/* 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.xorg.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.xlibsWrapper ]; 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 ]; stringi = [ pkgs.icu ]; survSNP = [ pkgs.gsl ]; sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; TAQMNGR = [ pkgs.zlib ]; tiff = [ pkgs.libtiff ]; TKF = [ pkgs.gsl ]; tkrplot = [ pkgs.xorg.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_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 "a4Classif" # broken build "a4Core" # broken build "a4" # depends on broken package annaffy-1.41.1 "a4Preproc" # broken build "a4Reporting" # depends on broken package annaffy-1.41.1 "ABAEnrichment" # broken build "ABarray" # broken build "abd" # depends on broken package nlopt-2.4.2 "aCGH" # broken build "ACME" # broken build "Actigraphy" # Build Is Broken "adabag" # depends on broken package nlopt-2.4.2 "ADaCGH2" # depends on broken package tilingArray-1.47.0 "adhoc" # broken build "adSplit" # build is broken "AER" # depends on broken package nlopt-2.4.2 "afex" # depends on broken package nlopt-2.4.2 "AffyCompatible" # broken build "affycomp" # broken build "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 "AGDEX" # broken build "AgiMicroRna" # depends on broken package affyio-1.37.0 "agRee" # depends on broken package nlopt-2.4.2 "AIMS" # broken build "ALDEx2" # broken build "aLFQ" # depends on broken package nlopt-2.4.2 "algstat" # broken build "AllelicImbalance" # depends on broken package Rsamtools-1.21.8 "alr3" # depends on broken package nlopt-2.4.2 "alr4" # depends on broken package nlopt-2.4.2 "alsace" # depends on broken nloptr-1.0.4 "altcdfenvs" # depends on broken package affyio-1.37.0 "ampliQueso" # depends on broken package Rsamtools-1.21.8 "anacor" # depends on broken package nlopt-2.4.2 "AnalysisPageServer" # broken build "animation" # broken build "anim_plots" # broken build "annaffy" # build is broken "annmap" # depends on broken package Rsamtools-1.21.8 "annotate" # broken build "AnnotationDbi" # broken build "AnnotationForge" # Build Is Broken "AnnotationFuncs" # broken build "AnnotationHubData" # depends on broken package r-AnnotationForge-1.11.19 "AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0 "annotationTools" # broken build "anota" # broken build "aods3" # depends on broken package nlopt-2.4.2 "aop" # broken build "apaTables" # depends on broken package r-car-2.1-0 "apComplex" # build is broken "apmsWAPP" # broken build "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 "ArrayBin" # broken build "ArrayExpress" # depends on broken package affyio-1.37.0 "ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8 "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 "ART" # depends on broken package ar-car-2.1-0 "ARTool" # depends on broken package nlopt-2.4.2 "AssetPricing" # broken build "AtelieR" # broken build "attract" # depends on broken package AnnotationForge-1.11.3 "AutoModel" # depends on broken package r-car-2.1-0 "babel" # broken build "BACA" # depends on broken package Category-2.35.1 "backShift" # broken build "BAGS" # build is broken "ballgown" # depends on broken package Rsamtools-1.21.8 "bamsignals" # build is broken "bapred" # depends on broken package r-lme4-1.1-9 "bartMachine" # depends on broken package nlopt-2.4.2 "Basic4Cseq" # depends on broken package Rsamtools-1.21.8 "bayesDem" # depends on broken package nlopt-2.4.2 "bayesLife" # depends on broken package nlopt-2.4.2 "BayesPeak" # broken build "bayesPop" # depends on broken package nlopt-2.4.2 "Bayesthresh" # depends on broken package nlopt-2.4.2 "bayou" # broken build "baySeq" # broken build "BBCAnalyzer" # depends on broken package r-Rsamtools-1.21.18 "BBRecapture" # depends on broken package nlopt-2.4.2 "BCA" # depends on broken package nlopt-2.4.2 "BcDiag" # broken build "BCRANK" # broken build "beadarray" # broken build "beadarrayFilter" # broken build "beadarrayMSV" # broken build "beadarraySNP" # broken build "BEAT" # depends on broken package Rsamtools-1.21.8 "bedr" # broken build "betr" # broken build "bgmm" # depends on broken package nlopt-2.4.2 "bgx" # depends on broken package affyio-1.37.0 "BicARE" # broken build "BIFIEsurvey" # depends on broken package nlopt-2.4.2 "bigGP" # build is broken "BiGGR" # depends on broken package rsbml-2.27.0 "bigmemoryExtras" # broken build "bioassayR" # broken build "Biobase" # broken build "BiocCaseStudies" # broken build "BiocCheck" # broken build "BiocGenerics" # broken build "biocGraph" # broken build "biocViews" # broken build "bioDist" # broken build "BiodiversityR" # depends on broken package nlopt-2.4.2 "biomaRt" # broken build "biomartr" # broken build "BioMVCClass" # broken build "biomvRCNS" # depends on broken package Rsamtools-1.21.8 "BioNet" # broken build "BioSeqClass" # broken build "Biostrings" # broken build "biosvd" # broken build "biotools" # depends on broken package rpanel-1.1-3 "biovizBase" # depends on broken package Rsamtools-1.21.8 "birta" # broken build "birte" # build is broken "bisectr" # broken build "BiSEp" # depends on broken package GOSemSim-1.27.3 "BiSeq" # depends on broken package Rsamtools-1.21.8 "BitSeq" # depends on broken package Rsamtools-1.21.8 "BLCOP" # depends on broken package Rsymphony-0.1-20 "blima" # broken build "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 "BMhyd" # broken build "bnclassify" # broken build "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 "BrailleR" # broken build "BRAIN" # broken build "BrainStars" # broken build "BrowserViz" # broken build "BrowserVizDemo" # broken build "brr" # broken build "BRugs" # build is broken "BSgenome" # depends on broken package Rsamtools-1.21.8 "bsseq" # broken build "BubbleTree" # depends on broken package r-biovizBase-1.17.2 "bumphunter" # depends on broken package Rsamtools-1.21.8 "CADFtest" # depends on broken package nlopt-2.4.2 "CAFE" # depends on broken package affyio-1.37.0 "CAGEr" # depends on broken package Rsamtools-1.21.8 "cAIC4" # depends on broken package nlopt-2.4.2 "CAMERA" # depends on broken package mzR-2.3.1 "cancerclass" # broken build "canceR" # depends on broken package Category-2.35.1 "CancerMutationAnalysis" # broken build "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 "Cardinal" # broken build "caret" # depends on broken package nlopt-2.4.2 "caretEnsemble" # depends on broken package nlopt-2.4.2 "caRpools" # broken build "CARrampsOcl" # depends on broken package OpenCL-0.1-3 "casper" # depends on broken package Rsamtools-1.21.8 "cate" # broken build "Category" # Build Is Broken "categoryCompare" # depends on broken package Category-2.35.1 "Causata" # broken build "CCpop" # depends on broken package nlopt-2.4.2 "cdcfluview" # broken build "cellHTS2" # depends on broken package Category-2.35.1 "cellHTS" # broken build "CellNOptR" # broken build "CexoR" # depends on broken package Rsamtools-1.21.8 "CGHbase" # broken build "CGHcall" # broken build "cghMCR" # broken build "CGHnormaliter" # broken build "CGHregions" # broken build "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 "ChemmineOB" # broken build "ChemmineR" # Build Is Broken "chimera" # depends on broken package Rsamtools-1.21.8 "ChIPComp" # depends on broken package r-Rsamtools-1.21.18 "chipenrich" # build is broken "chipPCR" # depends on broken nloptr-1.0.4 "ChIPpeakAnno" # depends on broken package Rsamtools-1.21.8 "ChIPQC" # depends on broken package AnnotationForge-1.11.3 "ChIPseeker" # depends on broken package Rsamtools-1.21.8 "chipseq" # 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 "ChIPXpress" # depends on broken package affyio-1.37.0 "chroGPS" # broken build "chromDraw" # broken build "ChromHeatMap" # depends on broken package Rsamtools-1.21.8 "Claddis" # broken build "classGraph" # broken build "ClassifyR" # broken build "cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8 "cleaver" # broken build "clere" # broken build "climwin" # depends on broken package nlopt-2.4.2 "clippda" # broken build "clipper" # depends on broken package Rsamtools-1.21.8 "CLME" # depends on broken package nlopt-2.4.2 "clpAPI" # build is broken "clusterPower" # depends on broken package nlopt-2.4.2 "clusterProfiler" # depends on broken package GOSemSim-1.27.3 "clusterSEs" # depends on broken AER-1.2-4 "clusterStab" # broken build "ClustGeo" # depends on broken FactoMineR-1.31.3 "CMA" # broken build "CNEr" # depends on broken package Rsamtools-1.21.8 "cn_farms" # depends on broken package affyio-1.37.0 "cn_mops" # depends on broken package Rsamtools-1.21.8 "CNORdt" # broken build "CNORfeeder" # broken build "CNORfuzzy" # depends on broken package nlopt-2.4.2 "CNORode" # broken build "CNTools" # broken build "cnvGSA" # broken build "CNVPanelizer" # depends on broken cn.mops-1.15.1 "CNVrd2" # depends on broken package Rsamtools-1.21.8 "cobindR" # depends on broken package Rsamtools-1.21.8 "CoCiteStats" # Build Is Broken "codelink" # broken build "CODEX" # depends on broken package Rsamtools-1.21.8 "cogena" # broken build "COHCAP" # build is broken "colorscience" "coMET" # depends on broken package Rsamtools-1.21.8 "compcodeR" # broken build "compendiumdb" # broken build "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 "conumee" # depends on broken package Rsamtools-1.21.8 "convert" # broken build "convevol" # broken build "copa" # broken build "CopyNumber450k" # depends on broken package Rsamtools-1.21.8 "copynumber" # broken build "CopywriteR" # depends on broken package Rsamtools-1.21.8 "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 "cosmiq" # depends on broken package mzR-2.3.1 "CosmoPhotoz" # depends on broken package nlopt-2.4.2 "CoverageView" # depends on broken package Rsamtools-1.21.8 "covmat" # depends on broken package r-VIM-4.4.1 "covr" # broken build "cp4p" # broken build "cpgen" # depends on broken package r-pedigreemm-0.3-3 "cplexAPI" # build is broken "cpvSNP" # depends on broken package Rsamtools-1.21.8 "creditr" # broken build "CRImage" # broken build "CRISPRseek" # depends on broken package Rsamtools-1.21.8 "crlmm" # depends on broken package affyio-1.37.0 "crmn" # broken build "Crossover" # Build Is Broken "CrypticIBDcheck" # depends on broken package nlopt-2.4.2 "CSAR" # broken build "csaw" # depends on broken package Rsamtools-1.21.8 "ctsem" # depends on broken package r-OpenMx-2.2.6 "cudaBayesreg" # build is broken "cummeRbund" # depends on broken package Rsamtools-1.21.8 "curvHDR" # broken build "customProDB" # depends on broken package Rsamtools-1.21.8 "cycle" # broken build "cytofkit" # broken build "D2C" # broken build "daff" # depends on broken package V8-0.6 "dagbag" # build is broken "dagLogo" # depends on broken package Rsamtools-1.21.8 "DAMisc" # depends on broken package nlopt-2.4.2 "DASiR" # broken build "datafsm" # depends on broken package r-caret-6.0-52 "DBChIP" # broken build "dbConnect" # broken build "DBKGrad" # depends on broken package rpanel-1.1-3 "dcGOR" # broken build "ddCt" # broken build "ddgraph" # broken build "ddst" # broken build "DECIPHER" # broken build "DeconRNASeq" # broken build "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 "deepSNV" # depends on broken package Rsamtools-1.21.8 "DEGraph" # depends on broken package RCytoscape-1.19.0 "DEGreport" # broken build "demi" # depends on broken package affyio-1.37.0 "derfinder" # depends on broken package Rsamtools-1.21.8 "derfinderHelper" # broken build "derfinderPlot" # depends on broken package Rsamtools-1.21.8 "DESeq2" # broken build "DESeq" # broken build "DESP" # broken build "destiny" # depends on broken package VIM-4.3.0 "DEXSeq" # depends on broken package Rsamtools-1.21.8 "dexus" # broken build "DFP" # broken build "DiagTest3Grp" # depends on broken package nlopt-2.4.2 "DiffBind" # depends on broken package AnnotationForge-1.11.3 "DiffCorr" # broken build "diffHic" # depends on broken package rhdf5-2.13.1 "difR" # depends on broken package nlopt-2.4.2 "diggit" # broken build "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 "DMRcaller" # broken build "DMRcate" # depends on broken package Rsamtools-1.21.8 "DMRforPairs" # depends on broken package Rsamtools-1.21.8 "dnet" # broken build "docxtractr" # broken build "domainsignatures" # build is broken "doMPI" # build is broken "DOQTL" # depends on broken package Rsamtools-1.21.8 "DOSE" # depends on broken package GOSemSim-1.27.3 "dpa" # depends on broken package nlopt-2.4.2 "dpcR" # depends on broken nloptr-1.0.4 "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 "DSS" # broken build "dualKS" # depends on broken package affyio-1.37.0 "dupRadar" # depends on broken package r-Rsubread-1.19.5 "dyebias" # broken build "dynlm" # depends on broken package nlopt-2.4.2 "easyanova" # depends on broken package nlopt-2.4.2 "easyRNASeq" # depends on broken package Rsamtools-1.21.8 "EBarrays" # broken build "EBcoexpress" # broken build "EBImage" # broken build "ecolitk" # broken build "EDASeq" # depends on broken package Rsamtools-1.21.8 "EDDA" # broken build "edge" # depends on broken package nlopt-2.4.2 "edgeR" # broken build "edgeRun" # broken build "edmr" # broken build "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 "ELMER" # depends on broken package Rsamtools-1.21.8 "EMA" # depends on broken package nlopt-2.4.2 "embryogrowth" # broken build "emg" # broken build "empiricalFDR_DESeq2" # broken build "ENmix" # depends on broken package affyio-1.37.0 "EnQuireR" # depends on broken package nlopt-2.4.2 "EnrichedHeatmap" # broken build "EnrichmentBrowser" # depends on broken package r-EDASeq-2.3.2 "ensembldb" # depends on broken package interactiveDisplayBase-1.7.0 "ensemblVEP" # depends on broken package Rsamtools-1.21.8 "epigenomix" # depends on broken package Rsamtools-1.21.8 "episplineDensity" # depends on broken package nlopt-2.4.2 "epivizr" # depends on broken package Rsamtools-1.21.8 "epoc" # broken build "epr" # depends on broken package nlopt-2.4.2 "erccdashboard" # broken build "erer" # depends on broken package nlopt-2.4.2 "erma" # depends on broken GenomicFiles-1.5.4 "erpR" # depends on broken package rpanel-1.1-3 "ESKNN" # depends on broken package r-caret-6.0-52 "eulerian" # broken build "evobiR" # broken build "evolqg" # broken build "ExiMiR" # depends on broken package affyio-1.37.0 "exomeCopy" # depends on broken package Rsamtools-1.21.8 "ExomeDepth" # depends on broken package Rsamtools-1.21.8 "exomePeak" # depends on broken package Rsamtools-1.21.8 "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 "fabia" # broken build "facopy" # depends on broken package nlopt-2.4.2 "factDesign" # broken build "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 "fastLiquidAssociation" # depends on broken package LiquidAssociation-1.23.0 "fastR" # depends on broken package nlopt-2.4.2 "fastseg" # broken build "fdrDiscreteNull" # broken build "FDRreg" # depends on broken package nlopt-2.4.2 "FedData" # broken build "FEM" # build is broken "ffpe" # depends on broken package affyio-1.37.0 "FIACH" # broken build "FindMyFriends" # broken build "FISHalyseR" # broken build "flagme" # depends on broken package mzR-2.3.1 "flipflop" # broken build "flowBeads" # broken build "flowBin" # broken build "flowcatchR" # broken build "flowCHIC" # broken build "flowCL" # broken build "flowClean" # broken build "flowClust" # broken build "flowCore" # broken build "flowDensity" # depends on broken package nlopt-2.4.2 "flowFit" # broken build "flowFP" # broken build "flowMatch" # broken build "flowMeans" # broken build "flowMerge" # broken build "flowPeaks" # build is broken "flowQB" # broken build "flowQ" # build is broken "FlowSOM" # depends on broken package ConsensusClusterPlus-1.23.0 "flowStats" # depends on broken package ncdfFlow-2.15.2 "flowTrans" # broken build "flowType" # broken build "flowUtils" # broken build "flowViz" # broken build "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 "focalCall" # broken build "FourCSeq" # depends on broken package Rsamtools-1.21.8 "fPortfolio" # depends on broken package Rsymphony-0.1-20 "fracprolif" # broken build "FreeSortR" # broken build "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 "frmqa" # broken build "fscaret" # depends on broken package nlopt-2.4.2 "fulltext" # broken build "FunciSNP" # depends on broken package snpStats-1.19.0 "FunctionalNetworks" # Build Is Broken "fxregime" # depends on broken package nlopt-2.4.2 "gaga" # broken build "gage" # broken build "gaggle" # broken build "gamclass" # depends on broken package nlopt-2.4.2 "gamlss_demo" # depends on broken package rpanel-1.1-3 "gamm4" # depends on broken package nlopt-2.4.2 "gaucho" # broken build "gaussquad" # broken build "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 "GeneAnswers" # broken build "GENE_E" # depends on broken package rhdf5-2.13.1 "GeneExpressionSignature" # depends on broken package annaffy-1.41.1 "genefilter" # broken build "genefu" # broken build "GeneMeta" # broken build "GeneNetworkBuilder" # broken build "geneplotter" # broken build "geneRecommender" # broken build "GeneRegionScan" # broken build "geneRxCluster" # broken build "GeneSelectMMD" # broken build "GeneSelector" # broken build "GENESIS" # broken build "geNetClassifier" # broken build "GeneticTools" # depends on broken package snpStats-1.19.0 "genomation" # depends on broken package Rsamtools-1.21.8 "GenomeGraphs" # broken build "GenomeInfoDb" # broken build "genomeIntervals" # broken build "genomes" # broken build "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 "GenomicRanges" # broken build "GenomicTuples" # broken build "Genominator" # broken build "genoset" # broken build "genotypeeval" # depends on broken package r-rtracklayer-1.29.12 "GenoView" # depends on broken package Rsamtools-1.21.8 "genridge" # depends on broken package nlopt-2.4.2 "geojsonio" # depends on broken package V8-0.6 "GEOmetadb" # broken build "geomorph" # broken build "GEOquery" # broken build "GEOsearch" # broken build "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 "GExMap" # broken build "gfcanalysis" # broken build "GGBase" # depends on broken package snpStats-1.19.0 "ggbio" # depends on broken package Rsamtools-1.21.8 "GGtools" # depends on broken package snpStats-1.19.0 "ggtree" # broken build "gimme" # depends on broken package nlopt-2.4.2 "girafe" # depends on broken package Rsamtools-1.21.8 "gitter" # broken build "GlobalAncova" # broken build "globaltest" # broken build "gmapR" # depends on broken package Rsamtools-1.21.8 "gmatrix" # depends on broken package cudatoolkit-5.5.22 "gMCP" # build is broken "GOexpress" # broken build "GOFunction" # build is broken "GOGANPA" # depends on broken package WGCNA-1.47 "GoogleGenomics" # depends on broken package Rsamtools-1.21.8 "googlesheets" # broken build "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 "GOTHiC" # depends on broken package Rsamtools-1.21.8 "goTools" # build is broken "GPC" # broken build "gplm" # depends on broken package nlopt-2.4.2 "gputools" # depends on broken package cudatoolkit-5.5.22 "gQTLBase" # depends on broken package r-GenomicFiles-1.5.8 "gQTLstats" # depends on broken package snpStats-1.19.0 "gRain" # broken build "granova" # depends on broken package nlopt-2.4.2 "GraphAT" # broken build "graph" # broken build "gRapHD" # broken build "graphicalVAR" # depends on broken package nlopt-2.4.2 "graphite" # broken build "GraphPAC" # broken build "GraphPCA" # depends on broken package nlopt-2.4.2 "gRbase" # broken build "gRc" # broken build "GreyListChIP" # depends on broken package Rsamtools-1.21.8 "gridDebug" # broken build "gridGraphviz" # broken build "gRim" # broken build "groHMM" # depends on broken package Rsamtools-1.21.8 "GSAgm" # broken build "GSCA" # depends on broken package rhdf5-2.13.1 "GSEABase" # broken build "GSEAlm" # broken build "gsheet" # broken build "GSRI" # broken build "GSVA" # broken build "GUIDE" # depends on broken package rpanel-1.1-3 "GUIProfiler" # broken build "Guitar" # depends on broken package r-GenomicAlignments-1.5.18 "Gviz" # depends on broken package Rsamtools-1.21.8 "GWAF" # depends on broken package nlopt-2.4.2 "gwascat" # depends on broken package interactiveDisplayBase-1.7.0 "GWASTools" # broken build "h2o" # build is broken "h5" # build is broken "h5vc" # depends on broken package rhdf5-2.13.1 "hapFabia" # broken build "Harshlight" # depends on broken package affyio-1.37.0 "hasseDiagram" # broken build "hbsae" # depends on broken package nlopt-2.4.2 "HCsnip" # broken build "hddplot" # broken build "HELP" # broken build "HEM" # broken build "heplots" # depends on broken package nlopt-2.4.2 "hiAnnotator" # depends on broken package Rsamtools-1.21.8 "HiDimMaxStable" # broken build "hierGWAS" "HierO" # Build Is Broken "highriskzone" "HilbertCurve" # broken build "HilbertVisGUI" # Build Is Broken "HiPLARM" # Build Is Broken "hiReadsProcessor" # depends on broken package Rsamtools-1.21.8 "hisse" # broken build "HistDAWass" # depends on broken package nlopt-2.4.2 "HiTC" # depends on broken package Rsamtools-1.21.8 "HLMdiag" # depends on broken package nlopt-2.4.2 "HMMcopy" # broken build "hopach" # broken build "hpcwld" # broken build "hpoPlot" # broken build "HTqPCR" # depends on broken package affyio-1.37.0 "HTSanalyzeR" # depends on broken package Category-2.35.1 "HTSCluster" # broken build "HTSeqGenie" # depends on broken package Rsamtools-1.21.8 "htSeqTools" # depends on broken package Rsamtools-1.21.8 "HTSFilter" # broken build "hwwntest" # broken build "HybridMTest" # broken build "HydeNet" # broken build "hyperdraw" # broken build "hypergraph" # broken build "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 "iBMQ" # broken build "iccbeta" # depends on broken package nlopt-2.4.2 "IdeoViz" # depends on broken package Rsamtools-1.21.8 "idiogram" # broken build "IdMappingAnalysis" # broken build "IdMappingRetrieval" # broken build "idm" # broken build "ifaTools" # depends on broken package r-OpenMx-2.2.6 "iFes" # depends on broken package cudatoolkit-5.5.22 "imageHTS" # depends on broken package Category-2.35.1 "imager" # broken build "immer" # depends on broken package r-sirt-1.8-9 "immunoClust" # build is broken "imputeLCMD" # broken build "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 "InPAS" # depends on broken package Rsamtools-1.21.8 "inSilicoDb" # broken build "inSilicoMerging" # build is broken "INSPEcT" # depends on broken GenomicFeatures-1.21.13 "intansv" # depends on broken package Rsamtools-1.21.8 "IntegratedJM" # broken build "interactiveDisplayBase" # build is broken "interactiveDisplay" # depends on broken package Category-2.35.1 "interplot" # depends on broken arm-1.8-5 "ioncopy" # broken build "ionflows" # broken build "IONiseR" # depends on broken rhdf5-2.13.4 "iPAC" # broken build "iptools" "IRanges" # broken build "iRefR" # broken build "IsingFit" # depends on broken package nlopt-2.4.2 "isobar" # broken build "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 "iteRates" # broken build "iterativeBMA" # broken build "iterpc" # broken build "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 "jetset" "jmosaics" # broken build "joda" # depends on broken package nlopt-2.4.2 "jomo" # build is broken "js" # depends on broken package V8-0.6 "KANT" # depends on broken package affyio-1.37.0 "KCsmart" # broken build "kebabs" # broken build "KEGGgraph" # broken build "keggorthology" # build is broken "KEGGprofile" # Build Is Broken "KEGGREST" # broken build "KoNLP" # broken build "ktspair" # broken build "kza" # broken build "kzft" # broken build "lapmix" # broken build "lawn" # depends on broken package V8-0.6 "ldamatch" # broken build "ldblock" # depends on broken package r-snpStats-1.19.3 "leapp" # broken build "learnstats" # depends on broken package nlopt-2.4.2 "LedPred" # broken build "lefse" # build is broken "lessR" # depends on broken package nlopt-2.4.2 "lfe" # build is broken "lgcp" # depends on broken package rpanel-1.1-3 "limmaGUI" # depends on broken package affyio-1.37.0 "LinRegInteractive" # depends on broken package rpanel-1.1-3 "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 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package DirichletMultinomial-1.11.1 "MaxPro" # depends on broken package nlopt-2.4.2 "MazamaSpatialUtils" # broken build "MBASED" # broken build "mbest" # depends on broken package nlopt-2.4.2 "MBmca" # depends on broken nloptr-1.0.4 "mBPCR" # depends on broken package affyio-1.37.0 "mcaGUI" # depends on broken package Rsamtools-1.21.8 "MCRestimate" # build is broken "mdgsa" # build is broken "meboot" # depends on broken package nlopt-2.4.2 "medflex" # depends on broken package r-car-2.1-0 "mediation" # depends on broken package r-lme4-1.1-8 "MEDIPS" # depends on broken package Rsamtools-1.21.8 "MEDME" # depends on broken package nlopt-2.4.2 "MEET" # broken build "MEIGOR" # broken build "MEMSS" # depends on broken package nlopt-2.4.2 "MergeMaid" # broken build "merTools" # depends on broken package r-arm-1.8-6 "MeSHDbi" # broken build "meshr" # depends on broken package Category-2.35.1 "meta4diag" # broken build "metaArray" # broken build "Metab" # depends on broken package mzR-2.3.1 "metabolomics" # broken build "metabomxtr" # broken build "metacom" # broken build "MetaDE" # broken build "metagear" # build is broken "metagene" # depends on broken package Rsamtools-1.21.8 "metagenomeSeq" # broken build "MetaLandSim" # broken build "metaMix" # build is broken "metaMS" # depends on broken package mzR-2.3.1 "metaplus" # depends on broken package nlopt-2.4.2 "metaSEM" # depends on broken package OpenMx-2.2.4 "metaSeq" # broken build "metaseqR" # depends on broken package affyio-1.37.0 "Metatron" # depends on broken package nlopt-2.4.2 "metaX" # depends on broken package r-CAMERA-1.25.2 "MethTargetedNGS" # broken build "methVisual" # broken build "methyAnalysis" # depends on broken package affyio-1.37.0 "MethylAid" # depends on broken package Rsamtools-1.21.8 "methylMnM" # broken build "methylPipe" # depends on broken package Rsamtools-1.21.8 "MethylSeekR" # depends on broken package Rsamtools-1.21.8 "methylumi" # depends on broken package Rsamtools-1.21.8 "Mfuzz" # 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build "Pasha" # depends on broken package GenomicAlignments-1.5.12 "pathClass" # depends on broken package affyio-1.37.0 "pathRender" # build is broken "pathview" # build is broken "PatternClass" # build is broken "Pbase" # depends on broken package affyio-1.37.0 "pbdBASE" # depends on broken package pbdSLAP-0.2-0 "PBD" # broken build "pbdDEMO" # depends on broken package pbdSLAP-0.2-0 "pbdDMAT" # depends on broken package pbdSLAP-0.2-0 "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 "pcaBootPlot" # depends on broken FactoMineR-1.31.3 "pcaGoPromoter" # broken build "pcaL1" # build is broken "pcalg" # broken build "pcaMethods" # broken build "PCGSE" # broken build "pcot2" # broken build "PCpheno" # depends on broken package Category-2.35.1 "PCS" # broken build "pdInfoBuilder" # depends on broken package affyio-1.37.0 "pdmclass" # build is broken "PDQutils" # broken build "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 "PepPrep" # broken build "pepStat" # broken build "pequod" # depends on broken package nlopt-2.4.2 "PerfMeas" # broken build "permGPU" # build is broken "PGA" # depends on broken package Rsamtools-1.21.8 "PGSEA" # depends on broken package annaffy-1.41.1 "PharmacoGx" "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 "phreeqc" # broken build "phylocurve" # depends on broken package nlopt-2.4.2 "phyloseq" # broken build "phyloTop" # depends on broken package nlopt-2.4.2 "phytools" # broken build "piano" # broken build "PICS" # depends on broken package Rsamtools-1.21.8 "PING" # depends on broken package Rsamtools-1.21.8 "pkgDepTools" # broken build "plateCore" # depends on broken package ncdfFlow-2.15.2 "plethy" # broken build "plfMA" # broken build "plgem" # broken build "plier" # depends on broken package affyio-1.37.0 "PLPE" # broken build "plrs" # broken build "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 "pmclust" # build is broken "pmm" # depends on broken package nlopt-2.4.2 "podkat" # depends on broken package Rsamtools-1.21.8 "polyester" # broken build "Polyfit" # broken build "polynom" # broken build "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 "prada" # broken build "prebs" # depends on broken package affyio-1.37.0 "PREDA" # broken build "predictionet" # broken build "predictmeans" # depends on broken package 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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 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GOSemSim-1.27.3 "ReadqPCR" # depends on broken package affyio-1.37.0 "REBayes" # depends on broken package Rmosek-1.2.5.1 "reb" # broken build "recluster" # broken build "REDseq" # depends on broken package Rsamtools-1.21.8 "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 "refund_shiny" # depends on broken package r-refund-0.1-13 "regioneR" # depends on broken package Rsamtools-1.21.8 "regionReport" # depends on broken package Rsamtools-1.21.8 "regRSM" # broken build "repijson" # depends on broken package V8-0.6 "Repitools" # depends on broken package affyio-1.37.0 "ReportingTools" # depends on broken package Category-2.35.1 "ReQON" # depends on broken package Rsamtools-1.21.8 "rerddap" # broken build "REST" # depends on broken package nlopt-2.4.2 "rfPred" # depends on broken package Rsamtools-1.21.8 "rGADEM" 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"RMySQL" # broken build "RNAinteract" # depends on broken package Category-2.35.1 "RNAither" # depends on broken package nlopt-2.4.2 "RNAprobR" # depends on broken package Rsamtools-1.21.8 "rnaSeqMap" # depends on broken package Rsamtools-1.21.8 "RnaSeqSampleSize" # Build Is Broken "RnavGraph" # build is broken "RnBeads" # depends on broken package Rsamtools-1.21.8 "Rnits" # depends on broken package affyio-1.37.0 "rNOMADS" # broken build "roar" # depends on broken package Rsamtools-1.21.8 "RobLoxBioC" # depends on broken package affyio-1.37.0 "RobLox" # broken build "robustlmm" # depends on broken package nlopt-2.4.2 "rockchalk" # depends on broken package nlopt-2.4.2 "RockFab" # broken build "ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20 "Roleswitch" # broken build "Rolexa" # depends on broken package Rsamtools-1.21.8 "rols" # build is broken "ROntoTools" # broken build "ROracle" # Build Is Broken "RPA" # depends on broken package affyio-1.37.0 "rpanel" # build is broken "Rphylopars" # broken build "Rpoppler" # broken build "RPPanalyzer" # broken build "RpsiXML" # broken build "rpubchem" # depends on broken package nlopt-2.4.2 "Rqc" # depends on broken package Rsamtools-1.21.8 "RQuantLib" # build is broken "rqubic" # broken build "rr" # depends on broken package nlopt-2.4.2 "rRDP" # broken build "Rsamtools" # Build Is Broken "RSAP" # build is broken "rsbml" # build is broken "rscala" # build is broken "RSDA" # depends on broken package nlopt-2.4.2 "RSeed" # broken build "rSFFreader" # depends on broken package Rsamtools-1.21.8 "RStoolbox" # depends on broken package r-caret-6.0-52 "Rsubread" # Build Is Broken "RSVSim" # depends on broken package Rsamtools-1.21.8 "Rsymphony" # build is broken "rTableICC" # broken build "rTANDEM" # build is broken "RTCA" # broken build "RTCGA" # depends on broken package r-rvest-0.3.0 "RTN" # depends on broken package nlopt-2.4.2 "RTopper" # broken build "rtracklayer" # depends on broken package Rsamtools-1.21.8 "Rtreemix" # broken build "rTRM" # broken build "rTRMui" # depends on broken package Rsamtools-1.21.8 "rugarch" # depends on broken package nlopt-2.4.2 "rUnemploymentData" # broken build "RUVcorr" # build is broken "RUVnormalize" # Build Is Broken "RUVSeq" # depends on broken package Rsamtools-1.21.8 "RVAideMemoire" # depends on broken package nlopt-2.4.2 "rvest" # broken build "RVFam" # depends on broken package nlopt-2.4.2 "RVideoPoker" # depends on broken package rpanel-1.1-3 "RWebServices" # broken build "ryouready" # depends on broken package nlopt-2.4.2 "S4Vectors" # broken build "sadists" # broken build "safe" # broken build "SAGx" # broken build "sampleSelection" # depends on broken package nlopt-2.4.2 "sangerseqR" # broken build "sapFinder" # depends on broken package rTANDEM-1.9.0 "saps" # broken build "SCAN_UPC" # depends on broken package affyio-1.37.0 "ScISI" # depends on broken package apComplex-2.35.0 "scmamp" # broken build "scsR" # broken build "sdcMicro" # depends on broken package nlopt-2.4.2 "sdcMicroGUI" # depends on broken package nlopt-2.4.2 "SDD" # depends on broken package rpanel-1.1-3 "seeg" # depends on broken package nlopt-2.4.2 "segmentSeq" # depends on broken package Rsamtools-1.21.8 "sejmRP" # depends on broken package r-rvest-0.3.0 "Sejong" # broken build "SELEX" # broken build "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 "SensMixed" # depends on broken package r-lme4-1.1-9 "SensoMineR" # depends on broken package nlopt-2.4.2 "SEPA" # depends on broken package topGO-2.21.0 "seq2pathway" # depends on broken package WGCNA-1.47 "SeqArray" # depends on broken package Rsamtools-1.21.8 "seqbias" # depends on broken package Rsamtools-1.21.8 "seqCNA" # build is broken "SeqFeatR" # broken build "SeqGrapheR" # Build Is Broken "SeqGSEA" # broken build "seqPattern" # broken build "seqplots" # depends on broken package Rsamtools-1.21.8 "seqTools" # build is broken "sequenza" # broken build "SeqVarTools" # depends on broken package Rsamtools-1.21.8 "SGSeq" # depends on broken package Rsamtools-1.21.8 "SharpeR" # broken build "shinyMethyl" # depends on broken package Rsamtools-1.21.8 "shinyTANDEM" # depends on broken package rTANDEM-1.9.0 "ShortRead" # depends on broken package Rsamtools-1.21.8 "SID" # broken build "sigaR" # broken build "SigCheck" # broken build "SigFuge" # broken build "siggenes" # broken build "sigsquared" # broken build "SigTree" # broken build "SIMAT" # depends on broken package mzR-2.3.1 "SimBindProfiles" # depends on broken package affyio-1.37.0 "SIM" # broken build "similaRpeak" # depends on broken package Rsamtools-1.21.8 "simpleaffy" # depends on broken package affyio-1.37.0 "simPop" # depends on broken package r-VIM-4.4.1 "SimRAD" # depends on broken package Rsamtools-1.21.8 "SimReg" # broken build "simulatorZ" # broken build "sirt" # depends on broken package nlopt-2.4.2 "SJava" # broken build "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 "smacof" # broken build "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 "snplist" # broken build "snpStats" # build is broken "snpStatsWriter" # depends on broken package snpStats-1.19.0 "SNPtools" # depends on broken package Rsamtools-1.21.8 "SOD" # depends on broken package cudatoolkit-5.5.22 "soGGi" # depends on broken package Rsamtools-1.21.8 "soilphysics" # depends on broken package rpanel-1.1-3 "SomatiCA" # broken build "SomaticSignatures" # depends on broken package Rsamtools-1.21.8 "sortinghat" # broken build "SoyNAM" # depends on broken package r-lme4-1.1-8 "SpacePAC" # broken build "spacom" # depends on broken package nlopt-2.4.2 "spade" # broken build "spdynmod" # broken build "specificity" # depends on broken package nlopt-2.4.2 "SpeCond" # broken build "SPEM" # broken build "SPIA" # broken build "spkTools" # broken build "splicegear" # broken build "spliceR" # depends on broken package Rsamtools-1.21.8 "spliceSites" # broken build "SplicingGraphs" # depends on broken package Rsamtools-1.21.8 "spocc" # depends on broken package V8-0.6 "spoccutils" # depends on broken spocc-0.3.0 "spsann" # depends on broken package r-pedometrics-0.6-2 "SRAdb" # broken build "srd" # broken build "sscore" # depends on broken package affyio-1.37.0 "ssizeRNA" # broken build "ssmrob" # depends on broken package nlopt-2.4.2 "ssviz" # depends on broken package Rsamtools-1.21.8 "stagePop" # depends on broken package PBSddesolve-1.11.29 "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 "Statomica" # broken build "stcm" # depends on broken package nlopt-2.4.2 "stepp" # depends on broken package nlopt-2.4.2 "stepwiseCM" # broken build "stream" # broken build "Streamer" # broken build "streamMOA" # broken build "stringgaussnet" # build is broken "structSSI" # broken build "strum" # broken build "SummarizedExperiment" # broken build "superbiclust" # broken build "Surrogate" # depends on broken package nlopt-2.4.2 "Sushi" # broken build "sva" # broken build "SVM2CRM" # depends on broken package Rsamtools-1.21.8 "sybilSBML" # build is broken "synapter" # depends on broken package affyio-1.37.0 "systemfit" # depends on broken package nlopt-2.4.2 "systemPipeRdata" # broken build "systemPipeR" # depends on broken package AnnotationForge-1.11.3 "TargetSearch" # depends on broken package mzR-2.3.1 "TCC" # broken build "TCGA2STAT" # broken build "TCGAbiolinks" # depends on broken package r-affy-1.47.1 "TcGSA" # depends on broken package nlopt-2.4.2 "TDARACNE" # broken build "TDMR" # depends on broken package nlopt-2.4.2 "TED" # broken build "TEQC" # depends on broken package Rsamtools-1.21.8 "TFBSTools" # depends on broken package DirichletMultinomial-1.11.1 "tigerstats" # depends on broken package nlopt-2.4.2 "tigre" # broken build "tilingArray" # depends on broken package affyio-1.37.0 "timecourse" # broken build "timeSeq" # broken build "TIN" # depends on broken package WGCNA-1.47 "TitanCNA" # depends on broken package Rsamtools-1.21.8 "TKF" # broken build "tmle" # broken build "tnam" # depends on broken package r-lme4-1.1-9 "ToPASeq" # depends on broken package Rsamtools-1.21.8 "topGO" # build is broken "topologyGSA" # depends on broken package Rsamtools-1.21.8 "TPP" # broken build "tracktables" # depends on broken package Rsamtools-1.21.8 "trackViewer" # depends on broken package Rsamtools-1.21.8 "translateSPSS2R" # depends on broken car-2.0-25 "tRanslatome" # depends on broken package GOSemSim-1.27.3 "TransView" # depends on broken package Rsamtools-1.21.8 "traseR" "triform" # broken build "trigger" # broken build "TriMatch" # depends on broken package nlopt-2.4.2 "triplex" # broken build "TROM" # depends on broken package topGO-2.21.0 "TRONCO" # broken build "TSdist" # broken build "TSMySQL" # broken build "tsoutliers" # broken build "tspair" # broken build "TSSi" # broken build "ttScreening" # broken build "TurboNorm" # depends on broken package affyio-1.37.0 "tweeDEseq" # broken build "twilight" # broken build "UBCRM" # broken build "umx" # depends on broken package r-OpenMx-2.2.6 "UNDO" # broken build "unifiedWMWqPCR" # depends on broken package affyio-1.37.0 "uniftest" # broken build "UniProt_ws" # broken build "untb" # broken build "userfriendlyscience" # depends on broken package nlopt-2.4.2 "V8" # build is broken "VanillaICE" # depends on broken package affyio-1.37.0 "varComp" # depends on broken package r-lme4-1.1-9 "variancePartition" # depends on broken package lme4-1.1-8 "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 "VBmix" # broken build "VegaMC" # broken build "VIM" # depends on broken package nlopt-2.4.2 "VIMGUI" # depends on broken package nlopt-2.4.2 "viper" # broken build "vmsbase" # depends on broken package PBSmapping-2.69.76 "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 "wavClusteR" # depends on broken package Rsamtools-1.21.8 "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 "wikipediatrend" # broken build "XBSeq" # broken build "xcms" # depends on broken package mzR-2.3.1 "XDE" # broken build "x_ent" # broken build "xergm" # depends on broken package nlopt-2.4.2 "xps" # build is broken "XVector" # broken build "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: { stringi = old.stringi.overrideDerivation (attrs: { postInstall = let icuName = "icudt52l"; icuSrc = pkgs.fetchzip { url = "http://static.rexamine.com/packages/${icuName}.zip"; sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj"; stripRoot = false; }; in '' ${attrs.postInstall or ""} cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs ''; }); xml2 = old.xml2.overrideDerivation (attrs: { preConfigure = '' export LIBXML_INCDIR=${pkgs.libxml2}/include/libxml2 patchShebangs configure ''; }); curl = old.curl.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); iFes = old.iFes.overrideDerivation (attrs: { 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.xorg.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 = "${pkgs.cudatoolkit}/include"; }); # It seems that we cannot override meta attributes with overrideDerivation. rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: { patches = [ ./patches/rpud.patch ]; CUDA_HOME = "${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