/* 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; }; # Generates package templates given per-repository settings # # some packages, e.g. cncaGUI, require X running while installation, # so that we use xvfb-run if requireX is true. mkDerive = {mkHomepage, mkUrls}: lib.makeOverridable ({ name, version, sha256, depends ? [], doCheck ? true, requireX ? false, broken ? false, hydraPlatforms ? R.meta.hydraPlatforms }: buildRPackage { name = "${name}-${version}"; src = fetchurl { inherit sha256; urls = mkUrls { inherit name version; }; }; inherit doCheck requireX; propagatedBuildInputs = depends; nativeBuildInputs = depends; meta.homepage = mkHomepage name; meta.platforms = R.meta.platforms; meta.hydraPlatforms = hydraPlatforms; meta.broken = broken; }); # Templates for generating Bioconductor and CRAN packages # from the name, version, sha256, and optional per-package arguments above # deriveBioc = mkDerive { mkHomepage = name: "http://cran.r-project.org/web/packages/${name}/"; mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ]; }; deriveCran = mkDerive { mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html"; mkUrls = {name, version}: [ "mirror://cran/src/contrib/${name}_${version}.tar.gz" "mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz" ]; }; # 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 ./bioc-packages.nix { inherit self; derive = deriveBioc; } // import ./cran-packages.nix { inherit self; derive = deriveCran; }; # tweaks for the individual packages and "in self" follow packagesWithRDepends = { FactoMineR = [ self.car ]; pander = [ self.codetools ]; }; packagesWithNativeBuildInputs = { abn = [ pkgs.gsl ]; adimpro = [ pkgs.imagemagick ]; audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl ]; BayesVarSel = [ pkgs.gsl ]; BayesXsrc = [ pkgs.readline pkgs.ncurses ]; bigGP = [ pkgs.openmpi ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; bnpmr = [ pkgs.gsl ]; BNSP = [ pkgs.gsl ]; cairoDevice = [ pkgs.gtk2 ]; Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ]; Cardinal = [ pkgs.which ]; CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ]; chebpol = [ pkgs.fftw ]; ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; cit = [ pkgs.gsl ]; curl = [ pkgs.curl ]; 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 ]; GLAD = [ pkgs.gsl ]; glpkAPI = [ pkgs.gmp pkgs.glpk ]; gmp = [ pkgs.gmp ]; graphscan = [ pkgs.gsl ]; gsl = [ pkgs.gsl ]; HiCseg = [ pkgs.gsl ]; iBMQ = [ 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 ]; pander = [ pkgs.pandoc pkgs.which ]; 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 ]; rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; 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 ]; rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ]; rgl = [ pkgs.mesa pkgs.x11 ]; Rglpk = [ pkgs.glpk ]; RGtk2 = [ pkgs.gtk2 ]; Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ]; Rhtslib = [ pkgs.zlib ]; 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 ]; xml2 = [ 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 = [ "accrual" "ade4TkGUI" "adehabitat" "analogue" "analogueExtra" "AnalyzeFMRI" "AnnotLists" "AnthropMMD" "aplpack" "aqfig" "arf3DS4" "asbio" "AtelieR" "BAT" "bayesDem" "BCA" "BEQI2" "betapart" "betaper" "BiodiversityR" "BioGeoBEARS" "bio_infer" "bipartite" "biplotbootGUI" "blender" "cairoDevice" "CCTpack" "cncaGUI" "cocorresp" "CommunityCorrelogram" "confidence" "constrainedKriging" "ConvergenceConcepts" "cpa" "DALY" "dave" "debug" "Deducer" "DeducerExtras" "DeducerPlugInExample" "DeducerPlugInScaling" "DeducerSpatial" "DeducerSurvival" "DeducerText" "Demerelate" "DescTools" "detrendeR" "dgmb" "DivMelt" "dpa" "DSpat" "dynamicGraph" "dynBiplotGUI" "EasyqpcR" "EcoVirtual" "ENiRG" "EnQuireR" "eVenn" "exactLoglinTest" "FAiR" "fat2Lpoly" "fbati" "FD" "feature" "FeedbackTS" "FFD" "fgui" "fisheyeR" "fit4NM" "forams" "forensim" "FreeSortR" "fscaret" "fSRM" "gcmr" "Geneland" "GeoGenetix" "geomorph" "geoR" "geoRglm" "georob" "GeoXp" "GGEBiplotGUI" "gnm" "GPCSIV" "GrammR" "GrapheR" "GroupSeq" "gsubfn" "GUniFrac" "gWidgets2RGtk2" "gWidgets2tcltk" "gWidgetsRGtk2" "gWidgetstcltk" "HH" "HiveR" "HomoPolymer" "iBUGS" "ic50" "iDynoR" "in2extRemes" "iplots" "isopam" "IsotopeR" "JGR" "KappaGUI" "likeLTD" "loe" "logmult" "LS2Wstat" "MAR1" "MareyMap" "memgene" "MergeGUI" "metacom" "Meth27QC" "MetSizeR" "MicroStrategyR" "migui" "miniGUI" "MissingDataGUI" "mixsep" "mlDNA" "MplusAutomation" "mpmcorrelogram" "mritc" "MTurkR" "multgee" "multibiplotGUI" "nodiv" "OligoSpecificitySystem" "onemap" "OpenRepGrid" "palaeoSig" "paleoMAS" "pbatR" "PBSadmb" "PBSmodelling" "PCPS" "pez" "phylotools" "picante" "PKgraph" "playwith" "plotSEMM" "plsRbeta" "plsRglm" "pmg" "PopGenReport" "poppr" "powerpkg" "PredictABEL" "prefmod" "PrevMap" "ProbForecastGOP" "QCAGUI" "qtbase" "qtpaint" "qtutils" "R2STATS" "r4ss" "RandomFields" "rareNMtests" "rAverage" "Rcmdr" "RcmdrPlugin_BCA" "RcmdrPlugin_coin" "RcmdrPlugin_depthTools" "RcmdrPlugin_DoE" "RcmdrPlugin_doex" "RcmdrPlugin_EACSPIR" "RcmdrPlugin_EBM" "RcmdrPlugin_EcoVirtual" "RcmdrPlugin_epack" "RcmdrPlugin_EZR" "RcmdrPlugin_FactoMineR" "RcmdrPlugin_HH" "RcmdrPlugin_IPSUR" "RcmdrPlugin_KMggplot2" "RcmdrPlugin_lfstat" "RcmdrPlugin_MA" "RcmdrPlugin_mosaic" "RcmdrPlugin_MPAStats" "RcmdrPlugin_orloca" "RcmdrPlugin_plotByGroup" "RcmdrPlugin_pointG" "RcmdrPlugin_qual" "RcmdrPlugin_ROC" "RcmdrPlugin_sampling" "RcmdrPlugin_SCDA" "RcmdrPlugin_SLC" "RcmdrPlugin_SM" "RcmdrPlugin_sos" "RcmdrPlugin_StatisticalURV" "RcmdrPlugin_steepness" "RcmdrPlugin_survival" "RcmdrPlugin_TeachingDemos" "RcmdrPlugin_temis" "RcmdrPlugin_UCA" "recluster" "relax" "relimp" "RenextGUI" "reportRx" "reshapeGUI" "rgl" "RHRV" "rich" "rioja" "ripa" "rite" "rnbn" "RNCEP" "RQDA" "RSDA" "rsgcc" "RSurvey" "RunuranGUI" "sdcMicroGUI" "sharpshootR" "simba" "Simile" "SimpleTable" "SOLOMON" "soundecology" "SPACECAP" "spacodiR" "spatsurv" "sqldf" "SRRS" "SSDforR" "statcheck" "StatDA" "STEPCAM" "stosim" "strvalidator" "stylo" "svDialogstcltk" "svIDE" "svSocket" "svWidgets" "SYNCSA" "SyNet" "tcltk2" "TDMR" "TED" "TestScorer" "TIMP" "titan" "tkrgl" "tkrplot" "tmap" "tspmeta" "TTAinterfaceTrendAnalysis" "twiddler" "vcdExtra" "VecStatGraphs3D" "vegan" "vegan3d" "vegclust" "VIMGUI" "WMCapacity" "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 = [ "a4Base" # depends on broken package annaffy-1.41.1 "a4" # depends on broken package annaffy-1.41.1 "a4Reporting" # depends on broken package annaffy-1.41.1 "abd" # depends on broken package nlopt-2.4.2 "adabag" # depends on broken package nlopt-2.4.2 "ADaCGH2" # depends on broken package tilingArray-1.47.0 "adSplit" # build is broken "AER" # depends on broken package nlopt-2.4.2 "afex" # depends on broken package nlopt-2.4.2 "affyContam" # depends on broken package affyio-1.37.0 "affycoretools" # depends on broken package affyio-1.37.0 "affy" # depends on broken package affyio-1.37.0 "AffyExpress" # depends on broken package affyio-1.37.0 "affyILM" # depends on broken package affyio-1.37.0 "affyio" # build is broken "affylmGUI" # depends on broken package affyio-1.37.0 "affyPara" # depends on broken package affyio-1.37.0 "affypdnn" # depends on broken package affyio-1.37.0 "affyPLM" # depends on broken package affyio-1.37.0 "affyQCReport" # depends on broken package affyio-1.37.0 "AffyRNADegradation" # depends on broken package affyio-1.37.0 "AffyTiling" # depends on broken package affyio-1.37.0 "AgiMicroRna" # depends on broken package affyio-1.37.0 "agRee" # depends on broken package nlopt-2.4.2 "aLFQ" # depends on broken package nlopt-2.4.2 "alr3" # depends on broken package nlopt-2.4.2 "alr4" # depends on broken package nlopt-2.4.2 "altcdfenvs" # depends on broken package affyio-1.37.0 "anacor" # depends on broken package nlopt-2.4.2 "annaffy" # build is broken "AnnotationForge" # Build Is Broken "AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0 "aods3" # depends on broken package nlopt-2.4.2 "apComplex" # build is broken "apt" # depends on broken package nlopt-2.4.2 "ArfimaMLM" # depends on broken package nlopt-2.4.2 "arm" # depends on broken package nlopt-2.4.2 "ArrayExpress" # depends on broken package affyio-1.37.0 "arrayMvout" # depends on broken package affyio-1.37.0 "arrayQualityMetrics" # depends on broken package affyio-1.37.0 "ArrayTools" # depends on broken package affyio-1.37.0 "ArrayTV" # depends on broken package affyio-1.37.0 "ARRmNormalization" # Build Is Broken "ARTool" # depends on broken package nlopt-2.4.2 "attract" # depends on broken package AnnotationForge-1.11.3 "BACA" # depends on broken package Category-2.35.1 "BAGS" # build is broken "bartMachine" # depends on broken package nlopt-2.4.2 "bayesDem" # depends on broken package nlopt-2.4.2 "bayesLife" # depends on broken package nlopt-2.4.2 "bayesPop" # depends on broken package nlopt-2.4.2 "Bayesthresh" # depends on broken package nlopt-2.4.2 "BBRecapture" # depends on broken package nlopt-2.4.2 "BCA" # depends on broken package nlopt-2.4.2 "bgmm" # depends on broken package nlopt-2.4.2 "bgx" # depends on broken package affyio-1.37.0 "BIFIEsurvey" # depends on broken package nlopt-2.4.2 "BiGGR" # depends on broken package rsbml-2.27.0 "BiodiversityR" # depends on broken package nlopt-2.4.2 "birte" # build is broken "BiSEp" # depends on broken package GOSemSim-1.27.3 "blmeco" # depends on broken package nlopt-2.4.2 "blme" # depends on broken package nlopt-2.4.2 "bmd" # depends on broken package nlopt-2.4.2 "bmem" # depends on broken package nlopt-2.4.2 "bootnet" # depends on broken package nlopt-2.4.2 "boss" # depends on broken package nlopt-2.4.2 "BradleyTerry2" # depends on broken package nlopt-2.4.2 "BRugs" # build is broken "CADFtest" # depends on broken package nlopt-2.4.2 "CAFE" # depends on broken package affyio-1.37.0 "cAIC4" # depends on broken package nlopt-2.4.2 "canceR" # depends on broken package Category-2.35.1 "candisc" # depends on broken package nlopt-2.4.2 "carcass" # depends on broken package nlopt-2.4.2 "car" # depends on broken package nlopt-2.4.2 "caret" # depends on broken package nlopt-2.4.2 "caretEnsemble" # depends on broken package nlopt-2.4.2 "Category" # Build Is Broken "categoryCompare" # depends on broken package Category-2.35.1 "CCpop" # depends on broken package nlopt-2.4.2 "cellHTS2" # depends on broken package Category-2.35.1 "ChainLadder" # depends on broken package nlopt-2.4.2 "ChAMP" # depends on broken package affyio-1.37.0 "charm" # depends on broken package affyio-1.37.0 "ChemmineR" # Build Is Broken "chipenrich" # build is broken "ChIPQC" # depends on broken package AnnotationForge-1.11.3 "ChIPXpress" # depends on broken package affyio-1.37.0 "climwin" # depends on broken package nlopt-2.4.2 "CLME" # depends on broken package nlopt-2.4.2 "clpAPI" # build is broken "clusterPower" # depends on broken package nlopt-2.4.2 "Actigraphy" # Build Is Broken "Crossover" # Build Is Broken "FunctionalNetworks" # Build Is Broken "HiPLARM" # Build Is Broken "HierO" # Build Is Broken "KEGGprofile" # Build Is Broken "MigClim" # Build Is Broken "ROracle" # Build Is Broken "Rcplex" # Build Is Broken "RcppAPT" # Build Is Broken "RnaSeqSampleSize" # Build Is Broken "Rsamtools" # Build Is Broken "SeqGrapheR" # Build Is Broken "bamsignals" # build is broken "bigGP" # build is broken "cudaBayesreg" # build is broken "dagbag" # build is broken "gMCP" # build is broken "h5" # build is broken "lefse" # build is broken "metaMix" # build is broken "mirIntegrator" # build is broken "pathview" # build is broken "pcaL1" # build is broken "permGPU" # build is broken "pmclust" # build is broken "qtbase" # build is broken "rDEA" # build is broken "rJPSGCS" # build is broken "rLindo" # build is broken "seqCNA" # build is broken "sybilSBML" # build is broken "AllelicImbalance" # depends on broken package Rsamtools-1.21.8 "ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8 "BEAT" # depends on broken package Rsamtools-1.21.8 "BLCOP" # depends on broken package Rsymphony-0.1-20 "BSgenome" # depends on broken package Rsamtools-1.21.8 "Basic4Cseq" # depends on broken package Rsamtools-1.21.8 "BiSeq" # depends on broken package Rsamtools-1.21.8 "BitSeq" # depends on broken package Rsamtools-1.21.8 "CAGEr" # depends on broken package Rsamtools-1.21.8 "CAMERA" # depends on broken package mzR-2.3.1 "CARrampsOcl" # depends on broken package OpenCL-0.1-3 "CNEr" # depends on broken package Rsamtools-1.21.8 "CNVrd2" # depends on broken package Rsamtools-1.21.8 "CODEX" # depends on broken package Rsamtools-1.21.8 "CRISPRseek" # depends on broken package Rsamtools-1.21.8 "CexoR" # depends on broken package Rsamtools-1.21.8 "ChIPpeakAnno" # depends on broken package Rsamtools-1.21.8 "ChIPseeker" # depends on broken package Rsamtools-1.21.8 "ChIPseqR" # depends on broken package Rsamtools-1.21.8 "ChIPsim" # depends on broken package Rsamtools-1.21.8 "ChromHeatMap" # depends on broken package Rsamtools-1.21.8 "CopyNumber450k" # depends on broken package Rsamtools-1.21.8 "CopywriteR" # depends on broken package Rsamtools-1.21.8 "CoverageView" # depends on broken package Rsamtools-1.21.8 "DBKGrad" # depends on broken package rpanel-1.1-3 "DEXSeq" # depends on broken package Rsamtools-1.21.8 "DMRcate" # depends on broken package Rsamtools-1.21.8 "DMRforPairs" # depends on broken package Rsamtools-1.21.8 "DOQTL" # depends on broken package Rsamtools-1.21.8 "EDASeq" # depends on broken package Rsamtools-1.21.8 "ELMER" # depends on broken package Rsamtools-1.21.8 "ExomeDepth" # depends on broken package Rsamtools-1.21.8 "FourCSeq" # depends on broken package Rsamtools-1.21.8 "GOGANPA" # depends on broken package WGCNA-1.47 "GOTHiC" # depends on broken package Rsamtools-1.21.8 "GUIDE" # depends on broken package rpanel-1.1-3 "GenoView" # depends on broken package Rsamtools-1.21.8 "GenomicAlignments" # depends on broken package Rsamtools-1.21.8 "GenomicFeatures" # depends on broken package Rsamtools-1.21.8 "GenomicFiles" # depends on broken package Rsamtools-1.21.8 "GenomicInteractions" # depends on broken package Rsamtools-1.21.8 "GoogleGenomics" # depends on broken package Rsamtools-1.21.8 "GreyListChIP" # depends on broken package Rsamtools-1.21.8 "Gviz" # depends on broken package Rsamtools-1.21.8 "HTSeqGenie" # depends on broken package Rsamtools-1.21.8 "HiTC" # depends on broken package Rsamtools-1.21.8 "IdeoViz" # depends on broken package Rsamtools-1.21.8 "InPAS" # depends on broken package Rsamtools-1.21.8 "LinRegInteractive" # depends on broken package rpanel-1.1-3 "LowMACA" # depends on broken package Rsamtools-1.21.8 "M3D" # depends on broken package Rsamtools-1.21.8 "MEDIPS" # depends on broken package Rsamtools-1.21.8 "MSeasy" # depends on broken package mzR-2.3.1 "MSeasyTkGUI" # depends on broken package mzR-2.3.1 "Metab" # depends on broken package mzR-2.3.1 "MethylAid" # depends on broken package Rsamtools-1.21.8 "MethylSeekR" # depends on broken package Rsamtools-1.21.8 "MotIV" # depends on broken package Rsamtools-1.21.8 "MotifDb" # depends on broken package Rsamtools-1.21.8 "OTUbase" # depends on broken package Rsamtools-1.21.8 "OrganismDbi" # depends on broken package Rsamtools-1.21.8 "PGA" # depends on broken package Rsamtools-1.21.8 "PICS" # depends on broken package Rsamtools-1.21.8 "PING" # depends on broken package Rsamtools-1.21.8 "Pviz" # depends on broken package Rsamtools-1.21.8 "QDNAseq" # depends on broken package Rsamtools-1.21.8 "QuasR" # depends on broken package Rsamtools-1.21.8 "R3CPET" # depends on broken package Rsamtools-1.21.8 "R453Plus1Toolbox" # depends on broken package Rsamtools-1.21.8 "RAPIDR" # depends on broken package Rsamtools-1.21.8 "REBayes" # depends on broken package Rmosek-1.2.5.1 "REDseq" # depends on broken package Rsamtools-1.21.8 "RIPSeeker" # depends on broken package Rsamtools-1.21.8 "RMassBank" # depends on broken package mzR-2.3.1 "RNAprobR" # depends on broken package Rsamtools-1.21.8 "ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20 "RSVSim" # depends on broken package Rsamtools-1.21.8 "RUVSeq" # depends on broken package Rsamtools-1.21.8 "RVideoPoker" # depends on broken package rpanel-1.1-3 "RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76 "Rariant" # depends on broken package Rsamtools-1.21.8 "Rcade" # depends on broken package Rsamtools-1.21.8 "ReQON" # depends on broken package Rsamtools-1.21.8 "RnBeads" # depends on broken package Rsamtools-1.21.8 "Rolexa" # depends on broken package Rsamtools-1.21.8 "Rqc" # depends on broken package Rsamtools-1.21.8 "SDD" # depends on broken package rpanel-1.1-3 "SGSeq" # depends on broken package Rsamtools-1.21.8 "SIMAT" # depends on broken package mzR-2.3.1 "SNPtools" # depends on broken package Rsamtools-1.21.8 "SVM2CRM" # depends on broken package Rsamtools-1.21.8 "SeqArray" # depends on broken package Rsamtools-1.21.8 "SeqVarTools" # depends on broken package Rsamtools-1.21.8 "ShortRead" # depends on broken package Rsamtools-1.21.8 "SimRAD" # depends on broken package Rsamtools-1.21.8 "SomaticSignatures" # depends on broken package Rsamtools-1.21.8 "SplicingGraphs" # depends on broken package Rsamtools-1.21.8 "TEQC" # depends on broken package Rsamtools-1.21.8 "TIN" # depends on broken package WGCNA-1.47 "TargetSearch" # depends on broken package mzR-2.3.1 "TitanCNA" # depends on broken package Rsamtools-1.21.8 "ToPASeq" # depends on broken package Rsamtools-1.21.8 "TransView" # depends on broken package Rsamtools-1.21.8 "VariantAnnotation" # depends on broken package Rsamtools-1.21.8 "VariantFiltering" # depends on broken package Rsamtools-1.21.8 "VariantTools" # depends on broken package Rsamtools-1.21.8 "ampliQueso" # depends on broken package Rsamtools-1.21.8 "annmap" # depends on broken package Rsamtools-1.21.8 "ballgown" # depends on broken package Rsamtools-1.21.8 "biomvRCNS" # depends on broken package Rsamtools-1.21.8 "biotools" # depends on broken package rpanel-1.1-3 "biovizBase" # depends on broken package Rsamtools-1.21.8 "bumphunter" # depends on broken package Rsamtools-1.21.8 "casper" # depends on broken package Rsamtools-1.21.8 "chimera" # depends on broken package Rsamtools-1.21.8 "chipseq" # depends on broken package Rsamtools-1.21.8 "cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8 "clipper" # depends on broken package Rsamtools-1.21.8 "cn_mops" # depends on broken package Rsamtools-1.21.8 "coMET" # depends on broken package Rsamtools-1.21.8 "cobindR" # depends on broken package Rsamtools-1.21.8 "conumee" # depends on broken package Rsamtools-1.21.8 "cosmiq" # depends on broken package mzR-2.3.1 "cpvSNP" # depends on broken package Rsamtools-1.21.8 "csaw" # depends on broken package Rsamtools-1.21.8 "cummeRbund" # depends on broken package Rsamtools-1.21.8 "customProDB" # depends on broken package Rsamtools-1.21.8 "daff" # depends on broken package V8-0.6 "dagLogo" # depends on broken package Rsamtools-1.21.8 "deepSNV" # depends on broken package Rsamtools-1.21.8 "derfinder" # depends on broken package Rsamtools-1.21.8 "derfinderPlot" # depends on broken package Rsamtools-1.21.8 "easyRNASeq" # depends on broken package Rsamtools-1.21.8 "ensemblVEP" # depends on broken package Rsamtools-1.21.8 "epigenomix" # depends on broken package Rsamtools-1.21.8 "epivizr" # depends on broken package Rsamtools-1.21.8 "erpR" # depends on broken package rpanel-1.1-3 "exomeCopy" # depends on broken package Rsamtools-1.21.8 "exomePeak" # depends on broken package Rsamtools-1.21.8 "fPortfolio" # depends on broken package Rsymphony-0.1-20 "fastLiquidAssociation" # depends on broken package LiquidAssociation-1.23.0 "flagme" # depends on broken package mzR-2.3.1 "gamlss_demo" # depends on broken package rpanel-1.1-3 "genomation" # depends on broken package Rsamtools-1.21.8 "geojsonio" # depends on broken package V8-0.6 "ggbio" # depends on broken package Rsamtools-1.21.8 "girafe" # depends on broken package Rsamtools-1.21.8 "gmapR" # depends on broken package Rsamtools-1.21.8 "groHMM" # depends on broken package Rsamtools-1.21.8 "hiAnnotator" # depends on broken package Rsamtools-1.21.8 "hiReadsProcessor" # depends on broken package Rsamtools-1.21.8 "htSeqTools" # depends on broken package Rsamtools-1.21.8 "intansv" # depends on broken package Rsamtools-1.21.8 "js" # depends on broken package V8-0.6 "lawn" # depends on broken package V8-0.6 "lgcp" # depends on broken package rpanel-1.1-3 "mcaGUI" # depends on broken package Rsamtools-1.21.8 "metaMS" # depends on broken package mzR-2.3.1 "metaSEM" # depends on broken package OpenMx-2.2.4 "metagene" # depends on broken package Rsamtools-1.21.8 "methylPipe" # depends on broken package Rsamtools-1.21.8 "methylumi" # depends on broken package Rsamtools-1.21.8 "minfi" # depends on broken package Rsamtools-1.21.8 "minimist" # depends on broken package V8-0.6 "missMethyl" # depends on broken package Rsamtools-1.21.8 "motifRG" # depends on broken package Rsamtools-1.21.8 "motifStack" # depends on broken package Rsamtools-1.21.8 "mygene" # depends on broken package Rsamtools-1.21.8 "nettools" # depends on broken package WGCNA-1.47 "nucleR" # depends on broken package Rsamtools-1.21.8 "optBiomarker" # depends on broken package rpanel-1.1-3 "ora" # depends on broken package ROracle-1.1-12 "pbdBASE" # depends on broken package pbdSLAP-0.2-0 "pbdDEMO" # depends on broken package pbdSLAP-0.2-0 "pbdDMAT" # depends on broken package pbdSLAP-0.2-0 "podkat" # depends on broken package Rsamtools-1.21.8 "proBAMr" # depends on broken package Rsamtools-1.21.8 "qpgraph" # depends on broken package Rsamtools-1.21.8 "qrqc" # depends on broken package Rsamtools-1.21.8 "qtpaint" # depends on broken package qtbase-1.0.9 "qtutils" # depends on broken package qtbase-1.0.9 "quantro" # depends on broken package Rsamtools-1.21.8 "r3Cseq" # depends on broken package Rsamtools-1.21.8 "rGADEM" # depends on broken package Rsamtools-1.21.8 "rSFFreader" # depends on broken package Rsamtools-1.21.8 "rTRMui" # depends on broken package Rsamtools-1.21.8 "regionReport" # depends on broken package Rsamtools-1.21.8 "regioneR" # depends on broken package Rsamtools-1.21.8 "repijson" # depends on broken package V8-0.6 "rfPred" # depends on broken package Rsamtools-1.21.8 "rgbif" # depends on broken package V8-0.6 "rgpui" # depends on broken package rgp-0.4-1 "rjade" # depends on broken package V8-0.6 "rnaSeqMap" # depends on broken package Rsamtools-1.21.8 "roar" # depends on broken package Rsamtools-1.21.8 "rtracklayer" # depends on broken package Rsamtools-1.21.8 "sapFinder" # depends on broken package rTANDEM-1.9.0 "segmentSeq" # depends on broken package Rsamtools-1.21.8 "seq2pathway" # depends on broken package WGCNA-1.47 "seqbias" # depends on broken package Rsamtools-1.21.8 "seqplots" # depends on broken package Rsamtools-1.21.8 "shinyMethyl" # depends on broken package Rsamtools-1.21.8 "shinyTANDEM" # depends on broken package rTANDEM-1.9.0 "similaRpeak" # depends on broken package Rsamtools-1.21.8 "soGGi" # depends on broken package Rsamtools-1.21.8 "soilphysics" # depends on broken package rpanel-1.1-3 "spliceR" # depends on broken package Rsamtools-1.21.8 "spocc" # depends on broken package V8-0.6 "ssviz" # depends on broken package Rsamtools-1.21.8 "stagePop" # depends on broken package PBSddesolve-1.11.29 "topologyGSA" # depends on broken package Rsamtools-1.21.8 "trackViewer" # depends on broken package Rsamtools-1.21.8 "tracktables" # depends on broken package Rsamtools-1.21.8 "vmsbase" # depends on broken package PBSmapping-2.69.76 "wavClusteR" # depends on broken package Rsamtools-1.21.8 "xcms" # depends on broken package mzR-2.3.1 "clusterProfiler" # depends on broken package GOSemSim-1.27.3 "cn_farms" # depends on broken package affyio-1.37.0 "CNORfuzzy" # depends on broken package nlopt-2.4.2 "CoCiteStats" # Build Is Broken "COHCAP" # build is broken "compEpiTools" # depends on broken package topGO-2.21.0 "CompGO" # depends on broken package Category-2.35.1 "conformal" # depends on broken package nlopt-2.4.2 "ConsensusClusterPlus" # Build Is Broken "corHMM" # depends on broken package nlopt-2.4.2 "Cormotif" # depends on broken package affyio-1.37.0 "coRNAi" # depends on broken package Category-2.35.1 "CosmoPhotoz" # depends on broken package nlopt-2.4.2 "cplexAPI" # build is broken "crlmm" # depends on broken package affyio-1.37.0 "CrypticIBDcheck" # depends on broken package nlopt-2.4.2 "DAMisc" # depends on broken package nlopt-2.4.2 "Deducer" # depends on broken package nlopt-2.4.2 "DeducerExtras" # depends on broken package nlopt-2.4.2 "DeducerPlugInExample" # depends on broken package nlopt-2.4.2 "DeducerPlugInScaling" # depends on broken package nlopt-2.4.2 "DeducerSpatial" # depends on broken package nlopt-2.4.2 "DeducerSurvival" # depends on broken package nlopt-2.4.2 "DeducerText" # depends on broken package nlopt-2.4.2 "DEGraph" # depends on broken package RCytoscape-1.19.0 "demi" # depends on broken package affyio-1.37.0 "DiagTest3Grp" # depends on broken package nlopt-2.4.2 "DiffBind" # depends on broken package AnnotationForge-1.11.3 "diffHic" # depends on broken package rhdf5-2.13.1 "difR" # depends on broken package nlopt-2.4.2 "DirichletMultinomial" # Build Is Broken "discSurv" # depends on broken package nlopt-2.4.2 "DistatisR" # depends on broken package nlopt-2.4.2 "diveRsity" # depends on broken package nlopt-2.4.2 "domainsignatures" # build is broken "doMPI" # build is broken "DOSE" # depends on broken package GOSemSim-1.27.3 "dpa" # depends on broken package nlopt-2.4.2 "drc" # depends on broken package nlopt-2.4.2 "drfit" # depends on broken package nlopt-2.4.2 "drsmooth" # depends on broken package nlopt-2.4.2 "DrugVsDisease" # depends on broken package affyio-1.37.0 "dualKS" # depends on broken package affyio-1.37.0 "dynlm" # depends on broken package nlopt-2.4.2 "easyanova" # depends on broken package nlopt-2.4.2 "edge" # depends on broken package nlopt-2.4.2 "eeptools" # depends on broken package nlopt-2.4.2 "EffectLiteR" # depends on broken package nlopt-2.4.2 "effects" # depends on broken package nlopt-2.4.2 "eiR" # depends on broken package ChemmineR-2.21.7 "eisa" # depends on broken package Category-2.35.1 "EMA" # depends on broken package nlopt-2.4.2 "ENmix" # depends on broken package affyio-1.37.0 "EnQuireR" # depends on broken package nlopt-2.4.2 "ensembldb" # depends on broken package interactiveDisplayBase-1.7.0 "episplineDensity" # depends on broken package nlopt-2.4.2 "epr" # depends on broken package nlopt-2.4.2 "erer" # depends on broken package nlopt-2.4.2 "ExiMiR" # depends on broken package affyio-1.37.0 "ExpressionView" # depends on broken package Category-2.35.1 "extRemes" # depends on broken package nlopt-2.4.2 "ez" # depends on broken package nlopt-2.4.2 "facopy" # depends on broken package nlopt-2.4.2 "FactoMineR" # depends on broken package nlopt-2.4.2 "Factoshiny" # depends on broken package nlopt-2.4.2 "faoutlier" # depends on broken package nlopt-2.4.2 "farms" # depends on broken package affyio-1.37.0 "fastR" # depends on broken package nlopt-2.4.2 "FDRreg" # depends on broken package nlopt-2.4.2 "FEM" # build is broken "ffpe" # depends on broken package affyio-1.37.0 "flowDensity" # depends on broken package nlopt-2.4.2 "flowPeaks" # build is broken "flowQ" # build is broken "FlowSOM" # depends on broken package ConsensusClusterPlus-1.23.0 "flowStats" # depends on broken package ncdfFlow-2.15.2 "flowVS" # depends on broken package ncdfFlow-2.15.2 "flowWorkspace" # depends on broken package ncdfFlow-2.15.2 "fmcsR" # depends on broken package ChemmineR-2.21.7 "freqweights" # depends on broken package nlopt-2.4.2 "frma" # depends on broken package affyio-1.37.0 "frmaTools" # depends on broken package affyio-1.37.0 "fscaret" # depends on broken package nlopt-2.4.2 "FunciSNP" # depends on broken package snpStats-1.19.0 "fxregime" # depends on broken package nlopt-2.4.2 "gamclass" # depends on broken package nlopt-2.4.2 "gamm4" # depends on broken package nlopt-2.4.2 "gCMAP" # depends on broken package Category-2.35.1 "gCMAPWeb" # depends on broken package Category-2.35.1 "gcmr" # depends on broken package nlopt-2.4.2 "gcrma" # depends on broken package affyio-1.37.0 "GDAtools" # depends on broken package nlopt-2.4.2 "GENE_E" # depends on broken package rhdf5-2.13.1 "GeneExpressionSignature" # depends on broken package annaffy-1.41.1 "GeneticTools" # depends on broken package snpStats-1.19.0 "genridge" # depends on broken package nlopt-2.4.2 "GEOsubmission" # depends on broken package affyio-1.37.0 "gespeR" # depends on broken package Category-2.35.1 "GEWIST" # depends on broken package nlopt-2.4.2 "GGBase" # depends on broken package snpStats-1.19.0 "GGtools" # depends on broken package snpStats-1.19.0 "gimme" # depends on broken package nlopt-2.4.2 "gmatrix" # depends on broken package cudatoolkit-5.5.22 "GOFunction" # build is broken "goProfiles" # build is broken "GOSemSim" # Build Is Broken "goseq" # build is broken "GOSim" # depends on broken package topGO-2.21.0 "GOstats" # depends on broken package AnnotationForge-1.11.3 "goTools" # build is broken "gplm" # depends on broken package nlopt-2.4.2 "gputools" # depends on broken package cudatoolkit-5.5.22 "gQTLstats" # depends on broken package snpStats-1.19.0 "granova" # depends on broken package nlopt-2.4.2 "graphicalVAR" # depends on broken package nlopt-2.4.2 "GraphPCA" # depends on broken package nlopt-2.4.2 "GSCA" # depends on broken package rhdf5-2.13.1 "GWAF" # depends on broken package nlopt-2.4.2 "gwascat" # depends on broken package interactiveDisplayBase-1.7.0 "h2o" # build is broken "h5vc" # depends on broken package rhdf5-2.13.1 "Harshlight" # depends on broken package affyio-1.37.0 "hbsae" # depends on broken package nlopt-2.4.2 "heplots" # depends on broken package nlopt-2.4.2 "HilbertVisGUI" # Build Is Broken "HistDAWass" # depends on broken package nlopt-2.4.2 "HLMdiag" # depends on broken package nlopt-2.4.2 "HTqPCR" # depends on broken package affyio-1.37.0 "HTSanalyzeR" # depends on broken package Category-2.35.1 "hysteresis" # depends on broken package nlopt-2.4.2 "IATscores" # depends on broken package nlopt-2.4.2 "ibd" # depends on broken package nlopt-2.4.2 "ibh" # build is broken "iccbeta" # depends on broken package nlopt-2.4.2 "iFes" # depends on broken package cudatoolkit-5.5.22 "imageHTS" # depends on broken package Category-2.35.1 "immunoClust" # build is broken "imputeR" # depends on broken package nlopt-2.4.2 "in2extRemes" # depends on broken package nlopt-2.4.2 "inferference" # depends on broken package nlopt-2.4.2 "influence_ME" # depends on broken package nlopt-2.4.2 "inSilicoMerging" # build is broken "interactiveDisplayBase" # build is broken "interactiveDisplay" # depends on broken package Category-2.35.1 "IsingFit" # depends on broken package nlopt-2.4.2 "IsoGene" # depends on broken package affyio-1.37.0 "IsoGeneGUI" # depends on broken package affyio-1.37.0 "ITALICS" # depends on broken package oligo-1.33.0 "IVAS" # depends on broken package nlopt-2.4.2 "ivpack" # depends on broken package nlopt-2.4.2 "JAGUAR" # depends on broken package nlopt-2.4.2 "joda" # depends on broken package nlopt-2.4.2 "jomo" # build is broken "KANT" # depends on broken package affyio-1.37.0 "keggorthology" # build is broken "learnstats" # depends on broken package nlopt-2.4.2 "lessR" # depends on broken package nlopt-2.4.2 "lfe" # build is broken "limmaGUI" # depends on broken package affyio-1.37.0 "LiquidAssociation" # build is broken "lmdme" # build is broken "lme4" # depends on broken package nlopt-2.4.2 "LMERConvenienceFunctions" # depends on broken package nlopt-2.4.2 "lmerTest" # depends on broken package nlopt-2.4.2 "LMGene" # depends on broken package affyio-1.37.0 "lmSupport" # depends on broken package nlopt-2.4.2 "LogisticDx" # depends on broken package nlopt-2.4.2 "logitT" # depends on broken package affyio-1.37.0 "longpower" # depends on broken package nlopt-2.4.2 "lumi" # depends on broken package affyio-1.37.0 "LVSmiRNA" # depends on broken package affyio-1.37.0 "MAIT" # depends on broken package nlopt-2.4.2 "makecdfenv" # depends on broken package affyio-1.37.0 "mAPKL" # build is broken "maPredictDSC" # depends on broken package nlopt-2.4.2 "marked" # depends on broken package nlopt-2.4.2 "maskBAD" # depends on broken package affyio-1.37.0 "MatrixRider" # depends on broken package DirichletMultinomial-1.11.1 "MaxPro" # depends on broken package nlopt-2.4.2 "mbest" # depends on broken package nlopt-2.4.2 "mBPCR" # depends on broken package affyio-1.37.0 "MCRestimate" # build is broken "mdgsa" # build is broken "meboot" # depends on broken package nlopt-2.4.2 "MEDME" # depends on broken package nlopt-2.4.2 "MEMSS" # depends on broken package nlopt-2.4.2 "meshr" # depends on broken package Category-2.35.1 "metagear" # build is broken "metaplus" # depends on broken package nlopt-2.4.2 "metaseqR" # depends on broken package affyio-1.37.0 "Metatron" # depends on broken package nlopt-2.4.2 "methyAnalysis" # depends on broken package affyio-1.37.0 "miceadds" # depends on broken package nlopt-2.4.2 "micEconAids" # depends on broken package nlopt-2.4.2 "micEconCES" # depends on broken package nlopt-2.4.2 "micEconSNQP" # depends on broken package nlopt-2.4.2 "mi" # depends on broken package nlopt-2.4.2 "migui" # depends on broken package nlopt-2.4.2 "MineICA" # depends on broken package AnnotationForge-1.11.3 "MinimumDistance" # depends on broken package affyio-1.37.0 "missMDA" # depends on broken package nlopt-2.4.2 "mitoODE" # build is broken "mixAK" # depends on broken package nlopt-2.4.2 "mixlm" # depends on broken package nlopt-2.4.2 "MixMAP" # depends on broken package nlopt-2.4.2 "mlmRev" # depends on broken package nlopt-2.4.2 "MLP" # depends on broken package affyio-1.37.0 "MLSeq" # depends on broken package nlopt-2.4.2 "mlVAR" # depends on broken package nlopt-2.4.2 "MMDiff" # depends on broken package AnnotationForge-1.11.3 "MmPalateMiRNA" # depends on broken package affyio-1.37.0 "mongolite" # build is broken "monocle" # build is broken "mosaic" # depends on broken package nlopt-2.4.2 "MSGFgui" # depends on broken package MSGFplus-1.3.0 "MSGFplus" # Build Is Broken "msmsEDA" # depends on broken package affyio-1.37.0 "msmsTests" # depends on broken package affyio-1.37.0 "MSnbase" # depends on broken package affyio-1.37.0 "MSnID" # depends on broken package affyio-1.37.0 "MSstats" # depends on broken package nlopt-2.4.2 "multiDimBio" # depends on broken package nlopt-2.4.2 "MultiRR" # depends on broken package nlopt-2.4.2 "muma" # depends on broken package nlopt-2.4.2 "mutossGUI" # build is broken "mvGST" # depends on broken package AnnotationForge-1.11.3 "mvinfluence" # depends on broken package nlopt-2.4.2 "mzR" # build is broken "NanoStringQCPro" # build is broken "nCal" # depends on broken package nlopt-2.4.2 "ncdfFlow" # build is broken "NCIgraph" # depends on broken package RCytoscape-1.19.0 "netbenchmark" # build is broken "NHPoisson" # depends on broken package nlopt-2.4.2 "nloptr" # depends on broken package nlopt-2.4.2 "nondetects" # depends on broken package affyio-1.37.0 "nonrandom" # depends on broken package nlopt-2.4.2 "NormqPCR" # depends on broken package affyio-1.37.0 "NORRRM" # build is broken "npIntFactRep" # depends on broken package nlopt-2.4.2 "oligoClasses" # depends on broken package affyio-1.37.0 "oligo" # depends on broken package affyio-1.37.0 "OmicsMarkeR" # depends on broken package nlopt-2.4.2 "oneChannelGUI" # depends on broken package affyio-1.37.0 "OpenCL" # build is broken "openCyto" # depends on broken package ncdfFlow-2.15.2 "OpenMx" # build is broken "OperaMate" # depends on broken package Category-2.35.1 "ordBTL" # depends on broken package nlopt-2.4.2 "OUwie" # depends on broken package nlopt-2.4.2 "PADOG" # build is broken "pamm" # depends on broken package nlopt-2.4.2 "PANDA" # build is broken "panelAR" # depends on broken package nlopt-2.4.2 "panp" # depends on broken package affyio-1.37.0 "papeR" # depends on broken package nlopt-2.4.2 "parboost" # depends on broken package nlopt-2.4.2 "parma" # depends on broken package nlopt-2.4.2 "pathClass" # depends on broken package affyio-1.37.0 "pathRender" # build is broken "PatternClass" # build is broken "Pbase" # depends on broken package affyio-1.37.0 "pbdSLAP" # build is broken "PBImisc" # depends on broken package nlopt-2.4.2 "pbkrtest" # depends on broken package nlopt-2.4.2 "PBSddesolve" # build is broken "PBSmapping" # build is broken "PCpheno" # depends on broken package Category-2.35.1 "pdInfoBuilder" # depends on broken package affyio-1.37.0 "pdmclass" # build is broken "PECA" # depends on broken package affyio-1.37.0 "pedigreemm" # depends on broken package nlopt-2.4.2 "pedometrics" # depends on broken package nlopt-2.4.2 "pequod" # depends on broken package nlopt-2.4.2 "PGSEA" # depends on broken package annaffy-1.41.1 "phenoDist" # depends on broken package Category-2.35.1 "phenoTest" # depends on broken package Category-2.35.1 "PhenStat" # depends on broken package nlopt-2.4.2 "phia" # depends on broken package nlopt-2.4.2 "phylocurve" # depends on broken package nlopt-2.4.2 "phyloTop" # depends on broken package nlopt-2.4.2 "plateCore" # depends on broken package ncdfFlow-2.15.2 "plier" # depends on broken package affyio-1.37.0 "plsRbeta" # depends on broken package nlopt-2.4.2 "plsRcox" # depends on broken package nlopt-2.4.2 "plsRglm" # depends on broken package nlopt-2.4.2 "plw" # depends on broken package affyio-1.37.0 "pmm" # depends on broken package nlopt-2.4.2 "polytomous" # depends on broken package nlopt-2.4.2 "pomp" # depends on broken package nlopt-2.4.2 "ppiPre" # depends on broken package GOSemSim-1.27.3 "ppiStats" # depends on broken package Category-2.35.1 "prebs" # depends on broken package affyio-1.37.0 "predictmeans" # depends on broken package nlopt-2.4.2 "prLogistic" # depends on broken package nlopt-2.4.2 "ProCoNA" # depends on broken package AnnotationForge-1.11.3 "pRoloc" # depends on broken package nlopt-2.4.2 "pRolocGUI" # depends on broken package nlopt-2.4.2 "proteoQC" # depends on broken package affyio-1.37.0 "PSAboot" # depends on broken package nlopt-2.4.2 "puma" # depends on broken package affyio-1.37.0 "pvac" # depends on broken package affyio-1.37.0 "pvca" # depends on broken package nlopt-2.4.2 "pwOmics" # depends on broken package interactiveDisplayBase-1.7.0 "qcmetrics" # build is broken "qgraph" # depends on broken package nlopt-2.4.2 "qpcrNorm" # depends on broken package affyio-1.37.0 "qtlnet" # depends on broken package nlopt-2.4.2 "QUALIFIER" # depends on broken package ncdfFlow-2.15.2 "quantification" # depends on broken package nlopt-2.4.2 "R2STATS" # depends on broken package nlopt-2.4.2 "radiant" # depends on broken package nlopt-2.4.2 "raincpc" # build is broken "rainfreq" # build is broken "RamiGO" # depends on broken package RCytoscape-1.19.0 "rasclass" # depends on broken package nlopt-2.4.2 "RbioRXN" # depends on broken package ChemmineR-2.21.7 "Rchemcpp" # depends on broken package ChemmineR-2.21.7 "Rcmdr" # depends on broken package nlopt-2.4.2 "RcmdrMisc" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_BCA" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_coin" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_depthTools" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_DoE" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_doex" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_EACSPIR" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_IPSUR" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_KMggplot2" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_lfstat" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_MA" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_mosaic" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_MPAStats" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_NMBU" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_orloca" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_plotByGroup" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_pointG" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_qual" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_RMTCJags" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_ROC" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_sampling" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_SCDA" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_seeg" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_SLC" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_SM" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_sos" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_StatisticalURV" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_steepness" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_survival" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_TeachingDemos" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_temis" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_UCA" # depends on broken package nlopt-2.4.2 "Rcpi" # depends on broken package ChemmineR-2.21.7 "RcppOctave" # build is broken "RcppRedis" # build is broken "RCytoscape" # Build Is Broken "RDAVIDWebService" # depends on broken package Category-2.35.1 "rdd" # depends on broken package nlopt-2.4.2 "RDieHarder" # build is broken "ReactomePA" # depends on broken package GOSemSim-1.27.3 "ReadqPCR" # depends on broken package affyio-1.37.0 "referenceIntervals" # depends on broken package nlopt-2.4.2 "RefNet" # depends on broken package interactiveDisplayBase-1.7.0 "RefPlus" # depends on broken package affyio-1.37.0 "refund" # depends on broken package nlopt-2.4.2 "Repitools" # depends on broken package affyio-1.37.0 "ReportingTools" # depends on broken package Category-2.35.1 "REST" # depends on broken package nlopt-2.4.2 "rgp" # build is broken "rgsepd" # depends on broken package goseq-1.21.1 "rhdf5" # build is broken "rHVDM" # depends on broken package affyio-1.37.0 "Ringo" # depends on broken package affyio-1.37.0 "Risa" # depends on broken package affyio-1.37.0 "rMAT" # build is broken "rmgarch" # depends on broken package nlopt-2.4.2 "rminer" # depends on broken package nlopt-2.4.2 "RmiR" # Build Is Broken "Rmosek" # build is broken "RNAinteract" # depends on broken package Category-2.35.1 "RNAither" # depends on broken package nlopt-2.4.2 "RnavGraph" # build is broken "Rnits" # depends on broken package affyio-1.37.0 "RobLoxBioC" # depends on broken package affyio-1.37.0 "robustlmm" # depends on broken package nlopt-2.4.2 "rockchalk" # depends on broken package nlopt-2.4.2 "rols" # build is broken "RPA" # depends on broken package affyio-1.37.0 "rpanel" # build is broken "rpubchem" # depends on broken package nlopt-2.4.2 "RQuantLib" # build is broken "rr" # depends on broken package nlopt-2.4.2 "RSAP" # build is broken "rsbml" # build is broken "rscala" # build is broken "RSDA" # depends on broken package nlopt-2.4.2 "Rsubread" # Build Is Broken "Rsymphony" # build is broken "rTANDEM" # build is broken "RTN" # depends on broken package nlopt-2.4.2 "rugarch" # depends on broken package nlopt-2.4.2 "RUVcorr" # build is broken "RUVnormalize" # Build Is Broken "RVAideMemoire" # depends on broken package nlopt-2.4.2 "RVFam" # depends on broken package nlopt-2.4.2 "ryouready" # depends on broken package nlopt-2.4.2 "sampleSelection" # depends on broken package nlopt-2.4.2 "SCAN_UPC" # depends on broken package affyio-1.37.0 "ScISI" # depends on broken package apComplex-2.35.0 "sdcMicro" # depends on broken package nlopt-2.4.2 "sdcMicroGUI" # depends on broken package nlopt-2.4.2 "seeg" # depends on broken package nlopt-2.4.2 "sem" # depends on broken package nlopt-2.4.2 "semdiag" # depends on broken package nlopt-2.4.2 "SemDist" # Build Is Broken "semGOF" # depends on broken package nlopt-2.4.2 "semPlot" # depends on broken package nlopt-2.4.2 "SensoMineR" # depends on broken package nlopt-2.4.2 "SEPA" # depends on broken package topGO-2.21.0 "seqTools" # build is broken "SimBindProfiles" # depends on broken package affyio-1.37.0 "simpleaffy" # depends on broken package affyio-1.37.0 "sirt" # depends on broken package nlopt-2.4.2 "sjPlot" # depends on broken package nlopt-2.4.2 "skewr" # depends on broken package affyio-1.37.0 "SLGI" # depends on broken package apComplex-2.35.0 "SNAGEE" # build is broken "snapCGH" # depends on broken package tilingArray-1.47.0 "snm" # depends on broken package nlopt-2.4.2 "SNPchip" # depends on broken package affyio-1.37.0 "snpEnrichment" # depends on broken package snpStats-1.19.0 "snpStats" # build is broken "snpStatsWriter" # depends on broken package snpStats-1.19.0 "SOD" # depends on broken package cudatoolkit-5.5.22 "spacom" # depends on broken package nlopt-2.4.2 "specificity" # depends on broken package nlopt-2.4.2 "sscore" # depends on broken package affyio-1.37.0 "ssmrob" # depends on broken package nlopt-2.4.2 "staRank" # depends on broken package Category-2.35.1 "Starr" # depends on broken package affyio-1.37.0 "STATegRa" # depends on broken package affyio-1.37.0 "stcm" # depends on broken package nlopt-2.4.2 "stepp" # depends on broken package nlopt-2.4.2 "stringgaussnet" # build is broken "Surrogate" # depends on broken package nlopt-2.4.2 "synapter" # depends on broken package affyio-1.37.0 "systemfit" # depends on broken package nlopt-2.4.2 "systemPipeR" # depends on broken package AnnotationForge-1.11.3 "TcGSA" # depends on broken package nlopt-2.4.2 "TDMR" # depends on broken package nlopt-2.4.2 "TFBSTools" # depends on broken package DirichletMultinomial-1.11.1 "tigerstats" # depends on broken package nlopt-2.4.2 "tilingArray" # depends on broken package affyio-1.37.0 "topGO" # build is broken "tRanslatome" # depends on broken package GOSemSim-1.27.3 "TriMatch" # depends on broken package nlopt-2.4.2 "TROM" # depends on broken package topGO-2.21.0 "TurboNorm" # depends on broken package affyio-1.37.0 "unifiedWMWqPCR" # depends on broken package affyio-1.37.0 "userfriendlyscience" # depends on broken package nlopt-2.4.2 "V8" # build is broken "VanillaICE" # depends on broken package affyio-1.37.0 "VIM" # depends on broken package nlopt-2.4.2 "VIMGUI" # depends on broken package nlopt-2.4.2 "vows" # depends on broken package nlopt-2.4.2 "vsn" # depends on broken package affyio-1.37.0 "vtpnet" # depends on broken package interactiveDisplayBase-1.7.0 "wateRmelon" # depends on broken package affyio-1.37.0 "waveTiling" # depends on broken package affyio-1.37.0 "webbioc" # depends on broken package affyio-1.37.0 "wfe" # depends on broken package nlopt-2.4.2 "WGCNA" # build is broken "wgsea" # depends on broken package snpStats-1.19.0 "WideLM" # depends on broken package cudatoolkit-5.5.22 "xergm" # depends on broken package nlopt-2.4.2 "xps" # build is broken "yaqcaffy" # depends on broken package affyio-1.37.0 "ZeligMultilevel" # depends on broken package nlopt-2.4.2 "zetadiv" # depends on broken package nlopt-2.4.2 ]; otherOverrides = old: new: { xml2 = old.xml2.overrideDerivation (attrs: { preConfigure = "export LIBXML_INCDIR=${pkgs.libxml2}/include/libxml2"; }); curl = old.curl.overrideDerivation (attrs: { preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include"; }); iFes = old.iFes.overrideDerivation (attrs: { patches = [ ./patches/iFes.patch ]; CUDA_HOME = "${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${pkgs.openblasCompat}/lib -lopenblas"; }); qtbase = old.qtbase.overrideDerivation (attrs: { patches = [ ./patches/qtbase.patch ]; }); Rmpi = old.Rmpi.overrideDerivation (attrs: { configureFlags = [ "--with-Rmpi-type=OPENMPI" ]; }); Rmpfr = old.Rmpfr.overrideDerivation (attrs: { configureFlags = [ "--with-mpfr-include=${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.openblasCompat}/lib -lopenblas"; }); SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: { PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas"; }); gputools = old.gputools.overrideDerivation (attrs: { patches = [ ./patches/gputools.patch ]; CUDA_HOME = "${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 ]; buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ]; }); 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${pkgs.nlopt}/lib -lnlopt_cxx -lm'" ]; }); V8 = old.V8.overrideDerivation (attrs: { preConfigure = "export V8_INCLUDES=${pkgs.v8}/include"; }); }; in self