+  "EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
+  "GeneticTools" # requires snpStats
+  "snpEnrichment" # requires snpStats
+  "snpStatsWriter" # requires snpStats
+  "wgsea" # requires snpStats
+  "rysgran" # requires soiltexture
+  "DSpat" # requires spatstat
+  "Digiroo2" # requires spatstat
+  "ETAS" # requires spatstat
+  "GriegSmith" # requires spatstat
+  "RImageJROI" # requires spatstat
+  "SGCS" # requires spatstat
+  "SpatialVx" # requires spatstat
+  "adaptsmoFMRI" # requires spatstat
+  "ads" # requires spatstat
+  "aoristic" # requires spatstat
+  "dbmss" # requires spatstat
+  "dixon" # requires spatstat
+  "dpcR" # requires spatstat
+  "ecespa" # requires spatstat
+  "ecospat" # requires spatstat
+  "intamapInteractive" # requires spatstat
+  "latticeDensity" # requires spatstat
+  "polyCub" # requires spatstat
+  "seeg" # requires spatstat
+  "siar" # requires spatstat
+  "siplab" # requires spatstat
+  "sparr" # requires spatstat
+  "spatialsegregation" # requires spatstat
+  "stpp" # requires spatstat
+  "trip" # requires spatstat
+  "dnet" # requires supraHex, graph, Rgraphviz, and Biobase
+  "plsRcox" # requires survcomp
+  "rsig" # requires survcomp
+  "ttScreening" # requires sva, and limma
+  "cudaBayesreg" # requres Rmath
+  "taxize" # requres bold
+  "rsprng" # requres sprng
+  "RNeXML" # requres taxize
+  "TR8" # requres taxize
+  "bdvis" # requres taxize
+  "evobiR" # requres taxiz
+]
--- a/pkgs/development/r-modules/packagesRequireingX.nix
+++ b/pkgs/development/r-modules/packagesRequireingX.nix
@ -0,0 +1,204 @@
+[
+  "AnalyzeFMRI"
+  "AnnotLists"
+  "AnthropMMD"
+  "AtelieR"
+  "BCA"
+  "BEQI2"
+  "BHMSMAfMRI"
+  "BiodiversityR"
+  "CCTpack"
+  "ConvergenceConcepts"
+  "DALY"
+  "DSpat"
+  "Deducer"
+  "DeducerExtras"
+  "DeducerPlugInExample"
+  "DeducerPlugInScaling"
+  "DeducerSpatial"
+  "DeducerSurvival"
+  "DeducerText"
+  "DescTools"
+  "DivMelt"
+  "ENiRG"
+  "EcoVirtual"
+  "EnQuireR"
+  "FFD"
+  "FeedbackTS"
+  "GGEBiplotGUI"
+  "GPCSIV"
+  "Geneland"
+  "GeoGenetix"
+  "GeoXp"
+  "GrapheR"
+  "GroupSeq"
+  "HH"
+  "HiveR"
+  "JGR"
+  "KappaGUI"
+  "LS2Wstat"
+  "MAR1"
+  "MTurkR"
+  "MareyMap"
+  "MergeGUI"
+  "Meth27QC"
+  "MissingDataGUI"
+  "MplusAutomation"
+  "OligoSpecificitySystem"
+  "OpenRepGrid"
+  "PBSadmb"
+  "PBSmodelling"
+  "PKmodelFinder"
+  "PoMoS"
+  "PredictABEL"
+  "PrevMap"
+  "ProbForecastGOP"
+  "QCAGUI"
+  "R2STATS"
+  "RHRV"
+  "RNCEP"
+  "RSDA"
+  "RSurvey"
+  "RandomFields"
+  "Rcmdr"
+  "RcmdrPlugin_BCA"
+  "RcmdrPlugin_DoE"
+  "RcmdrPlugin_EACSPIR"
+  "RcmdrPlugin_EBM"
+  "RcmdrPlugin_EZR"
+  "RcmdrPlugin_EcoVirtual"
+  "RcmdrPlugin_FactoMineR"
+  "RcmdrPlugin_HH"
+  "RcmdrPlugin_IPSUR"
+  "RcmdrPlugin_KMggplot2"
+  "RcmdrPlugin_MA"
+  "RcmdrPlugin_MPAStats"
+  "RcmdrPlugin_NMBU"
+  "RcmdrPlugin_ROC"
+  "RcmdrPlugin_SCDA"
+  "RcmdrPlugin_SLC"
+  "RcmdrPlugin_SM"
+  "RcmdrPlugin_StatisticalURV"
+  "RcmdrPlugin_TeachingDemos"
+  "RcmdrPlugin_UCA"
+  "RcmdrPlugin_coin"
+  "RcmdrPlugin_depthTools"
+  "RcmdrPlugin_doex"
+  "RcmdrPlugin_epack"
+  "RcmdrPlugin_lfstat"
+  "RcmdrPlugin_mosaic"
+  "RcmdrPlugin_orloca"
+  "RcmdrPlugin_plotByGroup"
+  "RcmdrPlugin_pointG"
+  "RcmdrPlugin_qual"
+  "RcmdrPlugin_sampling"
+  "RcmdrPlugin_sos"
+  "RcmdrPlugin_steepness"
+  "RcmdrPlugin_survival"
+  "RcmdrPlugin_temis"
+  "RenextGUI"
+  "RunuranGUI"
+  "SOLOMON"
+  "SPACECAP"
+  "SRRS"
+  "SSDforR"
+  "Simile"
+  "SimpleTable"
+  "StatDA"
+  "SyNet"
+  "TDMR"
+  "TED"
+  "TIMP"
+  "TTAinterfaceTrendAnalysis"
+  "TestScorer"
+  "VIMGUI"
+  "VecStatGraphs3D"
+  "VisuClust"
+  "WMCapacity"
+  "accrual"
+  "ade4TkGUI"
+  "adehabitat"
+  "aplpack"
+  "aqfig"
+  "arf3DS4"
+  "asbio"
+  "bio_infer"
+  "biplotbootGUI"
+  "cairoDevice"
+  "cncaGUI"
+  "confidence"
+  "constrainedKriging"
+  "cpa"
+  "debug"
+  "detrendeR"
+  "dgmb"
+  "dpa"
+  "dynBiplotGUI"
+  "dynamicGraph"
+  "eVenn"
+  "exactLoglinTest"
+  "fSRM"
+  "fat2Lpoly"
+  "fbati"
+  "feature"
+  "fgui"
+  "fisheyeR"
+  "fit4NM"
+  "forensim"
+  "fscaret"
+  "gWidgets2RGtk2"
+  "gWidgets2tcltk"
+  "gWidgetstcltk"
+  "gcmr"
+  "geoR"
+  "geoRglm"
+  "georob"
+  "gnm"
+  "gsubfn"
+  "ic50"
+  "in2extRemes"
+  "iplots"
+  "likeLTD"
+  "logmult"
+  "migui"
+  "miniGUI"
+  "mixsep"
+  "mlDNA"
+  "mritc"
+  "multgee"
+  "multibiplotGUI"
+  "onemap"
+  "pbatR"
+  "playwith"
+  "plotSEMM"
+  "powerpkg"
+  "prefmod"
+  "qtbase"
+  "qtpaint"
+  "qtutils"
+  "r4ss"
+  "rAverage"
+  "relax"
+  "relimp"
+  "reportRx"
+  "ringscale"
+  "ripa"
+  "rite"
+  "rnbn"
+  "rriskDistributions"
+  "rsgcc"
+  "sdcMicroGUI"
+  "spatsurv"
+  "sqldf"
+  "stosim"
+  "stylo"
+  "svDialogstcltk"
+  "svIDE"
+  "svSocket"
+  "svWidgets"
+  "titan"
+  "tkrgl"
+  "twiddler"
+  "vcdExtra"
+  "x12GUI"
+]
--- a/pkgs/development/r-modules/packagesToSkipTests.nix
+++ b/pkgs/development/r-modules/packagesToSkipTests.nix
@ -0,0 +1,6 @@
+[
+  "Rmpi" # tries to run MPI processes
+  "gmatrix" # requires CUDA runtime
+  "npRmpi" # tries to run MPI processes
+  "sprint" # tries to run MPI processes
+]
--- a/pkgs/development/r-modules/packagesWithBuildInputs.nix
+++ b/pkgs/development/r-modules/packagesWithBuildInputs.nix
@ -0,0 +1,37 @@
+pkgs: {
+  # sort -t '=' -k 2
+  qtpaint = [ pkgs.cmake ];
+  qtbase = [ pkgs.cmake pkgs.perl ];
+  gmatrix = [ pkgs.cudatoolkit ];
+  WideLM = [ pkgs.cudatoolkit ];
+  RCurl = [ pkgs.curl ];
+  Rgnuplot = [ pkgs.gnuplot ];
+  R2SWF = [ pkgs.pkgconfig ];
+  RGtk2 = [ pkgs.pkgconfig ];
+  RProtoBuf = [ pkgs.pkgconfig ];
+  Rpoppler = [ pkgs.pkgconfig ];
+  VBmix = [ pkgs.pkgconfig ];
+  XML = [ pkgs.pkgconfig ];
+  cairoDevice = [ pkgs.pkgconfig ];
+  chebpol = [ pkgs.pkgconfig ];
+  fftw = [ pkgs.pkgconfig ];
+  geoCount = [ pkgs.pkgconfig ];
+  kza = [ pkgs.pkgconfig ];
+  mwaved = [ pkgs.pkgconfig ];
+  showtext = [ pkgs.pkgconfig ];
+  spate = [ pkgs.pkgconfig ];
+  stringi = [ pkgs.pkgconfig ];
+  sysfonts = [ pkgs.pkgconfig ];
+  Cairo = [ pkgs.pkgconfig ];
+  Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
+  qtutils = [ pkgs.qt4 ];
+  tcltk2 = [ pkgs.tcl pkgs.tk ];
+  tikzDevice = [ pkgs.texLive ];
+  rPython = [ pkgs.which ];
+  CARramps = [ pkgs.which pkgs.cudatoolkit ];
+  gputools = [ pkgs.which pkgs.cudatoolkit ];
+  rpud = [ pkgs.which pkgs.cudatoolkit ];
+  adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
+  PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
+  dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
+}
--- a/pkgs/development/r-modules/packagesWithNativeBuildInputs.nix
+++ b/pkgs/development/r-modules/packagesWithNativeBuildInputs.nix
@ -0,0 +1,117 @@
+pkgs: {
+  # sort -t '=' -k 2
+  RAppArmor = [ pkgs.apparmor ];
+  SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
+  Rssa = [ pkgs.fftw ];
+  fftw = [ pkgs.fftw ];
+  fftwtools = [ pkgs.fftw ];
+  kza = [ pkgs.fftw ];
+  mwaved = [ pkgs.fftw ];
+  spate = [ pkgs.fftw ];
+  chebpol = [ pkgs.fftw ];
+  seewave = [ pkgs.fftw pkgs.libsndfile ];
+  rgeos = [ pkgs.geos ];
+  Rglpk = [ pkgs.glpk ];
+  RCA = [ pkgs.gmp ];
+  gmp = [ pkgs.gmp ];
+  rcdd = [ pkgs.gmp ];
+  igraph = [ pkgs.gmp ];
+  glpkAPI = [ pkgs.gmp pkgs.glpk ];
+  sdcTable = [ pkgs.gmp pkgs.glpk ];
+  Rmpfr = [ pkgs.gmp pkgs.mpfr ];
+  BNSP = [ pkgs.gsl ];
+  BayesSAE = [ pkgs.gsl ];
+  BayesVarSel = [ pkgs.gsl ];
+  HiCseg = [ pkgs.gsl ];
+  KFKSDS = [ pkgs.gsl ];
+  R2GUESS = [ pkgs.gsl ];
+  RcppZiggurat = [ pkgs.gsl ];
+  SemiCompRisks = [ pkgs.gsl ];
+  VBLPCM = [ pkgs.gsl ];
+  abn = [ pkgs.gsl ];
+  cit = [ pkgs.gsl ];
+  libamtrack = [ pkgs.gsl ];
+  mixcat = [ pkgs.gsl ];
+  outbreaker = [ pkgs.gsl ];
+  pcaPA = [ pkgs.gsl ];
+  ridge = [ pkgs.gsl ];
+  simplexreg = [ pkgs.gsl ];
+  stsm = [ pkgs.gsl ];
+  survSNP = [ pkgs.gsl ];
+  topicmodels = [ pkgs.gsl ];
+  RcppGSL = [ pkgs.gsl ];
+  bnpmr = [ pkgs.gsl ];
+  geoCount = [ pkgs.gsl ];
+  gsl = [ pkgs.gsl ];
+  mvabund = [ pkgs.gsl ];
+  diversitree = [ pkgs.gsl pkgs.fftw ];
+  VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
+  RGtk2 = [ pkgs.gtk2 ];
+  cairoDevice = [ pkgs.gtk2 ];
+  adimpro = [ pkgs.imagemagick ];
+  rjags = [ pkgs.jags ];
+  runjags = [ pkgs.jags ];
+  JavaGD = [ pkgs.jdk ];
+  RODBC = [ pkgs.libiodbc ];
+  RODBCext = [ pkgs.libiodbc ];
+  jpeg = [ pkgs.libjpeg ];
+  EMCluster = [ pkgs.liblapack ];
+  png = [ pkgs.libpng ];
+  rtiff = [ pkgs.libtiff ];
+  tiff = [ pkgs.libtiff ];
+  Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
+  XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
+  rpud = [ pkgs.linuxPackages.nvidia_x11 ];
+  CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
+  rgl = [ pkgs.mesa pkgs.x11 ];
+  ncdf = [ pkgs.netcdf ];
+  ncdf4 = [ pkgs.netcdf ];
+  pbdNCDF4 = [ pkgs.netcdf ];
+  RNetCDF = [ pkgs.netcdf pkgs.udunits ];
+  nloptr = [ pkgs.nlopt ];
+  npRmpi = [ pkgs.openmpi ];
+  pbdPROF = [ pkgs.openmpi ];
+  sprint = [ pkgs.openmpi ];
+  Rmpi = [ pkgs.openmpi ];
+  openssl = [ pkgs.openssl ];
+  PKI = [ pkgs.openssl ];
+  RSclient = [ pkgs.openssl ];
+  Rserve = [ pkgs.openssl ];
+  Rpoppler = [ pkgs.poppler ];
+  audio = [ pkgs.portaudio ];
+  rpg = [ pkgs.postgresql ];
+  RPostgreSQL = [ pkgs.postgresql ];
+  ssanv = [ pkgs.proj ];
+  proj4 = [ pkgs.proj ];
+  rgdal = [ pkgs.proj pkgs.gdal ];
+  RProtoBuf = [ pkgs.protobuf ];
+  rPython = [ pkgs.python ];
+  qtpaint = [ pkgs.qt4 ];
+  qtbase = [ pkgs.qt4 ];
+  BayesXsrc = [ pkgs.readline pkgs.ncurses ];
+  udunits2 = [ pkgs.udunits pkgs.expat ];
+  tkrplot = [ pkgs.xlibs.libX11 ];
+  rzmq = [ pkgs.zeromq2 ];
+  PopGenome = [ pkgs.zlib ];
+  RJaCGH = [ pkgs.zlib ];
+  RcppCNPy = [ pkgs.zlib ];
+  Rniftilib = [ pkgs.zlib ];
+  WhopGenome = [ pkgs.zlib ];
+  devEMF = [ pkgs.zlib ];
+  gdsfmt = [ pkgs.zlib ];
+  rbamtools = [ 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 ];
+  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 ];
+  rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
+  R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+  sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
+  showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
+  XBRL = [ pkgs.zlib pkgs.libxml2 ];
+  RMySQL = [ pkgs.zlib pkgs.mysql ];
+}
--- a/pkgs/development/r-modules/patches/BayesBridge.patch
+++ b/pkgs/development/r-modules/patches/BayesBridge.patch
@ -0,0 +1,9 @@
+diff -ru -x '*~' BayesBridge_orig/src/Makevars BayesBridge/src/Makevars
+--- BayesBridge_orig/src/Makevars	2014-07-19 05:08:55.000000000 +0900
+++ BayesBridge/src/Makevars	2014-10-25 18:35:01.398539305 +0900
+@@ -9,4 +9,4 @@
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -I../inst/include/ -DDISABLE_SINGLE -DNTHROW
+ PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -DDISABLE_SINGLE -DNTHROW
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wshadow  -ansi -Wsequence-point
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
--- a/pkgs/development/r-modules/patches/BayesBridge_cblas.patch
+++ b/pkgs/development/r-modules/patches/BayesBridge_cblas.patch
@ -0,0 +1,9 @@
+diff -ru -x '*~' BayesBridge_orig/src/Makevars BayesBridge/src/Makevars
+--- BayesBridge_orig/src/Makevars	2014-07-19 05:08:55.000000000 +0900
+++ BayesBridge/src/Makevars	2014-10-25 14:44:23.422592445 +0900
+@@ -9,4 +9,4 @@
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -I../inst/include/ -DDISABLE_SINGLE -DNTHROW
+ PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -DDISABLE_SINGLE -DNTHROW
+ # PKG_CPPFLAGS = -DUSE_R -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wshadow  -ansi -Wsequence-point
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
+PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -lcblas
--- a/pkgs/development/r-modules/patches/BayesLogit.patch
+++ b/pkgs/development/r-modules/patches/BayesLogit.patch
@ -0,0 +1,12 @@
+diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
+--- BayesLogit_orig/src/Makevars	2014-04-24 23:31:13.000000000 +0900
+++ BayesLogit/src/Makevars	2014-10-25 18:33:32.398572641 +0900
+@@ -6,7 +6,7 @@
+ ## W/OUT Dynamic Stuff
+ OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
+ 	PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+ # PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
+ PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW 
+ 
--- a/pkgs/development/r-modules/patches/BayesLogit_cblas.patch
+++ b/pkgs/development/r-modules/patches/BayesLogit_cblas.patch
@ -0,0 +1,12 @@
+diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
+--- BayesLogit_orig/src/Makevars	2014-04-24 23:31:13.000000000 +0900
+++ BayesLogit/src/Makevars	2014-10-21 21:00:15.570699136 +0900
+@@ -6,7 +6,7 @@
+ ## W/OUT Dynamic Stuff
+ OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
+ 	PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
+-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
+PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -llapack -lf77blas -lcblas -latlas -lgfortran
+ # PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
+ PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW 
+ 
--- a/pkgs/development/r-modules/patches/BayesXsrc.patch
+++ b/pkgs/development/r-modules/patches/BayesXsrc.patch
@ -0,0 +1,55 @@
+diff -ru -x '*~' BayesXsrc_org/MD5 BayesXsrc/MD5
+--- BayesXsrc_org/MD5	2013-11-22 21:59:01.000000000 +0900
+++ BayesXsrc/MD5	2014-10-14 22:50:46.040754675 +0900
+@@ -4,7 +4,7 @@
+ cba21fc7e2d39608d0241d8cedc4fd43 *R/run.bayesx.R
+ 112cb3aff0f8f0cd60bb146b14df1fcf *inst/CITATION
+ cf04425475f03ee67c06efcebbd8d476 *man/run.bayesx.Rd
+-1f73de4dba1228cdaa8d5435d1c1656b *src/Makefile
+658152ec0b336198a2654385bb27666d *src/Makefile
+ 2971212d003d1d647110264fb471e63b *src/Makefile.win
+ e0fd1515e0d2f8553d4034c3f7544fc5 *src/bayesxsrc/adaptiv/fullcond_adaptiv.cpp
+ 08cd954d541c3c0d635bbbd61cd05d15 *src/bayesxsrc/adaptiv/fullcond_adaptiv.h
+@@ -320,7 +320,7 @@
+ 465ac930657299f89a0a164232dc15d2 *src/dev-Makefile
+ d9aafe726622cd8c46bab760fef0d813 *src/dev-Makefile.win
+ 50413e579bc999d49037293a612190c0 *src/install.libs.R
+-1f73de4dba1228cdaa8d5435d1c1656b *src/rel-Makefile
+658152ec0b336198a2654385bb27666d *src/rel-Makefile
+ 2971212d003d1d647110264fb471e63b *src/rel-Makefile.win
+ 4d675785837670b6a9b2b3405812a910 *tests/data.raw
+ 1d3777462fcefa39559aa645305a65f2 *tests/mcmc.R
+diff -ru -x '*~' BayesXsrc_org/src/Makefile BayesXsrc/src/Makefile
+--- BayesXsrc_org/src/Makefile	2013-11-22 21:49:16.000000000 +0900
+++ BayesXsrc/src/Makefile	2014-10-14 22:47:15.458766001 +0900
+@@ -137,11 +137,11 @@
+ 	${PSPLINES_OBJS}\
+ 	${STRUCTADD_OBJS}\
+ 	bayesxsrc/main.o\
+-       	bayesxsrc/samson/multgaussian.o\
+	bayesxsrc/samson/multgaussian.o\
+ 	bayesxsrc/adaptiv/fullcond_adaptiv.o\
+ 	bayesxsrc/alex/mixture.o
+ 
+-LDFLAGS  += -L${R_HOME}/lib -lreadline -lcurses
+LDFLAGS  += -L${R_HOME}/lib -lreadline -lncurses
+ CPPFLAGS +=  -Ibayesxsrc/. -I"bayesxsrc/bib"  -I"bayesxsrc/alex"  -I"bayesxsrc/adaptiv"  -I"bayesxsrc/andrea"  -I"bayesxsrc/dag"  -I"bayesxsrc/graph"  -I"bayesxsrc/mcmc"  -I"bayesxsrc/psplines"  -I"bayesxsrc/samson"  -I"bayesxsrc/leyre"  -I"bayesxsrc/structadd"
+ CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
+ # CXXFLAGS += -O3 -ansi
+diff -ru -x '*~' BayesXsrc_org/src/rel-Makefile BayesXsrc/src/rel-Makefile
+--- BayesXsrc_org/src/rel-Makefile	2013-10-08 21:28:09.000000000 +0900
+++ BayesXsrc/src/rel-Makefile	2014-10-14 22:47:04.601766431 +0900
+@@ -137,11 +137,11 @@
+ 	${PSPLINES_OBJS}\
+ 	${STRUCTADD_OBJS}\
+ 	bayesxsrc/main.o\
+-       	bayesxsrc/samson/multgaussian.o\
+	bayesxsrc/samson/multgaussian.o\
+ 	bayesxsrc/adaptiv/fullcond_adaptiv.o\
+ 	bayesxsrc/alex/mixture.o
+ 
+-LDFLAGS  += -L${R_HOME}/lib -lreadline -lcurses
+LDFLAGS  += -L${R_HOME}/lib -lreadline -lncurses
+ CPPFLAGS +=  -Ibayesxsrc/. -I"bayesxsrc/bib"  -I"bayesxsrc/alex"  -I"bayesxsrc/adaptiv"  -I"bayesxsrc/andrea"  -I"bayesxsrc/dag"  -I"bayesxsrc/graph"  -I"bayesxsrc/mcmc"  -I"bayesxsrc/psplines"  -I"bayesxsrc/samson"  -I"bayesxsrc/leyre"  -I"bayesxsrc/structadd"
+ CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
+ # CXXFLAGS += -O3 -ansi
--- a/pkgs/development/r-modules/patches/CARramps.patch
+++ b/pkgs/development/r-modules/patches/CARramps.patch
@ -0,0 +1,24 @@
+diff -ru -x '*~' CARramps_orig/configure CARramps/configure
+--- CARramps_orig/configure	2011-12-01 22:27:06.000000000 +0900
+++ CARramps/configure	2014-10-25 14:56:04.599337748 +0900
+@@ -2395,7 +2395,7 @@
+ 
+ 
+ NCFLAGS="-arch=sm_13 -O2"
+-CUDA_INC=${CUDA_HOME}/include
+CUDA_INC=${CUDA_HOME}/usr_include
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for CUDA headers" >&5
+ $as_echo_n "checking for CUDA headers... " >&6; }
+ as_ac_File=`$as_echo "ac_cv_file_${CUDA_INC}/cublas.h" | $as_tr_sh`
+diff -ru -x '*~' CARramps_orig/src/combo1colForR1Q_d.cu CARramps/src/combo1colForR1Q_d.cu
+--- CARramps_orig/src/combo1colForR1Q_d.cu	2011-12-01 22:27:06.000000000 +0900
+++ CARramps/src/combo1colForR1Q_d.cu	2014-10-25 14:59:06.869299163 +0900
+@@ -4,7 +4,7 @@
+ #include <cuda.h>
+ #include <R.h>
+ #include <Rmath.h>
+-#include <combo1colForR1Q_d.h>
+#include "combo1colForR1Q_d.h"
+ 
+ #define BLOCKSIZE 256 
+ 
--- a/pkgs/development/r-modules/patches/EMCluster.patch
+++ b/pkgs/development/r-modules/patches/EMCluster.patch
@ -0,0 +1,6 @@
+diff -ru -x '*~' EMCluster_orig/src/Makevars EMCluster/src/Makevars
+--- EMCluster_orig/src/Makevars	2013-07-05 02:43:25.000000000 +0900
+++ EMCluster/src/Makevars	2014-10-25 18:10:19.190992120 +0900
+@@ -1 +1 @@
+-PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS)
+PKG_LIBS = $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
--- a/pkgs/development/r-modules/patches/RAppArmor.patch
+++ b/pkgs/development/r-modules/patches/RAppArmor.patch
@ -0,0 +1,20 @@
+diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure
+--- RAppArmor_orig/configure	2013-12-17 11:23:00.000000000 +0900
+++ RAppArmor/configure	2014-10-18 22:22:39.641341244 +0900
+@@ -1,15 +1,2 @@
+-if [ ! -e /usr/include/sys/apparmor.h ]
+-then
+-  echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi
+-
+-LIBFILE=$(/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
--- a/pkgs/development/r-modules/patches/Rserve.patch
+++ b/pkgs/development/r-modules/patches/Rserve.patch
@ -0,0 +1,15 @@
+diff -ru -x '*~' Rserve_orig/src/Makevars.in Rserve/src/Makevars.in
+--- Rserve_orig/src/Makevars.in	2013-08-22 06:09:33.000000000 +0900
+++ Rserve/src/Makevars.in	2014-11-09 21:36:31.184590320 +0900
+@@ -12,8 +12,9 @@
+ 	$(CC) -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(PKG_CPPFLAGS) $(PKG_CFLAGS) -o Rserve.dbg $(SERVER_SRC) $(ALL_LIBS) $(PKG_LIBS)
+ 
+ # merging to bin/Rserve works only if installed from sources, won't work for binary
+-	-./mergefat Rserve "$(R_HOME)/bin/Rserve"
+-	-./mergefat Rserve.dbg "$(R_HOME)/bin/Rserve.dbg"
+	mkdir $(out)/bin
+	-./mergefat Rserve "$(out)/bin/Rserve"
+	-./mergefat Rserve.dbg "$(out)/bin/Rserve.dbg"
+ 
+ client: config.h
+ 	cp config.h client/cxx/
--- a/pkgs/development/r-modules/patches/WideLM.patch
+++ b/pkgs/development/r-modules/patches/WideLM.patch
@ -0,0 +1,19 @@
+diff -ru -x '*~' WideLM_orig/src/Makefile.in WideLM/src/Makefile.in
+--- WideLM_orig/src/Makefile.in	2012-02-17 04:28:05.000000000 +0900
+++ WideLM/src/Makefile.in	2014-10-25 18:54:49.110011921 +0900
+@@ -12,12 +12,12 @@
+ #compiler/preprocessor options
+ R_INCS := @R_INCL@ @RCPP_INCL@
+ CC_ARGS := @CU_PARAMS@ -Xcompiler @R_CPIC@
+-CU_INCS := -I@CUDA_HOME@/include
+CU_INCS := -I@CUDA_HOME@/usr_include
+ CU_ARCH := -gencode arch=compute_20,code=sm_20
+ 
+ #linker options
+-LD_PARAMS := -Xlinker "@RCPP_LDFLAGS@"
+-RCU_LIBS :=  @R_LIB@ -L@CU_LIBDIR@ -lcublas
+LD_PARAMS := -Xlinker "--export-dynamic -fopenmp -L${R_HOME}/lib -lR"
+RCU_LIBS := -Xlinker "-L@CU_LIBDIR@ -lcublas"
+ 
+ all : WideLM.so
+ 
--- a/pkgs/development/r-modules/patches/dbarts.patch
+++ b/pkgs/development/r-modules/patches/dbarts.patch
@ -0,0 +1,12 @@
+diff -ru -x '*~' dbarts_orig/src/Makevars.in dbarts/src/Makevars.in
+--- dbarts_orig/src/Makevars.in	2014-07-01 02:30:57.000000000 +0900
+++ dbarts/src/Makevars.in	2014-10-25 19:25:58.910704279 +0900
+@@ -6,7 +6,7 @@
+ 
+ PKG_CPPFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
+ PKG_CPPXXFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
+-PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) dbarts/libdbarts.a external/libexternal.a @PTHREAD_LIBS@ 
+PKG_LIBS=dbarts/libdbarts.a external/libexternal.a $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @PTHREAD_LIBS@ 
+ 
+ .PHONY: all dbarts/libdbarts.a external/libexternal.a clean
+ 
--- a/pkgs/development/r-modules/patches/gmatrix.patch
+++ b/pkgs/development/r-modules/patches/gmatrix.patch
@ -0,0 +1,48 @@
+diff -ru -x '*~' gmatrix_orig/src/Makefile gmatrix/src/Makefile
+--- gmatrix_orig/src/Makefile	2014-08-27 02:42:04.000000000 +0900
+++ gmatrix/src/Makefile	2014-10-25 15:35:29.797202981 +0900
+@@ -21,6 +21,7 @@
+ # to the manual on the gmatrix install instructions)
+ CUDA_LIB_PATH ?= /usr/local/cuda/lib64
+ R_INC_PATH    ?= /usr/include/R
+CUDA_INC_PATH ?= /usr/local/cuda/include
+ 
+ 
+ # Nvidia CUDA Compiler
+@@ -49,25 +50,25 @@
+ # Build rules
+ build: $(OUT_OBJ)
+ 	$(R_CC) $(OUT_OBJ) -o $(OUT_SO) $(LIBS) -L$(CUDA_LIB_PATH)
+-	
+
+ conversions.o: 
+-	$(NVCC) -c conversions.cu -o conversions.o $(NVCC_FLAGS)  -I$(R_INC_PATH)
+-	
+	$(NVCC) -c conversions.cu -o conversions.o $(NVCC_FLAGS)  -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
+ manipulation.o: 
+-	$(NVCC) -c manipulation.cu -o manipulation.o $(NVCC_FLAGS)  -I$(R_INC_PATH)
+	$(NVCC) -c manipulation.cu -o manipulation.o $(NVCC_FLAGS)  -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+ 
+ general.o:
+-	$(NVCC) -c general.cu -o general.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+	$(NVCC) -c general.cu -o general.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+ 
+ matrix.o: 
+-	$(NVCC) -c matrix.cu -o matrix.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+- 	
+	$(NVCC) -c matrix.cu -o matrix.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
+ ops.o: 
+-	$(NVCC) -c ops.cu -o ops.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+-	
+	$(NVCC) -c ops.cu -o ops.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
+ dist.o: 
+-	$(NVCC) -c dist.cu -o dist.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+- 	
+	$(NVCC) -c dist.cu -o dist.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
+ 
+ clean:
+ 	-rm -f *.o core
--- a/pkgs/development/r-modules/patches/gputools.patch
+++ b/pkgs/development/r-modules/patches/gputools.patch
@ -0,0 +1,13 @@
+diff -ru -x '*~' gputools_orig/src/Makefile gputools/src/Makefile
+--- gputools_orig/src/Makefile	2013-05-09 01:43:32.000000000 +0900
+++ gputools/src/Makefile	2014-10-21 21:41:23.067148490 +0900
+@@ -6,6 +6,9 @@
+ 
+ R_HOME := $(shell R RHOME)
+ 
+CUDA_INC := $(CUDA_HOME)/usr_include
+CUDA_LIB := $(CUDA_HOME)/lib
+
+ #compiler/preprocessor options
+ INCS := -I. -I"$(CUDA_INC)" -I"$(R_INC)"
+ PARAMS := $(DEVICEOPTS) -Xcompiler $(CPICFLAGS)
--- a/pkgs/development/r-modules/patches/magma_cuda_include.patch
+++ b/pkgs/development/r-modules/patches/magma_cuda_include.patch
@ -0,0 +1,12 @@
+diff -ru -x '*~' magma_orig/configure magma/configure
+--- magma_orig/configure	2013-04-03 11:07:42.000000000 +0900
+++ magma/configure	2014-10-18 21:58:48.745890187 +0900
+@@ -2377,7 +2377,7 @@
+ 
+ 
+ NCFLAGS="-arch=sm_13 -O2 -DADD_"
+-CUDA_INC=${CUDA_HOME}/include
+CUDA_INC=${CUDA_HOME}/usr_include
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for CUDA headers" >&5
+ $as_echo_n "checking for CUDA headers... " >&6; }
+ as_ac_File=`$as_echo "ac_cv_file_${CUDA_INC}/cublas.h" | $as_tr_sh`
--- a/pkgs/development/r-modules/patches/openssl.patch
+++ b/pkgs/development/r-modules/patches/openssl.patch
@ -0,0 +1,28 @@
+diff -ru -x '*~' openssl_orig/configure openssl/configure
+--- openssl_orig/configure	2014-10-18 08:14:15.000000000 +0900
+++ openssl/configure	2014-11-03 15:05:25.122906126 +0900
+@@ -1,23 +1 @@
+-# Check for include
+-if [ ! -e /usr/include/openssl/rand.h ]
+-then
+-  echo "openssl/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
+-  exit 1
+-fi
+-
+-# Not linux. Probably OSX.
+-if [ ! -e /sbin/ldconfig ]
+-then
+-  exit 0
+-fi
+-
+-# looks like unix
+-LIBFILE=$(/sbin/ldconfig -p | egrep -ohm1 " [-_a-zA-Z0-9/]*/libssl[0-9]*.so$")
+-
+-if [ -z "$LIBFILE" ]
+-then
+-  echo "libssl.so not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
+-  exit 1
+-fi
+-
+-echo "PKG_LIBS= -L"$(dirname $LIBFILE)" -lssl -lcrypto" > src/Makevars
+echo "PKG_LIBS= -L"${OPENSSL_HOME}/lib" -lssl -lcrypto" > src/Makevars
--- a/pkgs/development/r-modules/patches/qtbase.patch
+++ b/pkgs/development/r-modules/patches/qtbase.patch
@ -0,0 +1,13 @@
+diff -ru -x '*~' qtbase_orig/src/Makefile qtbase/src/Makefile
+--- qtbase_orig/src/Makefile	2012-03-03 03:57:47.000000000 +0900
+++ qtbase/src/Makefile	2014-11-01 23:06:51.383876323 +0900
+@@ -10,6 +10,9 @@
+ 	      -DR_INCLUDES=${R_INCLUDE_DIR} \
+ 	      -DCMAKE_INSTALL_PREFIX=../src; \
+ 	make install
+# I could not control RPATH via CMake. HELP WANTED!
+	patchelf --set-rpath ${CMAKE_LIBRARY_PATH} qtbase.so
+	find ../inst/local/ -executable -type f -print0 | xargs -0 patchelf --set-rpath ${CMAKE_LIBRARY_PATH} 
+ 
+ clean:
+ 	rm -rf ../kdebindings-build
--- a/pkgs/development/r-modules/patches/rpud.patch
+++ b/pkgs/development/r-modules/patches/rpud.patch
@ -0,0 +1,29 @@
+diff -ru -x '*~' rpud_orig/configure rpud/configure
+--- rpud_orig/configure	2010-09-08 02:14:55.000000000 +0900
+++ rpud/configure	2014-10-25 16:46:39.479098648 +0900
+@@ -1794,7 +1794,7 @@
+ fi
+ 
+ LIBS="-L${CUDA_HOME}${CUDA_LIB_DIR} -lcublas -lcuda"
+-RPATHFLAG="-Wl,-rpath,${CUDA_HOME}${CUDA_LIB_DIR}"
+RPATHFLAG="-Xlinker -rpath=${CUDA_HOME}${CUDA_LIB_DIR}"
+ 
+ 
+ 
+diff -ru -x '*~' rpud_orig/src/Makefile.in rpud/src/Makefile.in
+--- rpud_orig/src/Makefile.in	2010-08-31 01:53:50.000000000 +0900
+++ rpud/src/Makefile.in	2014-10-25 16:45:30.248109883 +0900
+@@ -3,11 +3,11 @@
+ OBJS := rpud.o rpudist.o
+ 
+ #compiler/preprocessor options
+-INCS := -I@CUDA_HOME@/include
+INCS := -I@CUDA_HOME@/usr_include
+ PARAMS := -Xcompiler "@R_INCLUDE@ @CPICFLAGS@"
+ 
+ #linker options
+-LD_PARAMS := -Xlinker "@R_LIB@ @RPATHFLAG@"
+LD_PARAMS := -Xlinker "--export-dynamic -fopenmp -L${R_HOME}/lib -lR @RPATHFLAG@" 
+ LIBS :=  @LIBS@
+ 
+ TARGETS := rpud.so
--- a/pkgs/development/r-modules/patches/spMC.patch
+++ b/pkgs/development/r-modules/patches/spMC.patch
@ -0,0 +1,8 @@
+Only in spMC_orig: spMC
+diff -ru -x '*~' spMC_orig/src/Makevars spMC/src/Makevars
+--- spMC_orig/src/Makevars	2014-09-19 21:23:30.000000000 +0900
+++ spMC/src/Makevars	2014-10-25 18:14:48.366954769 +0900
+@@ -1,2 +1,2 @@
+ PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
+-PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(BLAS_LIBS) $(LAPACK_LIBS) $(FLIBS)
+PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
--- a/pkgs/development/r-modules/sources.nix
+++ b/pkgs/development/r-modules/sources.nix