/* This file defines the composition for CRAN (R) packages. */ { R, pkgs, overrides }: let inherit (pkgs) fetchurl stdenv lib; buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; }; # Package template # # some packages, e.g. cncaGUI, require X running while installation, # so that we use xvfb-run if requireX is true. derive = lib.makeOverridable ({ name, version, sha256, depends ? [], doCheck ? true, requireX ? false, broken ? false, hydraPlatforms ? R.meta.hydraPlatforms }: buildRPackage { name = "${name}-${version}"; src = fetchurl { urls = [ "mirror://cran/src/contrib/${name}_${version}.tar.gz" "mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz" ]; inherit sha256; }; inherit doCheck requireX; propagatedBuildInputs = depends; nativeBuildInputs = depends; meta.homepage = "http://cran.r-project.org/web/packages/${name}/"; meta.platforms = R.meta.platforms; meta.hydraPlatforms = hydraPlatforms; meta.broken = broken; }); # Overrides package definitions with nativeBuildInputs. # For example, # # overrideNativeBuildInputs { # foo = [ pkgs.bar ] # } old # # results in # # { # foo = old.foo.overrideDerivation (attrs: { # nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ]; # }); # } overrideNativeBuildInputs = overrides: old: lib.mapAttrs (name: value: (builtins.getAttr name old).overrideDerivation (attrs: { nativeBuildInputs = attrs.nativeBuildInputs ++ value; }) ) overrides; # Overrides package definitions with buildInputs. # For example, # # overrideBuildInputs { # foo = [ pkgs.bar ] # } old # # results in # # { # foo = old.foo.overrideDerivation (attrs: { # buildInputs = attrs.buildInputs ++ [ pkgs.bar ]; # }); # } overrideBuildInputs = overrides: old: lib.mapAttrs (name: value: (builtins.getAttr name old).overrideDerivation (attrs: { buildInputs = attrs.buildInputs ++ value; }) ) overrides; # Overrides package definitions with new R dependencies. # For example, # # overrideRDepends { # foo = [ self.bar ] # } old # # results in # # { # foo = old.foo.overrideDerivation (attrs: { # nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ]; # propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ]; # }); # } overrideRDepends = overrides: old: lib.mapAttrs (name: value: (builtins.getAttr name old).overrideDerivation (attrs: { nativeBuildInputs = attrs.nativeBuildInputs ++ value; propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value; }) ) overrides; # Overrides package definition requiring X running to install. # For example, # # overrideRequireX [ # "foo" # ] old # # results in # # { # foo = old.foo.override { # requireX = true; # }; # } overrideRequireX = packageNames: old: let nameValuePairs = map (name: { inherit name; value = (builtins.getAttr name old).override { requireX = true; }; }) packageNames; in builtins.listToAttrs nameValuePairs; # Overrides package definition to skip check. # For example, # # overrideSkipCheck [ # "foo" # ] old # # results in # # { # foo = old.foo.override { # doCheck = false; # }; # } overrideSkipCheck = packageNames: old: let nameValuePairs = map (name: { inherit name; value = (builtins.getAttr name old).override { doCheck = false; }; }) packageNames; in builtins.listToAttrs nameValuePairs; # Overrides package definition to mark it broken. # For example, # # overrideBroken [ # "foo" # ] old # # results in # # { # foo = old.foo.override { # broken = true; # }; # } overrideBroken = packageNames: old: let nameValuePairs = map (name: { inherit name; value = (builtins.getAttr name old).override { broken = true; }; }) packageNames; in builtins.listToAttrs nameValuePairs; defaultOverrides = old: new: let old0 = old; in let old1 = old0 // (overrideRequireX packagesRequireingX old0); old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1); old3 = old2 // (overrideRDepends packagesWithRDepends old2); old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3); old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4); old6 = old5 // (overrideBroken brokenPackages old5); old = old6; in old // (otherOverrides old new); # Recursive override pattern. # `_self` is a collection of packages; # `self` is `_self` with overridden packages; # packages in `_self` may depends on overridden packages. self = (defaultOverrides _self self) // overrides; _self = import ./cran-packages.nix { inherit self derive; }; # tweaks for the individual packages and "in self" follow packagesWithRDepends = { FactoMineR = [ self.car ]; }; packagesWithNativeBuildInputs = { abn = [ pkgs.gsl ]; adimpro = [ pkgs.imagemagick ]; audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl ]; BayesVarSel = [ pkgs.gsl ]; BayesXsrc = [ pkgs.readline pkgs.ncurses ]; bigGP = [ pkgs.openmpi ]; bnpmr = [ pkgs.gsl ]; BNSP = [ pkgs.gsl ]; cairoDevice = [ pkgs.gtk2 ]; Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ]; CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ]; chebpol = [ pkgs.fftw ]; cit = [ pkgs.gsl ]; curl = [ pkgs.curl pkgs.openldap ]; devEMF = [ pkgs.xlibs.libXft ]; diversitree = [ pkgs.gsl pkgs.fftw ]; EMCluster = [ pkgs.liblapack ]; fftw = [ pkgs.fftw ]; fftwtools = [ pkgs.fftw ]; Formula = [ pkgs.gmp ]; geoCount = [ pkgs.gsl ]; git2r = [ pkgs.zlib pkgs.openssl ]; glpkAPI = [ pkgs.gmp pkgs.glpk ]; gmp = [ pkgs.gmp ]; graphscan = [ pkgs.gsl ]; gsl = [ pkgs.gsl ]; HiCseg = [ pkgs.gsl ]; igraph = [ pkgs.gmp ]; JavaGD = [ pkgs.jdk ]; jpeg = [ pkgs.libjpeg ]; KFKSDS = [ pkgs.gsl ]; kza = [ pkgs.fftw ]; libamtrack = [ pkgs.gsl ]; mixcat = [ pkgs.gsl ]; mvabund = [ pkgs.gsl ]; mwaved = [ pkgs.fftw ]; ncdf4 = [ pkgs.netcdf ]; ncdf = [ pkgs.netcdf ]; nloptr = [ pkgs.nlopt ]; openssl = [ pkgs.openssl ]; outbreaker = [ pkgs.gsl ]; pbdMPI = [ pkgs.openmpi ]; pbdNCDF4 = [ pkgs.netcdf ]; pbdPROF = [ pkgs.openmpi ]; PKI = [ pkgs.openssl ]; png = [ pkgs.libpng ]; PopGenome = [ pkgs.zlib ]; proj4 = [ pkgs.proj ]; qtbase = [ pkgs.qt4 ]; qtpaint = [ pkgs.qt4 ]; R2GUESS = [ pkgs.gsl ]; R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; RAppArmor = [ pkgs.libapparmor ]; rbamtools = [ pkgs.zlib ]; RCA = [ pkgs.gmp ]; rcdd = [ pkgs.gmp ]; RcppCNPy = [ pkgs.zlib ]; RcppGSL = [ pkgs.gsl ]; RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ]; RcppZiggurat = [ pkgs.gsl ]; rgdal = [ pkgs.proj pkgs.gdal ]; rgeos = [ pkgs.geos ]; rgl = [ pkgs.mesa pkgs.x11 ]; Rglpk = [ pkgs.glpk ]; rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ]; RGtk2 = [ pkgs.gtk2 ]; Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ]; ridge = [ pkgs.gsl ]; RJaCGH = [ pkgs.zlib ]; rjags = [ pkgs.jags ]; rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ]; Rlibeemd = [ pkgs.gsl ]; rmatio = [ pkgs.zlib ]; Rmpfr = [ pkgs.gmp pkgs.mpfr ]; Rmpi = [ pkgs.openmpi ]; RMySQL = [ pkgs.zlib pkgs.mysql.lib ]; RNetCDF = [ pkgs.netcdf pkgs.udunits ]; RODBCext = [ pkgs.libiodbc ]; RODBC = [ pkgs.libiodbc ]; rpg = [ pkgs.postgresql ]; rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ]; Rpoppler = [ pkgs.poppler ]; RPostgreSQL = [ pkgs.postgresql ]; RProtoBuf = [ pkgs.protobuf ]; rpud = [ pkgs.linuxPackages.nvidia_x11 ]; rPython = [ pkgs.python ]; RSclient = [ pkgs.openssl ]; Rserve = [ pkgs.openssl ]; Rssa = [ pkgs.fftw ]; rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ]; rtiff = [ pkgs.libtiff ]; runjags = [ pkgs.jags ]; RVowpalWabbit = [ pkgs.zlib pkgs.boost ]; rzmq = [ pkgs.zeromq3 ]; SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ]; sdcTable = [ pkgs.gmp pkgs.glpk ]; seewave = [ pkgs.fftw pkgs.libsndfile ]; SemiCompRisks = [ pkgs.gsl ]; seqinr = [ pkgs.zlib ]; seqminer = [ pkgs.zlib pkgs.bzip2 ]; showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ]; simplexreg = [ pkgs.gsl ]; SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h spate = [ pkgs.fftw ]; sprint = [ pkgs.openmpi ]; ssanv = [ pkgs.proj ]; stsm = [ pkgs.gsl ]; survSNP = [ pkgs.gsl ]; sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; TAQMNGR = [ pkgs.zlib ]; tiff = [ pkgs.libtiff ]; TKF = [ pkgs.gsl ]; tkrplot = [ pkgs.xlibs.libX11 ]; topicmodels = [ pkgs.gsl ]; udunits2 = [ pkgs.udunits pkgs.expat ]; V8 = [ pkgs.v8 ]; VBLPCM = [ pkgs.gsl ]; VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ]; WhopGenome = [ pkgs.zlib ]; XBRL = [ pkgs.zlib pkgs.libxml2 ]; XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ]; }; packagesWithBuildInputs = { # sort -t '=' -k 2 svKomodo = [ pkgs.which ]; nat = [ pkgs.which ]; nat_nblast = [ pkgs.which ]; nat_templatebrains = [ pkgs.which ]; RMark = [ pkgs.which ]; RPushbullet = [ pkgs.which ]; qtpaint = [ pkgs.cmake ]; qtbase = [ pkgs.cmake pkgs.perl ]; gmatrix = [ pkgs.cudatoolkit ]; WideLM = [ pkgs.cudatoolkit ]; RCurl = [ pkgs.curl ]; R2SWF = [ pkgs.pkgconfig ]; rggobi = [ 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 ]; ecoretriever = [ pkgs.which ]; tcltk2 = [ pkgs.tcl pkgs.tk ]; tikzDevice = [ pkgs.which pkgs.texLive ]; rPython = [ pkgs.which ]; CARramps = [ pkgs.which pkgs.cudatoolkit ]; gridGraphics = [ pkgs.which ]; gputools = [ pkgs.which pkgs.cudatoolkit ]; rpud = [ pkgs.which pkgs.cudatoolkit ]; adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ]; PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ]; dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ]; }; packagesRequireingX = [ "AnalyzeFMRI" "AnnotLists" "AnthropMMD" "AtelieR" "BAT" "BCA" "BEQI2" "BHMSMAfMRI" "BioGeoBEARS" "BiodiversityR" "CCTpack" "CommunityCorrelogram" "ConvergenceConcepts" "DALY" "DSpat" "Deducer" "DeducerExtras" "DeducerPlugInExample" "DeducerPlugInScaling" "DeducerSpatial" "DeducerSurvival" "HomoPolymer" "MetSizeR" "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" "MareyMap" "MergeGUI" "Meth27QC" "MicroStrategyR" "MissingDataGUI" "MplusAutomation" "OligoSpecificitySystem" "OpenRepGrid" "PBSadmb" "PBSmodelling" "PCPS" "PKgraph" "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_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" "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" "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" ]; packagesToSkipCheck = [ "Rmpi" # tries to run MPI processes "gmatrix" # requires CUDA runtime "sprint" # tries to run MPI processes "pbdMPI" # tries to run MPI processes ]; # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ "ACNE" # requires aroma_affymetrix "Actigraphy" # SDMTools.so: undefined symbol: X "adaptsmoFMRI" # requires spatstat "ads" # requires spatstat "agridat" # requires pcaMethods "aLFQ" # requires protiq "AntWeb" # requires leafletR "aoristic" # requires spatstat "apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light "aroma_affymetrix" # requires aroma_core "aroma_cn" # requires PSCBS "aroma_core" # requires PSCBS "ArrayBin" # requires SAGx "babel" # requires edgeR "BACA" # requires RDAVIDWebService "BcDiag" # requires fabia "bdvis" # requres taxize "beadarrayFilter" # requires beadarray "beadarrayMSV" # requires Biobase, geneplotter, andlimma "bigGP" # requires MPI running. HELP WANTED! "bigpca" # requires NCmisc "Biograph" # requires mvna "biotools" # requires rpanel "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db "BLCOP" # depends on broken fPortfolio "bmrm" # requires clpAPI "branchLars" # requires Rgraphviz "BRugs" # requires OpenBUGS "calmate" # requires aroma_core "CARrampsOcl" # depends on OpenCL "CHAT" # requires DNAcopy "ChemoSpec" # depends on broken speaq "classGraph" # requires graph, and Rgraphviz "clpAPI" # requires clp "compendiumdb" # requires Biobase "CORM" # requires limma "cplexAPI" # requires CPLEX "crmn" # requires pcaMethods, and Biobase "Crossover" # fails self-test "CrypticIBDcheck" # requires rJPSGCS "cudaBayesreg" # requres Rmath "curvHDR" # requires flowCore "D2C" # requires gRbase "DAAGbio" # requires limma "daff" # requires V8 to build "dagbag" # requires Rlapack "DBKGrad" # requires SDD "dbmss" # requires spatstat "DCGL" # requires limma "dcGOR" # requires dnet "demi" # requires affy, affxparser, and oligo "DepthProc" # requires samr "DiagrammeR" # requires V8 to build "DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest' "Digiroo2" # requires spatstat "dixon" # requires spatstat "dnet" # requires supraHex, graph, Rgraphviz, and Biobase "doMPI" # requires MPI running. HELP WANTED! "dpcR" # requires spatstat "DSpat" # requires spatstat "ecespa" # requires spatstat "ecoengine" # requires leafletR "ecospat" # requires spatstat "edgeRun" # requires edgeR "EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges "epoc" # requires graph, and Rgraphviz "erpR" # requires rpanel "ETAS" # requires spatstat "eulerian" # requires graph "evobiR" # requres taxiz "evora" # requires qvalue "ExomeDepth" # requires GenomicRanges, and Rsamtools "FAMT" # requires impute "fdrDiscreteNull" # requires edgeR "FHtest" # requires interval "flexCWM" # depends on broken mixture "fPortfolio" # requires rneos "FunctionalNetworks" # requires breastCancerVDX, and Biobase "gamlss_demo" # requires rpanel "GeneticTools" # requires snpStats "geojsonio" # requires V8 to build "GExMap" # requires Biobase and multtest "gitter" # requires EBImage "glmgraph" # test suite says: "undefined symbol: dgemv_" "gmatrix" # depends on proprietary cudatoolkit "gMCP" # fails self-test "GOGANPA" # requires WGCNA "gputools" # depends on proprietary cudatoolkit "gRain" # requires gRbase "gRapHD" # requires graph "gRbase" # requires RBGL, and graph "gRc" # requires gRbase "gridDebug" # requires gridGraphviz "gridGraphviz" # requires graph, and Rgraphviz "GriegSmith" # requires spatstat "gRim" # requires gRbase "GSAgm" # requires edgeR "GUIDE" # requires rpanel "h2o" # tries to download some h2o.jar during its build "hasseDiagram" # requires Rgraphviz "hddplot" # requires multtest "HierO" # requires rneos "HiPLARM" # requires MAGMA or PLASMA "hpoPlot" # requires Rgraphviz "hsdar" # fails to build "HTSCluster" # requires edgeR "iFes" # depends on proprietary cudatoolkit "imputeLCMD" # requires pcaMethods, and impute "intamapInteractive" # requires spatstat "interval" # requires Icens "ionflows" # requires Biostrings "iRefR" # requires graph, and RBGL "IsoGene" # requires Biobase, and affy "isva" # requires qvalue "jomo" # linking errors "js" # requires broken V8 "KANT" # requires affy, and Biobase "ktspair" # requires Biobase "latticeDensity" # requires spatstat "leapp" # requires sva "lefse" # SDMTools.so: undefined symbol: X "lfe" # fails to compile "lgcp" # requires rpanel "LinRegInteractive" # requires Rpanel "LogisticDx" # requires gRbase "LOST" # requires pcaMethods "ltsk" # requires Rlapack and Rblas "magma" # requires MAGMA "MAMA" # requires metaMA "MEET" # requires pcaMethods, and seqLogo "metabolomics" # depends on broken crmn "MetaDE" # requires impute, and Biobase "MetaLandSim" # requires Biobase "metaMA" # requires limma "metaMix" # requires MPI running. HELP WANTED! "mGSZ" # requires Biobase, and limma "MigClim" # SDMTools.So: Undefined Symbol: X "minimist" # requires broken V8 "miRtest" # requires globaltest, GlobalAncova, and limma "MixGHD" # requires mixture to build "mixture" # mixture.so: undefined symbol: dtrmm_ "moduleColor" # requires impute "mongolite" # doesn't find OpenSSL "msarc" # requires AnnotationDbi "MSeasy" # requires mzR, and xcms "MSeasyTkGUI" # requires MSeasyTkGUI "MSIseq" # requires IRanges "msSurv" # requires graph "muir" # requires DiagrammeR to build "multiDimBio" # requires pcaMethods "mutossGUI" # requires mutoss "mutoss" # requires multtest "MXM" # depends on broken gRbase "NBPSeq" # requires qvalue "NCmisc" # requires BiocInstaller "netClass" # requires samr "nettools" # requires WGCNA "netweavers" # requires BiocGenerics, Biobase, and limma "NLPutils" # requires qdap "NORRRM" # can't load SDMTools properly "NSA" # requires aroma_core "OpenCL" # FIXME: requires CL/opencl.h "optBiomarker" # requires rpanel "ora" # requires ROracle "orQA" # requires genefilter "PairViz" # requires graph "PANDA" # requires GO.db "ParDNAcopy" # requires DNAcopy "pathClass" # requires affy, and Biobase "PatternClass" # SDMTools.So: Undefined Symbol: X "pbdBASE" # requires pbdMPI "pbdDEMO" # requires pbdMPI "pbdDMAT" # requires pbdMPI "pbdSLAP" # requires pbdMPI "PBSddesolve" # fails its test suite for unclear reasons "PBSmapping" # fails its test suite for unclear reasons "pcaL1" # requires clp "pcalg" # requires graph, and RBGL "PCGSE" # requires safe "PCS" # requires multtest "PepPrep" # requires biomaRt "PerfMeas" # requires limma, graph, and RBGL "permGPU" # requires Biobase "PhViD" # requires LBE "pi0" # requires qvalue "plmDE" # requires limma "plsRcox" # requires survcomp "PMA" # requires impute "pmcgd" # depends on broken mixture "pmclust" # requires MPI running. HELP WANTED! "polyCub" # requires spatstat "ppiPre" # requires AnnotationDbi, GOSemSim, GO.db "pRF" # requires multtest "propOverlap" # requires Biobase "protiq" # requires graph, and RBGL "PSCBS" # requires DNAcopy "pubmed_mineR" # requires SSOAP "PubMedWordcloud" # requires GOsummaries "qdap" # requires gender "qtlnet" # requires pcalg "qtpaint" # can't find QtCore libraries "QuACN" # requires graph, RBGL "quanteda" # fails to build "QuasiSeq" # requires edgeR "RADami" # requires Biostrings "raincpc" # SDMTools.so: undefined symbol: X "rainfreq" # SDMTools.so: undefined symbol: X "RAM" # requires Heatplus "RapidPolygonLookup" # depends on broken PBSmapping "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges "RbioRXN" # requires fmcsR, and KEGGREST "RcmdrPlugin_seeg" # requires seeg "Rcplex" # requires cplexAPI "RcppAPT" # configure script depends on /bin/sh "RcppRedis" # requires Hiredis "rDEA" # no such file or directory "RDieHarder" # requires libdieharder "reader" # requires NCmisc "REBayes" # requires Rmosek "RefFreeEWAS" # requires isva "retistruct" # depends on broken RImageJROI "rgp" # fails self-test "rgpui" # depends on broken rgp "RImageJROI" # requires spatstat "rjade" # requires V8 to build "rJPSGCS" # requires chopsticks "rLindo" # requires LINDO API "Rmosek" # requires mosek "RnavGraph" # requires graph, and RBGL "rneos" # requires XMLRPC "RNeXML" # requres taxize "RobLoxBioC" # requires Biobase "RobLox" # requires Biobase "RockFab" # requires EBImage "ROI_plugin_symphony" # depends on broken Rsymphony "ROracle" # requires OCI "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED! "RQuantLib" # requires QuantLib "RSAP" # requires SAPNWRFCSDK "RSeed" # requires RBGL, and graph "rsig" # requires survcomp "RSNPset" # requires qvalue "Rsymphony" # FIXME: requires SYMPHONY "RVideoPoker" # requires Rpanel "rysgran" # requires soiltexture "samr" # requires impute "SDD" # requires rpanel "seeg" # requires spatstat "selectspm" # depends on broken ecespa "semiArtificial" # requires RSNNS "SeqFeatR" # requires Biostrings, qvalue, and widgetTools "SeqGrapheR" # depends on Biostrings "sequenza" # requires copynumber "SGCS" # requires spatstat "siar" # requires spatstat "SID" # requires pcalg "SimRAD" # requires Biostrings, and ShortRead "SimSeq" # requires edgeR "siplab" # requires spatstat "smart" # requires PMA "snpEnrichment" # requires snpStats "snplist" # requires biomaRt "snpStatsWriter" # requires snpStats "SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools "SOD" # depends on proprietary cudatoolkit "soilphysics" # requires rpanel "sparr" # requires spatstat "spatialsegregation" # requires spatstat "SpatialVx" # requires spatstat "speaq" # requires MassSpecWavelet "spocc" # requires leafletR "SQDA" # requires limma "stagePop" # depends on broken PBSddesolve "statar" # depends on broken lfe "Statomica" # requires Biobase, multtest "stpp" # requires spatstat "structSSI" # requires multtest "strum" # requires Rgraphviz "superbiclust" # requires fabia "surveillance" # requires polyCub "swamp" # requires impute "sybilSBML" # requires libSBML "taxize" # requres bold "TcGSA" # requires multtest "topologyGSA" # requires gRbase "TR8" # requres taxize "trip" # requires spatstat "TROM" # misses undeclared dependencies topGO', 'AnnotationDbi', 'GO.db' "ttScreening" # requires sva, and limma "V8" # compilation error "vmsbase" # depends on broken PBSmapping "vows" # requires rpanel "WGCNA" # requires impute "wgsea" # requires snpStats "WideLM" # depends on proprietary cudatoolkit "x_ent" # requires opencpu "zoib" # tarball is invalid on server "timeSeq" # depends on missing edgeR "survJamda" # depends on missing survcomp "ssizeRNA" # depends on missing 'Biobase', 'edgeR', 'limma', 'qvalue' "h5" # depends on missing h5 system library ]; otherOverrides = old: new: { xml2 = old.xml2.overrideDerivation (attrs: { preConfigure = '' export LIBXML_INCDIR=${pkgs.libxml2}/include/libxml2 export LIBXML_LIBDIR=${pkgs.libxml2}/lib ''; }); curl = old.curl.overrideDerivation (attrs: { preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include/curl"; }); iFes = old.iFes.overrideDerivation (attrs: { patches = [ ./patches/iFes.patch ]; CUDA_HOME = "${pkgs.cudatoolkit}"; }); RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: { patchPhase = "patchShebangs configure"; }); rpf = old.rpf.overrideDerivation (attrs: { patchPhase = "patchShebangs configure"; }); BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: { patches = [ ./patches/BayesXsrc.patch ]; }); rJava = old.rJava.overrideDerivation (attrs: { preConfigure = '' export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ export JAVA_HOME=${pkgs.jdk} ''; }); JavaGD = old.JavaGD.overrideDerivation (attrs: { preConfigure = '' export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ export JAVA_HOME=${pkgs.jdk} ''; }); Mposterior = old.Mposterior.overrideDerivation (attrs: { PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; }); qtbase = old.qtbase.overrideDerivation (attrs: { patches = [ ./patches/qtbase.patch ]; }); Rmpi = old.Rmpi.overrideDerivation (attrs: { configureFlags = [ "--with-Rmpi-type=OPENMPI" ]; }); Rmpfr = old.Rmpfr.overrideDerivation (attrs: { configureFlags = [ "--with-mpfr-include=${pkgs.mpfr}/include" ]; }); RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: { configureFlags = [ "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib" ]; }); RAppArmor = old.RAppArmor.overrideDerivation (attrs: { patches = [ ./patches/RAppArmor.patch ]; LIBAPPARMOR_HOME = "${pkgs.libapparmor}"; }); RMySQL = old.RMySQL.overrideDerivation (attrs: { patches = [ ./patches/RMySQL.patch ]; MYSQL_DIR="${pkgs.mysql.lib}"; }); devEMF = old.devEMF.overrideDerivation (attrs: { NIX_CFLAGS_LINK = "-L${pkgs.xlibs.libXft}/lib -lXft"; }); slfm = old.slfm.overrideDerivation (attrs: { PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; }); SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: { PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas"; }); gputools = old.gputools.overrideDerivation (attrs: { patches = [ ./patches/gputools.patch ]; CUDA_HOME = "${pkgs.cudatoolkit}"; }); # 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=${pkgs.cudatoolkit}" ]; }); gmatrix = old.gmatrix.overrideDerivation (attrs: { patches = [ ./patches/gmatrix.patch ]; CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64"; R_INC_PATH = "${pkgs.R}/lib/R/include"; CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include"; }); # 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 = "${pkgs.cudatoolkit}"; }); WideLM = old.WideLM.overrideDerivation (attrs: { patches = [ ./patches/WideLM.patch ]; configureFlags = [ "--with-cuda-home=${pkgs.cudatoolkit}" ]; }); 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: { OPENSSL_INCLUDES = "${pkgs.openssl}/include"; }); Rserve = old.Rserve.overrideDerivation (attrs: { patches = [ ./patches/Rserve.patch ]; configureFlags = [ "--with-server" "--with-client" ]; }); nloptr = old.nloptr.overrideDerivation (attrs: { configureFlags = [ "--with-nlopt-cflags=-I${pkgs.nlopt}/include" "--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'" ]; }); }; in self