From 916e36940b416d98cd58ee0b3e9a0d80e9ef1ffc Mon Sep 17 00:00:00 2001 From: taku0 Date: Sat, 29 Nov 2014 22:13:11 +0900 Subject: [PATCH] cran-packages: combined packages definition files --- .../development/r-modules/broken-packages.nix | 291 ------ pkgs/development/r-modules/cran-packages.nix | 15 +- .../r-modules/default-overrides.nix | 969 +++++++++++++++--- .../r-modules/packages-requireing-x.nix | 270 ----- .../r-modules/packages-to-skip-check.nix | 6 - .../r-modules/packages-with-build-inputs.nix | 37 - .../packages-with-native-build-inputs.nix | 118 --- 7 files changed, 858 insertions(+), 848 deletions(-) delete mode 100644 pkgs/development/r-modules/broken-packages.nix delete mode 100644 pkgs/development/r-modules/packages-requireing-x.nix delete mode 100644 pkgs/development/r-modules/packages-to-skip-check.nix delete mode 100644 pkgs/development/r-modules/packages-with-build-inputs.nix delete mode 100644 pkgs/development/r-modules/packages-with-native-build-inputs.nix diff --git a/pkgs/development/r-modules/broken-packages.nix b/pkgs/development/r-modules/broken-packages.nix deleted file mode 100644 index 44ad69d47532..000000000000 --- a/pkgs/development/r-modules/broken-packages.nix +++ /dev/null @@ -1,291 +0,0 @@ -# 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! - "MigClim" # SDMTools.So: Undefined Symbol: X - "PatternClass" # SDMTools.So: Undefined Symbol: X - "Actigraphy" # 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 - "msarc" # requires AnnotationDbi - "MetaLandSim" # requires Biobase - "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 - "netweavers" # requires BiocGenerics, Biobase, and limma - "NCmisc" # requires BiocInstaller - "EMDomics" # requires BiocParallel - "RADami" # requires Biostrings - "ionflows" # 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 - "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges - "CHAT" # requires DNAcopy - "PSCBS" # requires DNAcopy - "ParDNAcopy" # requires DNAcopy - "Rcell" # requires EBImage - "RockFab" # requires EBImage - "gitter" # requires EBImage - "rggobi" # requires GGobi - "PANDA" # requires GO.db - "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db - "PubMedWordcloud" # requires GOsummaries - "ExomeDepth" # requires GenomicRanges, and Rsamtools - "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 - "cqrReg" # 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 - "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 - "D2C" # requires gRbase - "LogisticDx" # requires gRbase - "gRain" # 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 - "QuACN" # requires graph, RBGL - "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 - "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 - "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 - "agridat" # 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 - "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 - "leapp" # requires sva - "ttScreening" # requires sva, and limma - "cudaBayesreg" # requres Rmath - "taxize" # requres bold - "rsprng" # requres sprng - "evobiR" # requres taxiz - "RNeXML" # requres taxize - "TR8" # requres taxize - "bdvis" # requres taxize -] diff --git a/pkgs/development/r-modules/cran-packages.nix b/pkgs/development/r-modules/cran-packages.nix index d0aa2a6d4bcd..423ad4e5fa56 100644 --- a/pkgs/development/r-modules/cran-packages.nix +++ b/pkgs/development/r-modules/cran-packages.nix @@ -164,11 +164,13 @@ let 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; + inherit (import ./default-overrides.nix stdenv pkgs) + packagesWithNativeBuildInputs + packagesWithBuildInputs + packagesRequireingX + packagesToSkipCheck + brokenPackages + otherOverrides; defaultOverrides = old: new: let old0 = old; in @@ -179,8 +181,7 @@ let old4 = old3 // (overrideBuildInputs packagesWithBuildInputs old3); old5 = old4 // (overrideBroken brokenPackages old4); old = old5; - in old // (import ./default-overrides.nix stdenv pkgs old new); - + in old // (otherOverrides old new); # Recursive override pattern. # `_self` is a collection of packages; diff --git a/pkgs/development/r-modules/default-overrides.nix b/pkgs/development/r-modules/default-overrides.nix index 2f116faf940c..f5e3466dd675 100644 --- a/pkgs/development/r-modules/default-overrides.nix +++ b/pkgs/development/r-modules/default-overrides.nix @@ -1,146 +1,877 @@ -stdenv: pkgs: old: new: { - RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: { - patchPhase = "patchShebangs configure"; - }); +stdenv: pkgs: +{ + packagesWithNativeBuildInputs = { + # sort -t '=' -k 2 + RAppArmor = [ pkgs.apparmor ]; + SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h + curl = [ pkgs.curl pkgs.openldap ]; + 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 ]; + }; - rpf = old.rpf.overrideDerivation (attrs: { - patchPhase = "patchShebangs configure"; - }); + packagesWithBuildInputs = { + # 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 ]; + }; - BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: { - patches = [ ./patches/BayesXsrc.patch ]; - }); + packagesRequireingX = [ + "AnalyzeFMRI" + "AnnotLists" + "AnthropMMD" + "AtelieR" + "BAT" + "BCA" + "BEQI2" + "BHMSMAfMRI" + "BioGeoBEARS" + "BiodiversityR" + "CCTpack" + "CommunityCorrelogram" + "ConvergenceConcepts" + "DALY" + "DSpat" + "Deducer" + "DeducerExtras" + "DeducerPlugInExample" + "DeducerPlugInScaling" + "DeducerSpatial" + "DeducerSurvival" + "DeducerText" + "Demerelate" + "DescTools" + "DivMelt" + "ENiRG" + "EcoVirtual" + "EnQuireR" + "FAiR" + "FD" + "FFD" + "FeedbackTS" + "FreeSortR" + "GGEBiplotGUI" + "GPCSIV" + "GUniFrac" + "Geneland" + "GeoGenetix" + "GeoXp" + "GrammR" + "GrapheR" + "GroupSeq" + "HH" + "HiveR" + "IsotopeR" + "JGR" + "KappaGUI" + "LS2Wstat" + "MAR1" + "MTurkR" + "MVPARTwrap" + "MareyMap" + "MergeGUI" + "Meth27QC" + "MicroStrategyR" + "MissingDataGUI" + "MplusAutomation" + "OligoSpecificitySystem" + "OpenRepGrid" + "PBSadmb" + "PBSmodelling" + "PCPS" + "PKmodelFinder" + "PoMoS" + "PopGenReport" + "PredictABEL" + "PrevMap" + "ProbForecastGOP" + "QCAGUI" + "R2STATS" + "RHRV" + "RNCEP" + "RQDA" + "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" + "STEPCAM" + "SYNCSA" + "Simile" + "SimpleTable" + "StatDA" + "SyNet" + "TDMR" + "TED" + "TIMP" + "TTAinterfaceTrendAnalysis" + "TestScorer" + "VIMGUI" + "VecStatGraphs3D" + "VisuClust" + "WMCapacity" + "accrual" + "ade4TkGUI" + "adehabitat" + "analogue" + "analogueExtra" + "aplpack" + "aqfig" + "arf3DS4" + "asbio" + "bayesDem" + "betapart" + "betaper" + "bio_infer" + "bipartite" + "biplotbootGUI" + "blender" + "cairoDevice" + "cncaGUI" + "cocorresp" + "confidence" + "constrainedKriging" + "cpa" + "dave" + "debug" + "detrendeR" + "dgmb" + "dpa" + "dynBiplotGUI" + "dynamicGraph" + "eVenn" + "exactLoglinTest" + "fSRM" + "fat2Lpoly" + "fbati" + "feature" + "fgui" + "fisheyeR" + "fit4NM" + "forams" + "forensim" + "fscaret" + "gWidgets2RGtk2" + "gWidgets2tcltk" + "gWidgetsRGtk2" + "gWidgetstcltk" + "gcmr" + "geoR" + "geoRglm" + "geomorph" + "georob" + "gnm" + "gsubfn" + "iBUGS" + "iDynoR" + "ic50" + "in2extRemes" + "iplots" + "isopam" + "likeLTD" + "loe" + "logmult" + "memgene" + "metacom" + "migui" + "miniGUI" + "mixsep" + "mlDNA" + "mpmcorrelogram" + "mritc" + "multgee" + "multibiplotGUI" + "nodiv" + "onemap" + "palaeoSig" + "paleoMAS" + "pbatR" + "pez" + "phylotools" + "picante" + "playwith" + "plotSEMM" + "plsRbeta" + "plsRglm" + "pmg" + "poppr" + "powerpkg" + "prefmod" + "qtbase" + "qtpaint" + "qtutils" + "r4ss" + "rAverage" + "rareNMtests" + "recluster" + "relax" + "relimp" + "reportRx" + "reshapeGUI" + "rgl" + "rich" + "ringscale" + "rioja" + "ripa" + "rite" + "rnbn" + "rriskDistributions" + "rsgcc" + "sdcMicroGUI" + "sharpshootR" + "simba" + "soundecology" + "spacodiR" + "spatsurv" + "sqldf" + "statcheck" + "stosim" + "strvalidator" + "stylo" + "svDialogstcltk" + "svIDE" + "svSocket" + "svWidgets" + "tcltk2" + "titan" + "tkrgl" + "tkrplot" + "tmap" + "tspmeta" + "twiddler" + "vcdExtra" + "vegan" + "vegan3d" + "vegclust" + "x12GUI" + "xergm" + ]; - rJava = old.rJava.overrideDerivation (attrs: { - preConfigure = '' - export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ - export JAVA_HOME=${pkgs.jdk} - ''; - }); + packagesToSkipCheck = [ + "Rmpi" # tries to run MPI processes + "gmatrix" # requires CUDA runtime + "npRmpi" # tries to run MPI processes + "sprint" # tries to run MPI processes + ]; - JavaGD = old.JavaGD.overrideDerivation (attrs: { - preConfigure = '' - export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ - export JAVA_HOME=${pkgs.jdk} - ''; - }); + # Packages which cannot be installed due to lack of dependencies or other reasons. + brokenPackages = [ + # sort -t '#' -k 2 - Mposterior = old.Mposterior.overrideDerivation (attrs: { - PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; - }); + "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED! + "MigClim" # SDMTools.So: Undefined Symbol: X + "PatternClass" # SDMTools.So: Undefined Symbol: X + "Actigraphy" # 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 + "msarc" # requires AnnotationDbi + "MetaLandSim" # requires Biobase + "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 + "netweavers" # requires BiocGenerics, Biobase, and limma + "NCmisc" # requires BiocInstaller + "EMDomics" # requires BiocParallel + "RADami" # requires Biostrings + "ionflows" # 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 + "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges + "CHAT" # requires DNAcopy + "PSCBS" # requires DNAcopy + "ParDNAcopy" # requires DNAcopy + "Rcell" # requires EBImage + "RockFab" # requires EBImage + "gitter" # requires EBImage + "rggobi" # requires GGobi + "PANDA" # requires GO.db + "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db + "PubMedWordcloud" # requires GOsummaries + "ExomeDepth" # requires GenomicRanges, and Rsamtools + "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 + "cqrReg" # 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 + "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 + "D2C" # requires gRbase + "LogisticDx" # requires gRbase + "gRain" # 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 + "QuACN" # requires graph, RBGL + "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 + "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 + "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 + "agridat" # 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 + "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 + "leapp" # requires sva + "ttScreening" # requires sva, and limma + "cudaBayesreg" # requres Rmath + "taxize" # requres bold + "rsprng" # requres sprng + "evobiR" # requres taxiz + "RNeXML" # requres taxize + "TR8" # requres taxize + "bdvis" # requres taxize + ]; - qtbase = old.qtbase.overrideDerivation (attrs: { - patches = [ ./patches/qtbase.patch ]; - }); + otherOverrides = old: new: { + RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: { + patchPhase = "patchShebangs configure"; + }); - Rmpi = old.Rmpi.overrideDerivation (attrs: { - configureFlags = [ - "--with-Rmpi-type=OPENMPI" - ]; - }); + rpf = old.rpf.overrideDerivation (attrs: { + patchPhase = "patchShebangs configure"; + }); - npRmpi = old.npRmpi.overrideDerivation (attrs: { - configureFlags = [ - "--with-Rmpi-type=OPENMPI" - ]; - }); + BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: { + patches = [ ./patches/BayesXsrc.patch ]; + }); - Rmpfr = old.Rmpfr.overrideDerivation (attrs: { - configureFlags = [ - "--with-mpfr-include=${pkgs.mpfr}/include" - ]; - }); + rJava = old.rJava.overrideDerivation (attrs: { + preConfigure = '' + export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ + export JAVA_HOME=${pkgs.jdk} + ''; + }); - RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: { - configureFlags = [ - "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib" - ]; - }); + JavaGD = old.JavaGD.overrideDerivation (attrs: { + preConfigure = '' + export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ + export JAVA_HOME=${pkgs.jdk} + ''; + }); - RAppArmor = old.RAppArmor.overrideDerivation (attrs: { - patches = [ ./patches/RAppArmor.patch ]; - LIBAPPARMOR_HOME = "${pkgs.apparmor}"; - }); + Mposterior = old.Mposterior.overrideDerivation (attrs: { + PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; + }); - RMySQL = old.RMySQL.overrideDerivation (attrs: { - configureFlags = [ - "--with-mysql-dir=${pkgs.mysql}" - ]; - }); + qtbase = old.qtbase.overrideDerivation (attrs: { + patches = [ ./patches/qtbase.patch ]; + }); - slfm = old.slfm.overrideDerivation (attrs: { - PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; - }); + Rmpi = old.Rmpi.overrideDerivation (attrs: { + configureFlags = [ + "--with-Rmpi-type=OPENMPI" + ]; + }); - SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: { - PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; - }); + npRmpi = old.npRmpi.overrideDerivation (attrs: { + configureFlags = [ + "--with-Rmpi-type=OPENMPI" + ]; + }); - gputools = old.gputools.overrideDerivation (attrs: { - patches = [ ./patches/gputools.patch ]; - CUDA_HOME = "${pkgs.cudatoolkit}"; - }); + Rmpfr = old.Rmpfr.overrideDerivation (attrs: { + configureFlags = [ + "--with-mpfr-include=${pkgs.mpfr}/include" + ]; + }); - # It seems that we cannot override meta attributes with overrideDerivation. - CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: { - patches = [ ./patches/CARramps.patch ]; - configureFlags = [ - "--with-cuda-home=${pkgs.cudatoolkit}" - ]; - }); + RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: { + configureFlags = [ + "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib" + ]; + }); - gmatrix = old.gmatrix.overrideDerivation (attrs: { - patches = [ ./patches/gmatrix.patch ]; - CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64"; - R_INC_PATH = "${pkgs.R}/lib/R/include"; - CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include"; - }); + RAppArmor = old.RAppArmor.overrideDerivation (attrs: { + patches = [ ./patches/RAppArmor.patch ]; + LIBAPPARMOR_HOME = "${pkgs.apparmor}"; + }); - # It seems that we cannot override meta attributes with overrideDerivation. - rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: { - patches = [ ./patches/rpud.patch ]; - CUDA_HOME = "${pkgs.cudatoolkit}"; - }); + RMySQL = old.RMySQL.overrideDerivation (attrs: { + configureFlags = [ + "--with-mysql-dir=${pkgs.mysql}" + ]; + }); - WideLM = old.WideLM.overrideDerivation (attrs: { - patches = [ ./patches/WideLM.patch ]; - configureFlags = [ - "--with-cuda-home=${pkgs.cudatoolkit}" - ]; - }); + slfm = old.slfm.overrideDerivation (attrs: { + PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; + }); - EMCluster = old.EMCluster.overrideDerivation (attrs: { - patches = [ ./patches/EMCluster.patch ]; - }); + SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: { + PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; + }); - spMC = old.spMC.overrideDerivation (attrs: { - patches = [ ./patches/spMC.patch ]; - }); + gputools = old.gputools.overrideDerivation (attrs: { + patches = [ ./patches/gputools.patch ]; + CUDA_HOME = "${pkgs.cudatoolkit}"; + }); - BayesLogit = old.BayesLogit.overrideDerivation (attrs: { - patches = [ ./patches/BayesLogit.patch ]; - }); + # It seems that we cannot override meta attributes with overrideDerivation. + CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: { + patches = [ ./patches/CARramps.patch ]; + configureFlags = [ + "--with-cuda-home=${pkgs.cudatoolkit}" + ]; + }); - BayesBridge = old.BayesBridge.overrideDerivation (attrs: { - patches = [ ./patches/BayesBridge.patch ]; - }); + gmatrix = old.gmatrix.overrideDerivation (attrs: { + patches = [ ./patches/gmatrix.patch ]; + CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64"; + R_INC_PATH = "${pkgs.R}/lib/R/include"; + CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include"; + }); - openssl = old.openssl.overrideDerivation (attrs: { - patches = [ ./patches/openssl.patch ]; - OPENSSL_HOME = "${pkgs.openssl}"; - }); + # It seems that we cannot override meta attributes with overrideDerivation. + rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: { + patches = [ ./patches/rpud.patch ]; + CUDA_HOME = "${pkgs.cudatoolkit}"; + }); - Rserve = old.Rserve.overrideDerivation (attrs: { - patches = [ ./patches/Rserve.patch ]; - configureFlags = [ - "--with-server" "--with-client" - ]; - }); + WideLM = old.WideLM.overrideDerivation (attrs: { + patches = [ ./patches/WideLM.patch ]; + configureFlags = [ + "--with-cuda-home=${pkgs.cudatoolkit}" + ]; + }); - nloptr = old.nloptr.overrideDerivation (attrs: { - configureFlags = [ - "--with-nlopt-cflags=-I${pkgs.nlopt}/include" - "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'" - ]; - }); + EMCluster = old.EMCluster.overrideDerivation (attrs: { + patches = [ ./patches/EMCluster.patch ]; + }); + + spMC = old.spMC.overrideDerivation (attrs: { + patches = [ ./patches/spMC.patch ]; + }); + + BayesLogit = old.BayesLogit.overrideDerivation (attrs: { + patches = [ ./patches/BayesLogit.patch ]; + }); + + BayesBridge = old.BayesBridge.overrideDerivation (attrs: { + patches = [ ./patches/BayesBridge.patch ]; + }); + + openssl = old.openssl.overrideDerivation (attrs: { + patches = [ ./patches/openssl.patch ]; + OPENSSL_HOME = "${pkgs.openssl}"; + }); + + Rserve = old.Rserve.overrideDerivation (attrs: { + patches = [ ./patches/Rserve.patch ]; + configureFlags = [ + "--with-server" "--with-client" + ]; + }); + + nloptr = old.nloptr.overrideDerivation (attrs: { + configureFlags = [ + "--with-nlopt-cflags=-I${pkgs.nlopt}/include" + "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'" + ]; + }); + }; } + diff --git a/pkgs/development/r-modules/packages-requireing-x.nix b/pkgs/development/r-modules/packages-requireing-x.nix deleted file mode 100644 index 006c9caeb349..000000000000 --- a/pkgs/development/r-modules/packages-requireing-x.nix +++ /dev/null @@ -1,270 +0,0 @@ -[ - "AnalyzeFMRI" - "AnnotLists" - "AnthropMMD" - "AtelieR" - "BAT" - "BCA" - "BEQI2" - "BHMSMAfMRI" - "BioGeoBEARS" - "BiodiversityR" - "CCTpack" - "CommunityCorrelogram" - "ConvergenceConcepts" - "DALY" - "DSpat" - "Deducer" - "DeducerExtras" - "DeducerPlugInExample" - "DeducerPlugInScaling" - "DeducerSpatial" - "DeducerSurvival" - "DeducerText" - "Demerelate" - "DescTools" - "DivMelt" - "ENiRG" - "EcoVirtual" - "EnQuireR" - "FAiR" - "FD" - "FFD" - "FeedbackTS" - "FreeSortR" - "GGEBiplotGUI" - "GPCSIV" - "GUniFrac" - "Geneland" - "GeoGenetix" - "GeoXp" - "GrammR" - "GrapheR" - "GroupSeq" - "HH" - "HiveR" - "IsotopeR" - "JGR" - "KappaGUI" - "LS2Wstat" - "MAR1" - "MTurkR" - "MVPARTwrap" - "MareyMap" - "MergeGUI" - "Meth27QC" - "MicroStrategyR" - "MissingDataGUI" - "MplusAutomation" - "OligoSpecificitySystem" - "OpenRepGrid" - "PBSadmb" - "PBSmodelling" - "PCPS" - "PKmodelFinder" - "PoMoS" - "PopGenReport" - "PredictABEL" - "PrevMap" - "ProbForecastGOP" - "QCAGUI" - "R2STATS" - "RHRV" - "RNCEP" - "RQDA" - "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" - "STEPCAM" - "SYNCSA" - "Simile" - "SimpleTable" - "StatDA" - "SyNet" - "TDMR" - "TED" - "TIMP" - "TTAinterfaceTrendAnalysis" - "TestScorer" - "VIMGUI" - "VecStatGraphs3D" - "VisuClust" - "WMCapacity" - "accrual" - "ade4TkGUI" - "adehabitat" - "analogue" - "analogueExtra" - "aplpack" - "aqfig" - "arf3DS4" - "asbio" - "bayesDem" - "betapart" - "betaper" - "bio_infer" - "bipartite" - "biplotbootGUI" - "blender" - "cairoDevice" - "cncaGUI" - "cocorresp" - "confidence" - "constrainedKriging" - "cpa" - "dave" - "debug" - "detrendeR" - "dgmb" - "dpa" - "dynBiplotGUI" - "dynamicGraph" - "eVenn" - "exactLoglinTest" - "fSRM" - "fat2Lpoly" - "fbati" - "feature" - "fgui" - "fisheyeR" - "fit4NM" - "forams" - "forensim" - "fscaret" - "gWidgets2RGtk2" - "gWidgets2tcltk" - "gWidgetsRGtk2" - "gWidgetstcltk" - "gcmr" - "geoR" - "geoRglm" - "geomorph" - "georob" - "gnm" - "gsubfn" - "iBUGS" - "iDynoR" - "ic50" - "in2extRemes" - "iplots" - "isopam" - "likeLTD" - "loe" - "logmult" - "memgene" - "metacom" - "migui" - "miniGUI" - "mixsep" - "mlDNA" - "mpmcorrelogram" - "mritc" - "multgee" - "multibiplotGUI" - "nodiv" - "onemap" - "palaeoSig" - "paleoMAS" - "pbatR" - "pez" - "phylotools" - "picante" - "playwith" - "plotSEMM" - "plsRbeta" - "plsRglm" - "pmg" - "poppr" - "powerpkg" - "prefmod" - "qtbase" - "qtpaint" - "qtutils" - "r4ss" - "rAverage" - "rareNMtests" - "recluster" - "relax" - "relimp" - "reportRx" - "reshapeGUI" - "rgl" - "rich" - "ringscale" - "rioja" - "ripa" - "rite" - "rnbn" - "rriskDistributions" - "rsgcc" - "sdcMicroGUI" - "sharpshootR" - "simba" - "soundecology" - "spacodiR" - "spatsurv" - "sqldf" - "statcheck" - "stosim" - "strvalidator" - "stylo" - "svDialogstcltk" - "svIDE" - "svSocket" - "svWidgets" - "tcltk2" - "titan" - "tkrgl" - "tkrplot" - "tmap" - "tspmeta" - "twiddler" - "vcdExtra" - "vegan" - "vegan3d" - "vegclust" - "x12GUI" - "xergm" -] diff --git a/pkgs/development/r-modules/packages-to-skip-check.nix b/pkgs/development/r-modules/packages-to-skip-check.nix deleted file mode 100644 index b52b7518b1f4..000000000000 --- a/pkgs/development/r-modules/packages-to-skip-check.nix +++ /dev/null @@ -1,6 +0,0 @@ -[ - "Rmpi" # tries to run MPI processes - "gmatrix" # requires CUDA runtime - "npRmpi" # tries to run MPI processes - "sprint" # tries to run MPI processes -] diff --git a/pkgs/development/r-modules/packages-with-build-inputs.nix b/pkgs/development/r-modules/packages-with-build-inputs.nix deleted file mode 100644 index 4ddb33bea504..000000000000 --- a/pkgs/development/r-modules/packages-with-build-inputs.nix +++ /dev/null @@ -1,37 +0,0 @@ -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 ]; -} diff --git a/pkgs/development/r-modules/packages-with-native-build-inputs.nix b/pkgs/development/r-modules/packages-with-native-build-inputs.nix deleted file mode 100644 index a0beafb03162..000000000000 --- a/pkgs/development/r-modules/packages-with-native-build-inputs.nix +++ /dev/null @@ -1,118 +0,0 @@ -pkgs: { - # sort -t '=' -k 2 - RAppArmor = [ pkgs.apparmor ]; - SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h - curl = [ pkgs.curl pkgs.openldap ]; - 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 ]; -}