/* 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; inherit (pkgs.darwin.apple_sdk.frameworks) Cocoa Foundation; inherit (pkgs) gettext gfortran; }; # 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}: args: # XXX: not ideal ("2.2" would match "2.22") but sufficient assert (!(args ? rVersion) || lib.hasPrefix args.rVersion (lib.getVersion R)); 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 (args // { inherit name version; }); }; inherit doCheck requireX; propagatedBuildInputs = depends; nativeBuildInputs = depends; meta.homepage = mkHomepage (args // { inherit name; }); meta.platforms = R.meta.platforms; meta.hydraPlatforms = hydraPlatforms; meta.broken = broken; }); # Templates for generating Bioconductor, CRAN and IRkernel packages # from the name, version, sha256, and optional per-package arguments above # deriveBioc = mkDerive { mkHomepage = {name, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html"; mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ]; }; deriveBiocAnn = mkDerive { mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html"; mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ]; }; deriveBiocExp = mkDerive { mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html"; mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ]; }; deriveCran = mkDerive { mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/"; mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ]; }; deriveIRkernel = mkDerive { mkHomepage = {name}: "https://irkernel.github.io/"; mkUrls = {name, version}: [ "http://irkernel.github.io/src/contrib/${name}_${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 ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } // import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } // import ./cran-packages.nix { inherit self; derive = deriveCran; } // import ./irkernel-packages.nix { inherit self; derive = deriveIRkernel; }; # tweaks for the individual packages and "in self" follow packagesWithRDepends = { FactoMineR = [ self.car ]; pander = [ self.codetools ]; }; packagesWithNativeBuildInputs = { abn = [ pkgs.gsl_1 ]; adimpro = [ pkgs.imagemagick ]; audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl_1 ]; BayesVarSel = [ pkgs.gsl_1 ]; BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ]; bigGP = [ pkgs.openmpi ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; bnpmr = [ pkgs.gsl_1 ]; BNSP = [ pkgs.gsl_1 ]; cairoDevice = [ pkgs.gtk2.dev ]; Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ]; Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw ]; ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; cit = [ pkgs.gsl_1 ]; curl = [ pkgs.curl.dev ]; devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ]; diversitree = [ pkgs.gsl_1 pkgs.fftw ]; EMCluster = [ pkgs.liblapack ]; fftw = [ pkgs.fftw.dev ]; fftwtools = [ pkgs.fftw.dev ]; Formula = [ pkgs.gmp ]; geoCount = [ pkgs.gsl_1 ]; git2r = [ pkgs.zlib.dev pkgs.openssl.dev ]; GLAD = [ pkgs.gsl_1 ]; glpkAPI = [ pkgs.gmp pkgs.glpk ]; gmp = [ pkgs.gmp.dev ]; graphscan = [ pkgs.gsl_1 ]; gsl = [ pkgs.gsl_1 ]; h5 = [ pkgs.hdf5-cpp pkgs.which ]; h5vc = [ pkgs.zlib.dev ]; HiCseg = [ pkgs.gsl_1 ]; iBMQ = [ pkgs.gsl_1 ]; igraph = [ pkgs.gmp ]; JavaGD = [ pkgs.jdk ]; jpeg = [ pkgs.libjpeg.dev ]; KFKSDS = [ pkgs.gsl_1 ]; kza = [ pkgs.fftw.dev ]; libamtrack = [ pkgs.gsl_1 ]; mixcat = [ pkgs.gsl_1 ]; mvabund = [ pkgs.gsl_1 ]; mwaved = [ pkgs.fftw.dev ]; ncdf4 = [ pkgs.netcdf ]; nloptr = [ pkgs.nlopt ]; openssl = [ pkgs.openssl.dev ]; outbreaker = [ pkgs.gsl_1 ]; pander = [ pkgs.pandoc pkgs.which ]; pbdMPI = [ pkgs.openmpi ]; pbdNCDF4 = [ pkgs.netcdf ]; pbdPROF = [ pkgs.openmpi ]; PKI = [ pkgs.openssl.dev ]; png = [ pkgs.libpng.dev ]; PopGenome = [ pkgs.zlib.dev ]; proj4 = [ pkgs.proj ]; qtbase = [ pkgs.qt4 ]; qtpaint = [ pkgs.qt4 ]; R2GUESS = [ pkgs.gsl_1 ]; R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; RAppArmor = [ pkgs.libapparmor ]; rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; rbamtools = [ pkgs.zlib.dev ]; rcdd = [ pkgs.gmp.dev ]; RcppCNPy = [ pkgs.zlib.dev ]; RcppGSL = [ pkgs.gsl_1 ]; RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.octave ]; RcppZiggurat = [ pkgs.gsl_1 ]; rgdal = [ pkgs.proj pkgs.gdal ]; rgeos = [ pkgs.geos ]; rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ]; rgl = [ pkgs.mesa pkgs.xlibsWrapper ]; Rglpk = [ pkgs.glpk ]; RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; Rhtslib = [ pkgs.zlib.dev ]; RJaCGH = [ pkgs.zlib.dev ]; rjags = [ pkgs.jags ]; rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; Rlibeemd = [ pkgs.gsl_1 ]; rmatio = [ pkgs.zlib.dev ]; Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ]; 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.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ]; Rpoppler = [ pkgs.poppler ]; RPostgreSQL = [ pkgs.postgresql ]; RProtoBuf = [ pkgs.protobuf ]; 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.dev pkgs.libsndfile.dev ]; seqinr = [ pkgs.zlib ]; seqminer = [ pkgs.zlib pkgs.bzip2 ]; showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ]; simplexreg = [ pkgs.gsl_1 ]; SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h spate = [ pkgs.fftw ]; sprint = [ pkgs.openmpi ]; ssanv = [ pkgs.proj ]; stsm = [ pkgs.gsl_1 ]; stringi = [ pkgs.icu.dev ]; survSNP = [ pkgs.gsl_1 ]; sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; TAQMNGR = [ pkgs.zlib ]; tiff = [ pkgs.libtiff ]; TKF = [ pkgs.gsl_1 ]; tkrplot = [ pkgs.xorg.libX11 ]; topicmodels = [ pkgs.gsl_1 ]; udunits2 = [ pkgs.udunits pkgs.expat ]; V8 = [ pkgs.v8 ]; VBLPCM = [ pkgs.gsl_1 ]; VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ]; WhopGenome = [ pkgs.zlib ]; XBRL = [ pkgs.zlib pkgs.libxml2 ]; xml2 = [ pkgs.libxml2 ]; XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; affyPLM = [ pkgs.zlib ]; bamsignals = [ pkgs.zlib ]; BitSeq = [ pkgs.zlib ]; DiffBind = [ pkgs.zlib ]; ShortRead = [ pkgs.zlib.dev ]; oligo = [ pkgs.zlib ]; gmapR = [ pkgs.zlib ]; Rsubread = [ pkgs.zlib ]; XVector = [ pkgs.zlib.dev ]; Rsamtools = [ pkgs.zlib.dev ]; rtracklayer = [ pkgs.zlib ]; affyio = [ pkgs.zlib ]; VariantAnnotation = [ pkgs.zlib ]; snpStats = [ pkgs.zlib ]; }; 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 ]; RCurl = [ pkgs.curl.dev ]; 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.combined.scheme-medium ]; rPython = [ pkgs.which ]; gridGraphics = [ pkgs.which ]; gputools = [ 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 ]; mzR = [ pkgs.netcdf ]; }; 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" "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" "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 = [ "TED" # depends on broken package animation "streamMOA" # depends on broken package animation "stream" # depends on broken package animation "spdynmod" # depends on broken package animation "treeplyr" # depends on broken package animation "recluster" # depends on broken package animation "geomorph" # depends on broken package animation "phytools" # depends on broken package animation "animation" # broken build "srd" # broken build "paleotree" # broken build "ndtv" # broken build "mvMORPH" # broken build "mptools" # broken build "monogeneaGM" # broken build "molaR" # broken build "idm" # broken build "hisse" # broken build "gfcanalysis" # broken build "evolqg" # broken build "evobiR" # broken build "convevol" # broken build "bayou" # broken build "anim_plots" # broken build "TKF" # broken build "Rphylopars" # broken build "RAM" # broken build "PhySortR" # broken build "MonoPhy" # broken build "Momocs" # broken build "Evomorph" # broken build "PBD" # depends on broken package DDD "DDD" # broken build "BMhyd" # broken build "rscala" # broken build "rgpui" # depends on broken package rgp "rgp" # broken build "qcmetrics" # broken build "lfe" # broken build "interactiveDisplay" # depends on broken package interactiveDisplayBase "RefNet" # depends on broken package interactiveDisplayBase "pwOmics" # depends on broken package interactiveDisplayBase "grasp2db" # depends on broken package interactiveDisplayBase "EnsDb_Rnorvegicus_v79" # depends on broken package interactiveDisplayBase "EnsDb_Rnorvegicus_v75" # depends on broken package interactiveDisplayBase "EnsDb_Mmusculus_v79" # depends on broken package interactiveDisplayBase "EnsDb_Mmusculus_v75" # depends on broken package interactiveDisplayBase "EnsDb_Hsapiens_v79" # depends on broken package interactiveDisplayBase "EnsDb_Hsapiens_v75" # depends on broken package interactiveDisplayBase "ensembldb" # depends on broken package interactiveDisplayBase "AnnotationHubData" # depends on broken package interactiveDisplayBase "AnnotationHub" # depends on broken package interactiveDisplayBase "interactiveDisplayBase" # broken build "h2o" # broken build "funModeling" # broken build "brr" # broken build "bedr" # broken build "Sabermetrics" # broken build "RKEEL" # depends on broken package RKEELjars "RKEELjars" # broken build "RapidPolygonLookup" # depends on broken package PBSmapping "PBSmapping" # broken build "stagePop" # depends on broken package PBSddesolve "PBSddesolve" # broken build "Metab" # broken build "Crossover" # broken build "CardinalWorkflows" # broken build "spoccutils" # depends on broken package spocc "mapr" # depends on broken package spocc "vmsbase" # broken build "vcfR" # broken build "strataG" # broken build "SSDM" # broken build "SimInf" # broken build "shazam" # broken build "rsvg" # broken build "Rothermel" # broken build "rfPermute" # broken build "redland" # broken build "RAppArmor" # broken build "permGPU" # broken build "pdftools" # broken build "OceanView" # broken build "MSeasyTkGUI" # broken build "mrMLM" # broken build "MonetDBLite" # broken build "MixGHD" # broken build "LCMCR" # broken build "hunspell" # broken build "googleformr" # broken build "ggseas" # depends on broken package x13binary "seasonal" # depends on broken package x13binary "gunsales" # depends on broken package x13binary "x13binary" # broken build "fds" # broken build "exifr" # broken build "rite" # depends on broken package euroMix "MBCB" # depends on broken package euroMix "forensim" # depends on broken package euroMix "dynBiplotGUI" # depends on broken package euroMix "cncaGUI" # depends on broken package euroMix "biplotbootGUI" # depends on broken package euroMix "AnthropMMD" # depends on broken package euroMix "ilc" # depends on broken package demography "demography" # broken build "webbioc" # depends on broken package limma "davidTiling" # depends on broken package limma "tilingArray" # depends on broken package limma "NAPPA" # depends on broken package limma "NanoStringNorm" # depends on broken package limma "synapterdata" # depends on broken package limma "synapter" # depends on broken package limma "RforProteomics" # depends on broken package limma "pRolocdata" # depends on broken package limma "ProCoNA" # depends on broken package limma "Pbase" # depends on broken package limma "MSnID" # depends on broken package limma "msmsEDA" # depends on broken package limma "MSnbase" # depends on broken package limma "staRank" # depends on broken package limma "phenoDist" # depends on broken package limma "imageHTS" # depends on broken package limma "Mulder2012" # depends on broken package limma "HTSanalyzeR" # depends on broken package limma "gespeR" # depends on broken package limma "cellHTS2" # depends on broken package limma "affyPara" # depends on broken package limma "vsn" # depends on broken package limma "ttScreening" # depends on broken package limma "metaX" # depends on broken package limma "SSPA" # depends on broken package limma "SQDA" # depends on broken package limma "ADaCGH2" # depends on broken package limma "snapCGH" # depends on broken package limma "Shrinkage" # depends on broken package limma "SafeQuant" # depends on broken package limma "RTopper" # depends on broken package limma "RTCGAToolbox" # depends on broken package limma "RPPanalyzer" # depends on broken package limma "Rnits" # depends on broken package limma "RNAinteractMAPK" # depends on broken package limma "RNAinteract" # depends on broken package limma "SimBindProfiles" # depends on broken package limma "ccTutorial" # depends on broken package limma "Ringo" # depends on broken package limma "rCGH" # depends on broken package limma "qusage" # depends on broken package limma "qpcrNorm" # depends on broken package limma "prot2D" # depends on broken package limma "polyester" # depends on broken package limma "plmDE" # depends on broken package limma "phenoTest" # depends on broken package limma "RANKS" # depends on broken package limma "PerfMeas" # depends on broken package limma "pepStat" # depends on broken package limma "PECA" # depends on broken package limma "PADOG" # depends on broken package limma "OGSA" # depends on broken package limma "nethet" # depends on broken package limma "lpNet" # depends on broken package limma "nem" # depends on broken package limma "monocle" # depends on broken package limma "MmPalateMiRNA" # depends on broken package limma "miRtest" # depends on broken package limma "miRLAB" # depends on broken package limma "mGSZ" # depends on broken package limma "MAMA" # depends on broken package limma "metaMA" # depends on broken package limma "msd16s" # depends on broken package limma "metagenomeSeq" # depends on broken package limma "metabolomics" # depends on broken package limma "maSigPro" # depends on broken package limma "timecourse" # depends on broken package limma "stepNorm" # depends on broken package limma "RBM" # depends on broken package limma "saps" # depends on broken package limma "PharmacoGx" # depends on broken package limma "piano" # depends on broken package limma "OLINgui" # depends on broken package limma "OLIN" # depends on broken package limma "nnNorm" # depends on broken package limma "ListerEtAlBSseq" # depends on broken package limma "compEpiTools" # depends on broken package limma "methylPipe" # depends on broken package limma "dyebiasexamples" # depends on broken package limma "dyebias" # depends on broken package limma "CluMix" # depends on broken package limma "HCsnip" # depends on broken package limma "sigaR" # depends on broken package limma "plrs" # depends on broken package limma "CGHregions" # depends on broken package limma "QDNAseq_mm10" # depends on broken package limma "QDNAseq_hg19" # depends on broken package limma "QDNAseq" # depends on broken package limma "GeneBreak" # depends on broken package limma "focalCall" # depends on broken package limma "CGHnormaliter" # depends on broken package limma "CGHcall" # depends on broken package limma "CGHbase" # depends on broken package limma "beta7" # depends on broken package limma "marray" # depends on broken package limma "LVSmiRNA" # depends on broken package limma "lmdme" # depends on broken package limma "limmaGUI" # depends on broken package limma "InPAS" # depends on broken package limma "iChip" # depends on broken package limma "unifiedWMWqPCR" # depends on broken package limma "nondetects" # depends on broken package limma "HTqPCR" # depends on broken package limma "HD2013SGI" # depends on broken package limma "vtpnet" # depends on broken package limma "gwascat" # depends on broken package limma "gQTLstats" # depends on broken package limma "GOsummaries" # depends on broken package limma "yri1kgv" # depends on broken package limma "hmyriB36" # depends on broken package limma "cheung2010" # depends on broken package limma "GGtools" # depends on broken package limma "GGdata" # depends on broken package limma "encoDnaseI" # depends on broken package limma "dsQTL" # depends on broken package limma "ceuhm3" # depends on broken package limma "ceu1kgv" # depends on broken package limma "ceu1kg" # depends on broken package limma "GGBase" # depends on broken package limma "GeneSelector" # depends on broken package limma "GeneSelectMMD" # depends on broken package limma "gCMAPWeb" # depends on broken package limma "gCMAP" # depends on broken package limma "flowBin" # depends on broken package limma "Fletcher2013a" # depends on broken package limma "FEM" # depends on broken package limma "explorase" # depends on broken package limma "ExiMiR" # depends on broken package limma "tweeDEseq" # depends on broken package limma "tRanslatome" # depends on broken package limma "ToPASeq" # depends on broken package limma "timeSeq" # depends on broken package limma "TCGAbiolinks" # depends on broken package limma "TCC" # depends on broken package limma "systemPipeR" # depends on broken package limma "STATegRa" # depends on broken package limma "ssizeRNA" # depends on broken package limma "RUVSeq" # depends on broken package limma "RnaSeqSampleSizeData" # depends on broken package limma "RnaSeqSampleSize" # depends on broken package limma "rnaSeqMap" # depends on broken package limma "ReportingTools" # depends on broken package limma "QuasiSeq" # depends on broken package limma "PROPER" # depends on broken package limma "myTAI" # depends on broken package limma "msmsTests" # depends on broken package limma "methylMnM" # depends on broken package limma "metaseqR" # depends on broken package limma "MEDIPS" # depends on broken package limma "manta" # depends on broken package limma "HTSFilter" # depends on broken package limma "HTSCluster" # depends on broken package limma "GSAgm" # depends on broken package limma "fdrDiscreteNull" # depends on broken package limma "erccdashboard" # depends on broken package limma "EnrichmentBrowser" # depends on broken package limma "edgeRun" # depends on broken package limma "EDDA" # depends on broken package limma "RnaSeqTutorial" # depends on broken package limma "easyRNASeq" # depends on broken package limma "DEGreport" # depends on broken package limma "Imetagene" # depends on broken package limma "metagene" # depends on broken package limma "DBChIP" # depends on broken package limma "babel" # depends on broken package limma "apmsWAPP" # depends on broken package limma "ampliQueso" # depends on broken package limma "edgeR" # depends on broken package limma "MMDiff" # depends on broken package limma "ChIPQC" # depends on broken package limma "DiffBind" # depends on broken package limma "DCGL" # depends on broken package limma "Prostar" # depends on broken package limma "DAPAR" # depends on broken package limma "DAAGbio" # depends on broken package limma "csaw" # depends on broken package limma "cp4p" # depends on broken package limma "coRNAi" # depends on broken package limma "Cormotif" # depends on broken package limma "CORM" # depends on broken package limma "TurboNorm" # depends on broken package limma "maigesPack" # depends on broken package limma "convert" # depends on broken package limma "compcodeR" # depends on broken package limma "codelink" # depends on broken package limma "clippda" # depends on broken package limma "REDseq" # depends on broken package limma "GUIDEseq" # depends on broken package limma "ggtut" # depends on broken package limma "FunciSNP" # depends on broken package limma "ChIPpeakAnno" # depends on broken package limma "ChIPComp" # depends on broken package limma "ChimpHumanBrainData" # depends on broken package limma "charmData" # depends on broken package limma "charm" # depends on broken package limma "cghMCR" # depends on broken package limma "CCl4" # depends on broken package limma "casper" # depends on broken package limma "CancerMutationAnalysis" # depends on broken package limma "CALIB" # depends on broken package limma "quantro" # depends on broken package limma "RnBeads" # depends on broken package limma "mvoutData" # depends on broken package limma "MineICA" # depends on broken package limma "methyAnalysis" # depends on broken package limma "MAQCsubsetILM" # depends on broken package limma "MAQCsubset" # depends on broken package limma "lumiRatIDMapping" # depends on broken package limma "lumiMouseIDMapping" # depends on broken package limma "lumiHumanIDMapping" # depends on broken package limma "lumiBarnes" # depends on broken package limma "iCheck" # depends on broken package limma "ffpeExampleData" # depends on broken package limma "arrayMvout" # depends on broken package limma "lumi" # depends on broken package limma "ffpe" # depends on broken package limma "methylumi" # depends on broken package limma "shinyMethyl" # depends on broken package limma "MethylAidData" # depends on broken package limma "MethylAid" # depends on broken package limma "IlluminaHumanMethylation450kmanifest" # depends on broken package limma "skewr" # depends on broken package limma "wateRmelon" # depends on broken package limma "missMethyl" # depends on broken package limma "minfiData" # depends on broken package limma "IlluminaHumanMethylation450kanno_ilmn12_hg19" # depends on broken package limma "IlluminaHumanMethylation27kmanifest" # depends on broken package limma "FlowSorted_DLPFC_450k" # depends on broken package limma "FlowSorted_Blood_450k" # depends on broken package limma "ENmix" # depends on broken package limma "ELMER" # depends on broken package limma "MEAL" # depends on broken package limma "DMRcate" # depends on broken package limma "CopyNumber450kData" # depends on broken package limma "CopyNumber450k" # depends on broken package limma "conumee" # depends on broken package limma "ChAMP" # depends on broken package limma "minfi" # depends on broken package limma "regionReport" # depends on broken package limma "derfinderPlot" # depends on broken package limma "derfinder" # depends on broken package limma "bumphunter" # depends on broken package limma "birta" # depends on broken package limma "betr" # depends on broken package limma "beadarrayMSV" # depends on broken package limma "RobLoxBioC" # depends on broken package limma "maGUI" # depends on broken package limma "epigenomix" # depends on broken package limma "blima" # depends on broken package limma "BeadArrayUseCases" # depends on broken package limma "beadarrayFilter" # depends on broken package limma "beadarrayExampleData" # depends on broken package limma "beadarray" # depends on broken package limma "ballgown" # depends on broken package limma "attract" # depends on broken package limma "ArrayTools" # depends on broken package limma "arrayQuality" # depends on broken package limma "DrugVsDisease" # depends on broken package limma "ArrayExpress" # depends on broken package limma "oneChannelGUI" # depends on broken package limma "affylmGUI" # depends on broken package limma "AffyExpress" # depends on broken package limma "AgiMicroRna" # depends on broken package limma "affycoretools" # depends on broken package limma "ABSSeq" # depends on broken package limma "a4" # depends on broken package limma "a4Base" # depends on broken package limma "limma" # broken build "TransView" # broken build "Starr" # broken build "SICtools" # broken build "ReQON" # depends on broken package seqbias "seqbias" # broken build "Repitools" # broken build "QuasR" # broken build "qrqc" # broken build "ProteomicsAnnotationHubData" # broken build "podkat" # broken build "PING" # depends on broken package PICS "PICS" # broken build "mcaGUI" # broken build "deepSNV" # broken build "motifbreakR" # depends on broken package MotIV "LowMACA" # depends on broken package MotIV "dagLogo" # depends on broken package MotIV "motifStack" # depends on broken package MotIV "MotIV" # broken build "CNEr" # broken build "canceR" # broken build "BubbleTree" # broken build "arrayQualityMetrics" # broken build "ArrayExpressHTS" # broken build "TargetSearchData" # depends on broken package TargetSearch "TargetSearch" # broken build "ptw" # depends on broken package nloptr "gpuR" # broken build "erma" # broken build "MBmca" # depends on broken package chipPCR "dpcR" # depends on broken package chipPCR "chipPCR" # broken build "alsace" # broken build "rrlda" # depends on broken package VIM "qrfactor" # depends on broken package VIM "MVN" # depends on broken package VIM "mvoutlier" # depends on broken package VIM "robCompositions" # depends on broken package VIM "DiagrammeRsvg" # depends on broken package V8 "dagitty" # depends on broken package V8 "remoter" # depends on broken package sodium "Fletcher2013b" # depends on broken package RTN "apaStyle" # depends on broken package ReporteRs "categoryCompare" # depends on broken package RCytoscape "preseqR" # depends on broken package polynom "permutations" # depends on broken package partitions "GLMMRR" # depends on broken package lme4 "replicationInterval" # depends on broken package lme4 "GWASdata" # depends on broken package GWASTools "EnsemblePCReg" # depends on broken package EnsembleBase "EnsembleCV" # depends on broken package EnsembleBase "cpgen" # depends on broken package pedigreemm "mitml" # depends on broken package jomo "IlluminaHumanMethylation450k_db" # broken build "gahgu95ecdf" # broken build "gahgu95dcdf" # broken build "gahgu95ccdf" # broken build "gahgu95bcdf" # broken build "gahgu95av2cdf" # broken build "PREDAsampledata" # depends on broken package gahgu133plus2cdf "gahgu133plus2cdf" # broken build "gahgu133bcdf" # broken build "gahgu133acdf" # broken build "annmap" # depends on broken package RMySQL "choroplethr" # depends on broken package acs "acs" # broken build "spray" # depends on broken package partitions "CNVrd2" # broken build "proteoQC" # depends on broken package rTANDEM "PGA" # depends on broken package rTANDEM "MBESS" # depends on broken package OpenMx "DOQTL" # depends on broken package rhdf5 "DmelSGI" # depends on broken package rhdf5 "flowDiv" # depends on broken package ncdfFlow "ChemmineDrugs" # depends on broken package ChemmineR "stpm" # depends on broken package nloptr "sjmisc" # depends on broken package nloptr "rstanarm" # depends on broken package nloptr "glmmsr" # depends on broken package nloptr "FDboost" # depends on broken package nloptr "faraway" # depends on broken package nloptr "interplot" # depends on broken package nloptr "VSE" # depends on broken package car "VARSEDIG" # depends on broken package car "translateSPSS2R" # depends on broken package car "tadaatoolbox" # depends on broken package car "lavaan_shiny" # depends on broken package car "RcmdrPlugin_GWRM" # depends on broken package car "TextoMineR" # depends on broken package car "pcaBootPlot" # depends on broken package car "ClustGeo" # depends on broken package car "preproviz" # depends on broken package car "hsdar" # depends on broken package car "DecisionCurve" # depends on broken package car "CONDOP" # depends on broken package car "EnsemblePenReg" # depends on broken package car "EnsembleBase" # depends on broken package car "fullfact" # depends on broken package car "clusterSEs" # depends on broken package car "ggiraph" # depends on broken package gdtools "rvg" # depends on broken package gdtools "ggpmisc" # depends on broken package polynom "mlt_docreg" # depends on broken package polynom "mlt" # depends on broken package polynom "basefun" # depends on broken package polynom "rtable" # depends on broken package ReporteRs "Mediana" # depends on broken package ReporteRs "ReporteRs" # broken build "abd" # depends on broken package nlopt "adabag" # depends on broken package nlopt "adhoc" # broken build "AER" # depends on broken package nlopt "afex" # depends on broken package nlopt "agRee" # depends on broken package nlopt "aLFQ" # depends on broken package nlopt "algstat" # broken build "alr3" # depends on broken package nlopt "alr4" # depends on broken package nlopt "alsace" # depends on broken nloptr "anacor" # depends on broken package nlopt "aods3" # depends on broken package nlopt "apaTables" # depends on broken package car "apt" # depends on broken package nlopt "ArfimaMLM" # depends on broken package nlopt "arm" # depends on broken package nlopt "ART" # depends on broken package car "ARTool" # depends on broken package nlopt "AssetPricing" # broken build "AtelieR" # broken build "auRoc" # depends on broken package MBESS "AutoModel" # depends on broken package car "bamdit" # broken build "bapred" # depends on broken package lme4 "bartMachine" # depends on broken package nlopt "bayesDem" # depends on broken package nlopt "bayesLife" # depends on broken package nlopt "BayesMed" # broken build "bayesmix" # broken build "bayesPop" # depends on broken package nlopt "Bayesthresh" # depends on broken package nlopt "BaySIC" # broken build "BBRecapture" # depends on broken package nlopt "BCA" # depends on broken package nlopt "bdynsys" # depends on broken package car "BEST" # broken build "bgmm" # depends on broken package nlopt "BIFIEsurvey" # depends on broken package nlopt "BiGGR" # depends on broken package rsbml "bioassayR" # broken build "BiodiversityR" # depends on broken package nlopt "biotools" # depends on broken package rpanel "birte" # build is broken "BLCOP" # depends on broken package Rsymphony "blmeco" # depends on broken package nlopt "blme" # depends on broken package nlopt "bmd" # depends on broken package nlopt "bmem" # depends on broken package nlopt "bmeta" # depends on broken package R2jags "bootnet" # depends on broken package nlopt "boral" # broken build "BradleyTerry2" # depends on broken package nlopt "BrailleR" # broken build "brainGraph" # build is broken "brms" # build is broken "BRugs" # build is broken "BTSPAS" # broken build "CADFtest" # depends on broken package nlopt "cAIC4" # depends on broken package nlopt "candisc" # depends on broken package nlopt "carcass" # depends on broken package nlopt "car" # depends on broken package nlopt "caret" # depends on broken package nlopt "caretEnsemble" # depends on broken package nlopt "CARrampsOcl" # depends on broken package OpenCL "Causata" # broken build "CCpop" # depends on broken package nlopt "CCTpack" # broken build "ChainLadder" # depends on broken package nlopt "ChemmineR" # Build Is Broken "chipenrich" # build is broken "chipPCR" # depends on broken nloptr "classify" # broken build "climwin" # depends on broken package nlopt "CLME" # depends on broken package nlopt "clpAPI" # build is broken "clusterPower" # depends on broken package nlopt "clusterSEs" # depends on broken AER "ClustGeo" # depends on broken FactoMineR "CNORfuzzy" # depends on broken package nlopt "CNVPanelizer" # depends on broken cn.mops "COHCAP" # build is broken "colorscience" # broken build "compendiumdb" # broken build "conformal" # depends on broken package nlopt "corHMM" # depends on broken package nlopt "CosmoPhotoz" # depends on broken package nlopt "covmat" # depends on broken package VIM "cplexAPI" # build is broken "cquad" # depends on broken package car "CrypticIBDcheck" # depends on broken package nlopt "ctsem" # depends on broken package OpenMx "cudaBayesreg" # build is broken "daff" # depends on broken package V8 "dagbag" # build is broken "DAMisc" # depends on broken package nlopt "datafsm" # depends on broken package caret "dbConnect" # broken build "DBKGrad" # depends on broken package rpanel #"dcmle" # broken build "ddst" # broken build "Deducer" # depends on broken package nlopt "DeducerExtras" # depends on broken package nlopt "DeducerPlugInExample" # depends on broken package nlopt "DeducerPlugInScaling" # depends on broken package nlopt "DeducerSpatial" # depends on broken package nlopt "DeducerSurvival" # depends on broken package nlopt "DeducerText" # depends on broken package nlopt "DEGraph" # depends on broken package RCytoscape "destiny" # depends on broken package VIM "DiagTest3Grp" # depends on broken package nlopt "diffHic" # depends on broken package edgeR "difR" # depends on broken package nlopt "DirichletMultinomial" # Build Is Broken "DistatisR" # depends on broken package nlopt "diveRsity" # depends on broken package nlopt "DJL" # depends on broken package car "dpa" # depends on broken package nlopt "dpcR" # depends on broken nloptr "drc" # depends on broken package nlopt "drfit" # depends on broken package nlopt "drsmooth" # depends on broken package nlopt "dynlm" # depends on broken package nlopt "easyanova" # depends on broken package nlopt "ecd" # depends on broken package polynom "edge" # depends on broken package nlopt "edgeR" # broken url "eeptools" # depends on broken package nlopt "EffectLiteR" # depends on broken package nlopt "effects" # depends on broken package nlopt "eiR" # depends on broken package ChemmineR "EMA" # depends on broken package nlopt "embryogrowth" # broken build "emg" # broken build "EnQuireR" # depends on broken package nlopt "episplineDensity" # depends on broken package nlopt "epr" # depends on broken package nlopt "erer" # depends on broken package nlopt "erma" # depends on broken GenomicFiles "erpR" # depends on broken package rpanel "ESKNN" # depends on broken package caret "euroMix" # build is broken "extRemes" # depends on broken package nlopt "ez" # depends on broken package nlopt "ezec" # depends on broken package drc "facopy" # depends on broken package nlopt "FactoMineR" # depends on broken package nlopt "Factoshiny" # depends on broken package nlopt "faoutlier" # depends on broken package nlopt "fastR" # depends on broken package nlopt "FDRreg" # depends on broken package nlopt "fishmethods" # depends on broken package lme4 "flipflop" # broken build "flowDensity" # depends on broken package nlopt "flowPeaks" # build is broken "flowQ" # build is broken "flowStats" # depends on broken package ncdfFlow "flowVS" # depends on broken package ncdfFlow "flowWorkspace" # depends on broken package ncdfFlow "fmcsR" # depends on broken package ChemmineR "fPortfolio" # depends on broken package Rsymphony "fracprolif" # broken build "FreeSortR" # broken build "freqweights" # depends on broken package nlopt "frmqa" # broken build "FSA" # depends on broken package car "fscaret" # depends on broken package nlopt "funcy" # depends on broken package car "fxregime" # depends on broken package nlopt "gamclass" # depends on broken package nlopt "gamlss_demo" # depends on broken package rpanel "gamm4" # depends on broken package nlopt "gaussquad" # broken build "gcmr" # depends on broken package nlopt "GDAtools" # depends on broken package nlopt "gdtools" # broken build "GENESIS" # broken build "genridge" # depends on broken package nlopt "geojsonio" # depends on broken package V8 "GEWIST" # depends on broken package nlopt "ggtree" # broken build "gimme" # depends on broken package nlopt "gmatrix" # depends on broken package cudatoolkit "gMCP" # build is broken "gmum_r" # broken build "Goslate" # depends on broken package PythonInR "GPC" # broken build "gplm" # depends on broken package nlopt "gpuR" # depends on GPU-specific header files "gputools" # depends on broken package cudatoolkit "granova" # depends on broken package nlopt "graphicalVAR" # depends on broken package nlopt "GraphPAC" # broken build "gridGraphics" # build is broken "GSCA" # depends on broken package rhdf5 "GUIDE" # depends on broken package rpanel "GWAF" # depends on broken package nlopt "GWASTools" # broken build "hbsae" # depends on broken package nlopt "heplots" # depends on broken package nlopt "HiDimMaxStable" # broken build "HierO" # Build Is Broken "HilbertVisGUI" # Build Is Broken "HiPLARM" # Build Is Broken "HistDAWass" # depends on broken package nlopt "HLMdiag" # depends on broken package nlopt "homomorpheR" # broken build "hpcwld" # broken build "hwwntest" # broken build "HydeNet" # broken build "hysteresis" # depends on broken package nlopt "IATscores" # depends on broken package nlopt "ibd" # depends on broken package nlopt "iccbeta" # depends on broken package nlopt "iClick" # depends on broken package rugarch "ifaTools" # depends on broken package OpenMx "imager" # broken build "immunoClust" # build is broken "in2extRemes" # depends on broken package nlopt "inferference" # depends on broken package nlopt "influence_ME" # depends on broken package nlopt "inSilicoMerging" # build is broken "INSPEcT" # depends on broken GenomicFeatures "interplot" # depends on broken arm "IsingFit" # depends on broken package nlopt "ITEMAN" # depends on broken package car "iteRates" # broken build "iterpc" # broken build "IUPS" # broken build "IVAS" # depends on broken package nlopt "ivpack" # depends on broken package nlopt "jagsUI" # broken build "JAGUAR" # depends on broken package nlopt "joda" # depends on broken package nlopt "jomo" # build is broken "js" # depends on broken package V8 "KoNLP" # broken build "kzft" # broken build "LaplaceDeconv" # depends on broken package orthopolynom "lawn" # depends on broken package V8 "ldamatch" # broken build "learnstats" # depends on broken package nlopt "lefse" # build is broken "lessR" # depends on broken package nlopt "lgcp" # depends on broken package rpanel "Libra" # broken build "LinRegInteractive" # depends on broken package rpanel "lira" # broken build "littler" # broken build "lme4" # depends on broken package nlopt "LMERConvenienceFunctions" # depends on broken package nlopt "lmerTest" # depends on broken package nlopt "lmSupport" # depends on broken package nlopt "LOGIT" # depends on broken package caret "longpower" # depends on broken package nlopt "LPTime" # broken build "MAIT" # depends on broken package nlopt "mAPKL" # build is broken "maPredictDSC" # depends on broken package nlopt "mar1s" # broken build "marked" # depends on broken package nlopt "matchingMarkets" # broken build "MatrixRider" # depends on broken package DirichletMultinomial "MaxPro" # depends on broken package nlopt "mbest" # depends on broken package nlopt "MBmca" # depends on broken nloptr "mBvs" # build is broken "meboot" # depends on broken package nlopt "medflex" # depends on broken package car "mediation" # depends on broken package lme4 "MEDME" # depends on broken package nlopt "MEMSS" # depends on broken package nlopt "merTools" # depends on broken package arm "meta4diag" # broken build "metagear" # build is broken "metaheur" # depends on broken package preprocomb "metamisc" # broken build "metaplus" # depends on broken package nlopt "metaSEM" # depends on broken package OpenMx "Metatron" # depends on broken package nlopt "miceadds" # depends on broken package nlopt "micEconAids" # depends on broken package nlopt "micEconCES" # depends on broken package nlopt "micEconSNQP" # depends on broken package nlopt "mi" # depends on broken package nlopt "MigClim" # Build Is Broken "migui" # depends on broken package nlopt "minimist" # depends on broken package V8 "missMDA" # depends on broken package nlopt "mitoODE" # build is broken "mixAK" # depends on broken package nlopt "MixedPoisson" # broken build "mixlm" # depends on broken package nlopt "MixMAP" # depends on broken package nlopt "mlma" # depends on broken package lme4 "mlmRev" # depends on broken package nlopt "MLSeq" # depends on broken package nlopt "mlVAR" # depends on broken package nlopt "MM" # broken build "mongolite" # build is broken "mosaic" # depends on broken package nlopt "mpoly" # broken build "mRMRe" # broken build "msa" # broken build "MSGFgui" # depends on broken package MSGFplus "MSGFplus" # Build Is Broken "MSstats" # depends on broken package nlopt "MultiRR" # depends on broken package nlopt "muma" # depends on broken package nlopt "munsellinterpol" # broken build "mutossGUI" # build is broken "mvinfluence" # depends on broken package nlopt "MXM" # broken build "NanoStringDiff" # broken build "NanoStringQCPro" # build is broken "nCal" # depends on broken package nlopt "ncdfFlow" # build is broken "NCIgraph" # depends on broken package RCytoscape "NHPoisson" # depends on broken package nlopt "nloptr" # depends on broken package nlopt "nlsem" # broken build "nlts" # broken build "nonrandom" # depends on broken package nlopt "NORRRM" # build is broken "npIntFactRep" # depends on broken package nlopt "NSM3" # broken build "omics" # depends on broken package lme4 "OmicsMarkeR" # depends on broken package nlopt "OPDOE" # broken build "OpenCL" # build is broken "openCyto" # depends on broken package ncdfFlow "OpenMx" # build is broken "optBiomarker" # depends on broken package rpanel "ora" # depends on broken package ROracle "ordBTL" # depends on broken package nlopt "ordPens" # depends on broken package lme4 "orthopolynom" # broken build "OUwie" # depends on broken package nlopt "oz" # broken build "PAA" # broken build "pamm" # depends on broken package nlopt "panelAR" # depends on broken package nlopt "papeR" # depends on broken package nlopt "parboost" # depends on broken package nlopt "parma" # depends on broken package nlopt "partitions" # broken build "PatternClass" # build is broken "PBImisc" # depends on broken package nlopt "pcaBootPlot" # depends on broken FactoMineR "pcaL1" # build is broken "pcnetmeta" # broken build "PDQutils" # broken build "pedigreemm" # depends on broken package nlopt "pequod" # depends on broken package nlopt "pglm" # depends on broken package car "PhenStat" # depends on broken package nlopt "phia" # depends on broken package nlopt "phylocurve" # depends on broken package nlopt "piecewiseSEM" # depends on broken package lme4 "plateCore" # depends on broken package ncdfFlow "plfMA" # broken build "plm" # depends on broken package car "plsRbeta" # depends on broken package nlopt "plsRcox" # depends on broken package nlopt "plsRglm" # depends on broken package nlopt "pmm" # depends on broken package nlopt "polynom" # broken build "pomp" # depends on broken package nlopt "predictmeans" # depends on broken package nlopt "preprocomb" # depends on broken package caret "prevalence" # broken build "prLogistic" # depends on broken package nlopt "pRoloc" # depends on broken package nlopt "pRolocGUI" # depends on broken package nlopt "PSAboot" # depends on broken package nlopt "ptw" # depends on broken nloptr "PurBayes" # broken build "pvca" # depends on broken package nlopt "PythonInR" # broken build "QFRM" # broken build "qgraph" # depends on broken package nlopt "qtbase" # build is broken "qtlnet" # depends on broken package nlopt "qtpaint" # depends on broken package qtbase "qtutils" # depends on broken package qtbase "QUALIFIER" # depends on broken package ncdfFlow "quantification" # depends on broken package nlopt "QuartPAC" # broken build "R2jags" # broken build "R2STATS" # depends on broken package nlopt "rain" # broken build "raincpc" # build is broken "rainfreq" # build is broken "RamiGO" # depends on broken package RCytoscape "RareVariantVis" # depends on broken VariantAnnotation "rasclass" # depends on broken package nlopt "rationalfun" # broken build "RBerkeley" # broken build "RbioRXN" # depends on broken package ChemmineR "Rblpapi" # broken build "Rchemcpp" # depends on broken package ChemmineR "rchess" # depends on broken package V8 "Rchoice" # depends on broken package car "Rcmdr" # depends on broken package nlopt "RcmdrMisc" # depends on broken package nlopt "RcmdrPlugin_BCA" # depends on broken package nlopt "RcmdrPlugin_coin" # depends on broken package nlopt "RcmdrPlugin_depthTools" # depends on broken package nlopt "RcmdrPlugin_DoE" # depends on broken package nlopt "RcmdrPlugin_doex" # depends on broken package nlopt "RcmdrPlugin_EACSPIR" # depends on broken package nlopt "RcmdrPlugin_EBM" # depends on broken package nlopt "RcmdrPlugin_EcoVirtual" # depends on broken package nlopt "RcmdrPlugin_epack" # depends on broken package nlopt "RcmdrPlugin_Export" # depends on broken package Rcmdr "RcmdrPlugin_EZR" # depends on broken package nlopt "RcmdrPlugin_FactoMineR" # depends on broken package nlopt "RcmdrPlugin_HH" # depends on broken package nlopt "RcmdrPlugin_IPSUR" # depends on broken package nlopt "RcmdrPlugin_KMggplot2" # depends on broken package nlopt "RcmdrPlugin_lfstat" # depends on broken package nlopt "RcmdrPlugin_MA" # depends on broken package nlopt "RcmdrPlugin_mosaic" # depends on broken package nlopt "RcmdrPlugin_MPAStats" # depends on broken package nlopt "RcmdrPlugin_NMBU" # depends on broken package nlopt "RcmdrPlugin_orloca" # depends on broken package nlopt "RcmdrPlugin_plotByGroup" # depends on broken package nlopt "RcmdrPlugin_pointG" # depends on broken package nlopt "RcmdrPlugin_qual" # depends on broken package nlopt "RcmdrPlugin_RMTCJags" # depends on broken package nlopt "RcmdrPlugin_ROC" # depends on broken package nlopt "RcmdrPlugin_sampling" # depends on broken package nlopt "RcmdrPlugin_SCDA" # depends on broken package nlopt "RcmdrPlugin_seeg" # depends on broken package nlopt "RcmdrPlugin_SLC" # depends on broken package nlopt "RcmdrPlugin_SM" # depends on broken package nlopt "RcmdrPlugin_sos" # depends on broken package nlopt "RcmdrPlugin_steepness" # depends on broken package nlopt "RcmdrPlugin_survival" # depends on broken package nlopt "RcmdrPlugin_TeachingDemos" # depends on broken package nlopt "RcmdrPlugin_temis" # depends on broken package nlopt "RcmdrPlugin_UCA" # depends on broken package nlopt "Rcpi" # depends on broken package ChemmineR "Rcplex" # Build Is Broken "RcppAPT" # Build Is Broken "RcppRedis" # build is broken "rcrypt" # broken build "RCytoscape" # Build Is Broken "rdd" # depends on broken package nlopt "rddtools" # depends on broken package AER "rDEA" # build is broken "RDieHarder" # build is broken "REBayes" # depends on broken package Rmosek "referenceIntervals" # depends on broken package nlopt "refund" # depends on broken package nlopt "refund_shiny" # depends on broken package refund "REndo" # depends on broken package AER "repijson" # depends on broken package V8 "REST" # depends on broken package nlopt "rgbif" # depends on broken package V8 "Rgnuplot" # broken build "rjade" # depends on broken package V8 "rJPSGCS" # build is broken "rLindo" # build is broken "RLRsim" # depends on broken package lme4 "RMallow" # broken build "rMAT" # build is broken "rmgarch" # depends on broken package nlopt "rminer" # depends on broken package nlopt "Rmosek" # build is broken "RMySQL" # broken build "RNAither" # depends on broken package nlopt "RnavGraph" # build is broken "rnetcarto" # broken build "robustlmm" # depends on broken package nlopt "rockchalk" # depends on broken package nlopt "ROI_plugin_symphony" # depends on broken package Rsymphony "rols" # build is broken "ROracle" # Build Is Broken "rpanel" # build is broken "Rpoppler" # broken build "rpubchem" # depends on broken package nlopt "RQuantLib" # build is broken "rr" # depends on broken package nlopt "RRreg" # depends on broken package lme4 "RSAP" # build is broken "rsbml" # build is broken "RSDA" # depends on broken package nlopt "Rsomoclu" # broken build "RStoolbox" # depends on broken package caret "Rsymphony" # build is broken "rTableICC" # broken build "rTANDEM" # build is broken "RTN" # depends on broken package nlopt "rugarch" # depends on broken package nlopt "rUnemploymentData" # broken build "RVAideMemoire" # depends on broken package nlopt "RVFam" # depends on broken package nlopt "RVideoPoker" # depends on broken package rpanel "RWebServices" # broken build "ryouready" # depends on broken package nlopt "sadists" # broken build "sampleSelection" # depends on broken package nlopt "sapFinder" # depends on broken package rTANDEM "sdcMicro" # depends on broken package nlopt "sdcMicroGUI" # depends on broken package nlopt "SDD" # depends on broken package rpanel "seeg" # depends on broken package nlopt "Sejong" # broken build "sem" # depends on broken package nlopt "semdiag" # depends on broken package nlopt "semGOF" # depends on broken package nlopt "semPlot" # depends on broken package nlopt "SensMixed" # depends on broken package lme4 "SensoMineR" # depends on broken package nlopt "seqCNA" # build is broken "SeqFeatR" # broken build "SeqGrapheR" # Build Is Broken "seqHMM" # depends on broken package nloptr "seqTools" # build is broken "SharpeR" # broken build "shinyTANDEM" # depends on broken package rTANDEM "SIBER" # broken build "simPop" # depends on broken package VIM "simr" # depends on broken package lme4 "SJava" # broken build "sjPlot" # depends on broken package nlopt "smacof" # broken build "SNAGEE" # build is broken "snm" # depends on broken package nlopt "SOD" # depends on broken package cudatoolkit "sodium" # broken build "soilphysics" # depends on broken package rpanel "sortinghat" # broken build "SoyNAM" # depends on broken package lme4 "spacom" # depends on broken package nlopt "SparseLearner" # depends on broken package qgraph "specificity" # depends on broken package nlopt "specmine" # depends on broken package caret "splm" # depends on broken package car "spocc" # depends on broken package V8 "spoccutils" # depends on broken spocc "ssmrob" # depends on broken package nlopt "StatMethRank" # broken build "stepp" # depends on broken package nlopt "stringgaussnet" # build is broken "Surrogate" # depends on broken package nlopt "svglite" # depends on broken package gdtools "sybilSBML" # build is broken "systemfit" # depends on broken package nlopt "TcGSA" # depends on broken package nlopt "TDMR" # depends on broken package nlopt "TextoMineR" # depends on broken package FactoMineR "TFBSTools" # depends on broken package DirichletMultinomial "tigerstats" # depends on broken package nlopt "TLBC" # depends on broken package caret "tmle" # broken build "tnam" # depends on broken package lme4 "tolBasis" # depends on broken package polynom "translateSPSS2R" # depends on broken car "TriMatch" # depends on broken package nlopt "TSMySQL" # broken build "tsoutliers" # broken build "UBCRM" # broken build "umx" # depends on broken package OpenMx "uniftest" # broken build "untb" # broken build "userfriendlyscience" # depends on broken package nlopt "V8" # build is broken "varComp" # depends on broken package lme4 "varian" # build is broken "variancePartition" # depends on broken package lme4 "VBmix" # broken build "VIM" # depends on broken package nlopt "VIMGUI" # depends on broken package nlopt "vows" # depends on broken package nlopt "webp" # build is broken "wfe" # depends on broken package nlopt "wordbankr" # depends on broken package RMySQL "xergm" # depends on broken package nlopt "xps" # build is broken "ZeligChoice" # depends on broken package AER "Zelig" # depends on broken package AER "zetadiv" # depends on broken package nlopt "zoib" # broken build ]; 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.dev}/include/libxml2 patchShebangs configure ''; }); Cairo = old.Cairo.overrideDerivation (attrs: { NIX_LDFLAGS = "-lfontconfig"; }); curl = old.curl.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); 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.dev}/include" ]; }); RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: { configureFlags = [ "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/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${pkgs.xorg.libXft.out}/lib -lXft"; NIX_LDFLAGS = "-lX11"; }); slfm = old.slfm.overrideDerivation (attrs: { PKG_LIBS = "-L${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}"; }); 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 = "${pkgs.cudatoolkit}/include"; }); EMCluster = old.EMCluster.overrideDerivation (attrs: { patches = [ ./patches/EMCluster.patch ]; }); spMC = old.spMC.overrideDerivation (attrs: { patches = [ ./patches/spMC.patch ]; }); BayesLogit = old.BayesLogit.overrideDerivation (attrs: { patches = [ ./patches/BayesLogit.patch ]; buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ]; }); BayesBridge = old.BayesBridge.overrideDerivation (attrs: { patches = [ ./patches/BayesBridge.patch ]; }); openssl = old.openssl.overrideDerivation (attrs: { OPENSSL_INCLUDES = "${pkgs.openssl.dev}/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