/* This file defines the composition for CRAN (R) packages. */ { R, pkgs, overrides }: let inherit (pkgs) cacert 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, hydraPlatforms ? null}: args: let hydraPlatforms' = hydraPlatforms; in lib.makeOverridable ({ name, version, sha256, depends ? [], doCheck ? true, requireX ? false, broken ? false, platforms ? R.meta.platforms, hydraPlatforms ? if hydraPlatforms' != null then hydraPlatforms' else platforms, maintainers ? [] }: 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 = platforms; meta.hydraPlatforms = hydraPlatforms; meta.broken = broken; meta.maintainers = maintainers; }); # Templates for generating Bioconductor and CRAN packages # from the name, version, sha256, and optional per-package arguments above # deriveBioc = mkDerive { mkHomepage = {name, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html"; mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz" "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz" "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ]; }; deriveBiocAnn = mkDerive { mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html"; mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ]; hydraPlatforms = []; }; deriveBiocExp = mkDerive { mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html"; mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ]; hydraPlatforms = []; }; deriveCran = mkDerive { mkHomepage = {name, ...}: "https://cran.r-project.org/web/packages/${name}/"; mkUrls = {name, version}: [ "mirror://cran/${name}_${version}.tar.gz" "mirror://cran/Archive/${name}/${name}_${version}.tar.gz" ]; }; # Overrides package definitions with nativeBuildInputs. # For example, # # overrideNativeBuildInputs { # foo = [ pkgs.bar ] # } old # # results in # # { # foo = old.foo.overrideAttrs (attrs: { # nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ]; # }); # } overrideNativeBuildInputs = overrides: old: lib.mapAttrs (name: value: (builtins.getAttr name old).overrideAttrs (attrs: { nativeBuildInputs = attrs.nativeBuildInputs ++ value; }) ) overrides; # Overrides package definitions with buildInputs. # For example, # # overrideBuildInputs { # foo = [ pkgs.bar ] # } old # # results in # # { # foo = old.foo.overrideAttrs (attrs: { # buildInputs = attrs.buildInputs ++ [ pkgs.bar ]; # }); # } overrideBuildInputs = overrides: old: lib.mapAttrs (name: value: (builtins.getAttr name old).overrideAttrs (attrs: { buildInputs = attrs.buildInputs ++ value; }) ) overrides; # Overrides package definitions with maintainers. # For example, # # overrideMaintainers { # foo = [ lib.maintainers.jsmith ] # } old # # results in # # { # foo = old.foo.override { # maintainers = [ lib.maintainers.jsmith ]; # }; # } overrideMaintainers = overrides: old: lib.mapAttrs (name: value: (builtins.getAttr name old).override { maintainers = value; }) overrides; # Overrides package definitions with new R dependencies. # For example, # # overrideRDepends { # foo = [ self.bar ] # } old # # results in # # { # foo = old.foo.overrideAttrs (attrs: { # nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ]; # propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ]; # }); # } overrideRDepends = overrides: old: lib.mapAttrs (name: value: (builtins.getAttr name old).overrideAttrs (attrs: { nativeBuildInputs = (attrs.nativeBuildInputs or []) ++ value; propagatedNativeBuildInputs = (attrs.propagatedNativeBuildInputs or []) ++ 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 requiring a home directory to install or to # run tests. # For example, # # overrideRequireHome [ # "foo" # ] old # # results in # # { # foo = old.foo.overrideAttrs (oldAttrs: { # preInstall = '' # ${oldAttrs.preInstall or ""} # export HOME=$(mktemp -d) # ''; # }); # } overrideRequireHome = packageNames: old: let nameValuePairs = map (name: { inherit name; value = (builtins.getAttr name old).overrideAttrs (oldAttrs: { preInstall = '' ${oldAttrs.preInstall or ""} export HOME=$(mktemp -d) ''; }); }) 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 packagesRequiringX old0); old2 = old1 // (overrideRequireHome packagesRequiringHome old1); old3 = old2 // (overrideSkipCheck packagesToSkipCheck old2); old4 = old3 // (overrideRDepends packagesWithRDepends old3); old5 = old4 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old4); old6 = old5 // (overrideBuildInputs packagesWithBuildInputs old5); old7 = old6 // (overrideBroken brokenPackages old6); old8 = old7 // (overrideMaintainers packagesWithMaintainers old7); old = old8; 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 = { inherit buildRPackage; } // 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; }; # tweaks for the individual packages and "in self" follow packagesWithMaintainers = with lib.maintainers; { data_table = [ jbedo ]; BiocManager = [ jbedo ]; ggplot2 = [ jbedo ]; svaNUMT = [ jbedo ]; svaRetro = [ jbedo ]; StructuralVariantAnnotation = [ jbedo ]; }; packagesWithRDepends = { FactoMineR = [ self.car ]; pander = [ self.codetools ]; }; packagesWithNativeBuildInputs = { arrow = [ pkgs.pkg-config pkgs.arrow-cpp ]; adimpro = [ pkgs.imagemagick ]; animation = [ pkgs.which ]; audio = [ pkgs.portaudio ]; BayesSAE = [ pkgs.gsl ]; BayesVarSel = [ pkgs.gsl ]; BayesXsrc = with pkgs; [ readline.dev ncurses gsl ]; bigGP = [ pkgs.mpi ]; bio3d = [ pkgs.zlib ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; bnpmr = [ pkgs.gsl ]; cairoDevice = [ pkgs.gtk2.dev ]; Cairo = with pkgs; [ libtiff libjpeg cairo.dev xorg.libXt.dev fontconfig.lib ]; Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw.dev ]; ChemmineOB = with pkgs; [ openbabel pkg-config ]; curl = [ pkgs.curl.dev ]; data_table = with pkgs; [ pkg-config zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; devEMF = with pkgs; [ xorg.libXft.dev ]; diversitree = with pkgs; [ gsl fftw ]; exactextractr = [ pkgs.geos ]; EMCluster = [ pkgs.lapack ]; fftw = [ pkgs.fftw.dev ]; fftwtools = with pkgs; [ fftw.dev pkg-config ]; Formula = [ pkgs.gmp ]; gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ]; ggiraph = with pkgs; [ pkgs.libpng.dev ]; git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ]; GLAD = [ pkgs.gsl ]; glpkAPI = with pkgs; [ gmp glpk ]; gmp = [ pkgs.gmp.dev ]; graphscan = [ pkgs.gsl ]; gsl = [ pkgs.gsl ]; gert = [ pkgs.libgit2 ]; haven = with pkgs; [ zlib.dev ]; h5vc = [ pkgs.zlib.dev ]; HiCseg = [ pkgs.gsl ]; imager = [ pkgs.xorg.libX11.dev ]; iBMQ = [ pkgs.gsl ]; igraph = with pkgs; [ gmp libxml2.dev ]; JavaGD = [ pkgs.jdk ]; jpeg = [ pkgs.libjpeg.dev ]; jqr = [ pkgs.jq.dev ]; KFKSDS = [ pkgs.gsl ]; kza = [ pkgs.fftw.dev ]; lpsymphony = with pkgs; [ pkg-config gfortran gettext ]; lwgeom = with pkgs; [ proj geos gdal ]; rvg = [ pkgs.libpng.dev ]; magick = [ pkgs.imagemagick.dev ]; ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; mvabund = [ pkgs.gsl ]; mwaved = [ pkgs.fftw.dev ]; mzR = with pkgs; [ zlib netcdf ]; nanonext = with pkgs; [ mbedtls nng ]; ncdf4 = [ pkgs.netcdf ]; nloptr = with pkgs; [ nlopt pkg-config ]; n1qn1 = [ pkgs.gfortran ]; odbc = [ pkgs.unixODBC ]; pander = with pkgs; [ pandoc which ]; pbdMPI = [ pkgs.mpi ]; pbdPROF = [ pkgs.mpi ]; pbdZMQ = [ pkgs.pkg-config ] ++ lib.optionals stdenv.isDarwin [ pkgs.which ]; pdftools = [ pkgs.poppler.dev ]; phytools = [ pkgs.which ]; PKI = [ pkgs.openssl.dev ]; png = [ pkgs.libpng.dev ]; protolite = [ pkgs.protobuf ]; R2SWF = with pkgs; [ zlib libpng freetype.dev ]; RAppArmor = [ pkgs.libapparmor ]; rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; rcdd = [ pkgs.gmp.dev ]; RcppCNPy = [ pkgs.zlib.dev ]; RcppGSL = [ pkgs.gsl ]; RcppZiggurat = [ pkgs.gsl ]; reprex = [ pkgs.which ]; rgdal = with pkgs; [ proj.dev gdal ]; rgeos = [ pkgs.geos ]; Rglpk = [ pkgs.glpk ]; RGtk2 = [ pkgs.gtk2.dev ]; rhdf5 = [ pkgs.zlib ]; Rhdf5lib = with pkgs; [ zlib.dev ]; Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ]; Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ]; rjags = [ pkgs.jags ]; rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ]; Rlibeemd = [ pkgs.gsl ]; rmatio = [ pkgs.zlib.dev ]; Rmpfr = with pkgs; [ gmp mpfr.dev ]; Rmpi = [ pkgs.mpi ]; RMySQL = with pkgs; [ zlib libmysqlclient openssl.dev ]; RNetCDF = with pkgs; [ netcdf udunits ]; RODBC = [ pkgs.libiodbc ]; rpanel = [ pkgs.bwidget ]; Rpoppler = [ pkgs.poppler ]; RPostgreSQL = with pkgs; [ postgresql postgresql ]; RProtoBuf = [ pkgs.protobuf ]; RSclient = [ pkgs.openssl.dev ]; Rserve = [ pkgs.openssl ]; Rssa = [ pkgs.fftw.dev ]; rsvg = [ pkgs.pkg-config ]; runjags = [ pkgs.jags ]; xslt = [ pkgs.pkg-config ]; RVowpalWabbit = with pkgs; [ zlib.dev boost ]; rzmq = with pkgs; [ zeromq pkg-config ]; httpuv = [ pkgs.zlib.dev ]; clustermq = [ pkgs.zeromq ]; SAVE = with pkgs; [ zlib bzip2 icu xz pcre ]; sdcTable = with pkgs; [ gmp glpk ]; seewave = with pkgs; [ fftw.dev libsndfile.dev ]; seqinr = [ pkgs.zlib.dev ]; seqminer = with pkgs; [ zlib.dev bzip2 ]; sf = with pkgs; [ gdal proj geos ]; terra = with pkgs; [ gdal proj geos ]; showtext = with pkgs; [ zlib libpng icu freetype.dev ]; simplexreg = [ pkgs.gsl ]; spate = [ pkgs.fftw.dev ]; ssanv = [ pkgs.proj ]; stsm = [ pkgs.gsl ]; stringi = [ pkgs.icu.dev ]; survSNP = [ pkgs.gsl ]; svglite = [ pkgs.libpng.dev ]; sysfonts = with pkgs; [ zlib libpng freetype.dev ]; systemfonts = with pkgs; [ fontconfig.dev freetype.dev ]; TAQMNGR = [ pkgs.zlib.dev ]; tesseract = with pkgs; [ tesseract leptonica ]; tiff = [ pkgs.libtiff.dev ]; tkrplot = with pkgs; [ xorg.libX11 tk.dev ]; topicmodels = [ pkgs.gsl ]; udunits2 = with pkgs; [ udunits expat ]; units = [ pkgs.udunits ]; V8 = [ pkgs.v8 ]; XBRL = with pkgs; [ zlib libxml2.dev ]; xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ]; XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ]; affyPLM = [ pkgs.zlib.dev ]; bamsignals = [ pkgs.zlib.dev ]; BitSeq = [ pkgs.zlib.dev ]; DiffBind = [ pkgs.zlib ]; ShortRead = [ pkgs.zlib.dev ]; oligo = [ pkgs.zlib.dev ]; gmapR = [ pkgs.zlib.dev ]; Rsubread = [ pkgs.zlib.dev ]; XVector = [ pkgs.zlib.dev ]; Rsamtools = with pkgs; [ zlib.dev curl.dev ]; rtracklayer = [ pkgs.zlib.dev ]; affyio = [ pkgs.zlib.dev ]; VariantAnnotation = with pkgs; [ zlib.dev curl.dev ]; snpStats = [ pkgs.zlib.dev ]; hdf5r = [ pkgs.hdf5.dev ]; httpgd = with pkgs; [ cairo.dev ]; SymTS = [ pkgs.gsl ]; VBLPCM = [ pkgs.gsl ]; dynr = [ pkgs.gsl ]; mixlink = [ pkgs.gsl ]; ridge = [ pkgs.gsl ]; smam = [ pkgs.gsl ]; rnetcarto = [ pkgs.gsl ]; rGEDI = [ pkgs.gsl ]; mmpca = [ pkgs.gsl ]; monoreg = [ pkgs.gsl ]; mvst = [ pkgs.gsl ]; mixture = [ pkgs.gsl ]; jSDM = [ pkgs.gsl ]; immunoClust = [ pkgs.gsl ]; hSDM = [ pkgs.gsl ]; flowPeaks = [ pkgs.gsl ]; fRLR = [ pkgs.gsl ]; eaf = [ pkgs.gsl ]; diseq = [ pkgs.gsl ]; cit = [ pkgs.gsl ]; abn = [ pkgs.gsl ]; SimInf = [ pkgs.gsl ]; RJMCMCNucleosomes = [ pkgs.gsl ]; RDieHarder = [ pkgs.gsl ]; QF = [ pkgs.gsl ]; PICS = [ pkgs.gsl ]; RcppCWB = [ pkgs.pkg-config ]; rrd = [ pkgs.pkg-config ]; trackViewer = [ pkgs.zlib.dev ]; themetagenomics = [ pkgs.zlib.dev ]; NanoMethViz = [ pkgs.zlib.dev ]; RcppMeCab = [ pkgs.pkg-config ]; HilbertVisGUI = with pkgs; [ pkg-config which ]; textshaping = [ pkgs.pkg-config ]; ragg = [ pkgs.pkg-config ]; qqconf = [ pkgs.pkg-config ]; }; packagesWithBuildInputs = { # sort -t '=' -k 2 svKomodo = [ pkgs.which ]; nat = [ pkgs.which ]; nat_templatebrains = [ pkgs.which ]; pbdZMQ = [ pkgs.zeromq ] ++ lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ]; bigmemory = lib.optionals stdenv.isLinux [ pkgs.libuuid.dev ]; clustermq = [ pkgs.pkg-config ]; RMark = [ pkgs.which ]; RPushbullet = [ pkgs.which ]; RCurl = [ pkgs.curl.dev ]; R2SWF = [ pkgs.pkg-config ]; rgl = with pkgs; [ libGLU libGLU.dev libGL xorg.libX11.dev freetype.dev libpng.dev ]; RGtk2 = [ pkgs.pkg-config ]; RProtoBuf = [ pkgs.pkg-config ]; Rpoppler = [ pkgs.pkg-config ]; XML = [ pkgs.pkg-config ]; cairoDevice = [ pkgs.pkg-config ]; chebpol = [ pkgs.pkg-config ]; fftw = [ pkgs.pkg-config ]; gdtools = [ pkgs.pkg-config ]; jqr = [ pkgs.jq.lib ]; kza = [ pkgs.pkg-config ]; lwgeom = with pkgs; [ pkg-config proj.dev sqlite.dev ]; magick = [ pkgs.pkg-config ]; mwaved = [ pkgs.pkg-config ]; odbc = [ pkgs.pkg-config ]; openssl = [ pkgs.pkg-config ]; pdftools = [ pkgs.pkg-config ]; sf = with pkgs; [ pkg-config sqlite.dev proj.dev ]; terra = with pkgs; [ pkg-config sqlite.dev proj.dev ]; showtext = [ pkgs.pkg-config ]; spate = [ pkgs.pkg-config ]; stringi = [ pkgs.pkg-config ]; sysfonts = [ pkgs.pkg-config ]; systemfonts = [ pkgs.pkg-config ]; tesseract = [ pkgs.pkg-config ]; Cairo = [ pkgs.pkg-config ]; CLVTools = [ pkgs.gsl ]; JMcmprsk = [ pkgs.gsl ]; mashr = [ pkgs.gsl ]; hadron = [ pkgs.gsl ]; AMOUNTAIN = [ pkgs.gsl ]; Rsymphony = with pkgs; [ pkg-config doxygen graphviz subversion ]; tcltk2 = with pkgs; [ tcl tk ]; tikzDevice = with pkgs; [ which texlive.combined.scheme-medium ]; gridGraphics = [ pkgs.which ]; adimpro = with pkgs; [ which xorg.xdpyinfo ]; rsvg = [ pkgs.librsvg.dev ]; ssh = with pkgs; [ libssh ]; s2 = [ pkgs.openssl.dev ]; ArrayExpressHTS = with pkgs; [ zlib.dev curl.dev which ]; bbl = with pkgs; [ gsl ]; writexl = with pkgs; [ zlib.dev ]; xslt = with pkgs; [ libxslt libxml2 ]; qpdf = with pkgs; [ libjpeg.dev zlib.dev ]; vcfR = with pkgs; [ zlib.dev ]; bio3d = with pkgs; [ zlib.dev ]; arrangements = with pkgs; [ gmp.dev ]; spp = with pkgs; [ zlib.dev ]; Rbowtie = with pkgs; [ zlib.dev ]; gaston = with pkgs; [ zlib.dev ]; csaw = with pkgs; [ zlib.dev curl ]; DirichletMultinomial = with pkgs; [ gsl ]; DiffBind = with pkgs; [ zlib.dev ]; CNEr = with pkgs; [ zlib ]; GMMAT = with pkgs; [ zlib.dev bzip2.dev ]; HiCDCPlus = [ pkgs.zlib.dev ]; PopGenome = [ pkgs.zlib.dev ]; QuasR = [ pkgs.zlib.dev ]; Rbowtie2 = [ pkgs.zlib.dev ]; Rmmquant = [ pkgs.zlib.dev ]; SICtools = with pkgs; [ zlib.dev ncurses.dev ]; Signac = [ pkgs.zlib.dev ]; TransView = [ pkgs.zlib.dev ]; bigsnpr = [ pkgs.zlib.dev ]; divest = [ pkgs.zlib.dev ]; hipread = [ pkgs.zlib.dev ]; jackalope = with pkgs; [ zlib.dev xz.dev ]; largeList = [ pkgs.zlib.dev ]; mappoly = [ pkgs.zlib.dev ]; matchingMarkets = [ pkgs.zlib.dev ]; methylKit = [ pkgs.zlib.dev ]; ndjson = [ pkgs.zlib.dev ]; podkat = [ pkgs.zlib.dev ]; qrqc = [ pkgs.zlib.dev ]; rJPSGCS = [ pkgs.zlib.dev ]; rhdf5filters = with pkgs; [ zlib.dev bzip2.dev ]; symengine = with pkgs; [ mpfr symengine flint ]; rtk = [ pkgs.zlib.dev ]; scPipe = [ pkgs.zlib.dev ]; seqTools = [ pkgs.zlib.dev ]; seqbias = [ pkgs.zlib.dev ]; sparkwarc = [ pkgs.zlib.dev ]; RoBMA = [ pkgs.jags ]; rGEDI = with pkgs; [ libgeotiff.dev libaec zlib.dev hdf5.dev ]; rawrr = [ pkgs.mono ]; HDF5Array = [ pkgs.zlib.dev ]; FLAMES = [ pkgs.zlib.dev ]; ncdfFlow = [ pkgs.zlib.dev ]; proj4 = [ pkgs.proj.dev ]; rtmpt = [ pkgs.gsl ]; rmarkdown = [ pkgs.pandoc ]; mixcat = [ pkgs.gsl ]; libstableR = [ pkgs.gsl ]; landsepi = [ pkgs.gsl ]; flan = [ pkgs.gsl ]; econetwork = [ pkgs.gsl ]; crandep = [ pkgs.gsl ]; catSurv = [ pkgs.gsl ]; ccfindR = [ pkgs.gsl ]; SPARSEMODr = [ pkgs.gsl ]; RKHSMetaMod = [ pkgs.gsl ]; LCMCR = [ pkgs.gsl ]; BNSP = [ pkgs.gsl ]; scModels = [ pkgs.mpfr.dev ]; multibridge = [ pkgs.mpfr.dev ]; RcppCWB = with pkgs; [ pcre.dev glib.dev ]; RmecabKo = [ pkgs.mecab ]; PoissonBinomial = [ pkgs.fftw.dev ]; rrd = [ pkgs.rrdtool ]; flowWorkspace = [ pkgs.zlib.dev ]; RcppMeCab = [ pkgs.mecab ]; PING = [ pkgs.gsl ]; RcppAlgos = [ pkgs.gmp.dev ]; RcppBigIntAlgos = [ pkgs.gmp.dev ]; HilbertVisGUI = [ pkgs.gtkmm2.dev ]; textshaping = with pkgs; [ harfbuzz.dev freetype.dev fribidi libpng ]; DropletUtils = [ pkgs.zlib.dev ]; RMariaDB = [ pkgs.libmysqlclient.dev ]; ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ]; qqconf = [ pkgs.fftw.dev ]; }; packagesRequiringX = [ "accrual" "ade4TkGUI" "analogue" "analogueExtra" "AnalyzeFMRI" "AnnotLists" "AnthropMMD" "aplpack" "asbio" "BAT" "BCA" "betapart" "BiodiversityR" "bio_infer" "bipartite" "biplotbootGUI" "blender" "cairoDevice" "canceR" "CCTpack" "cncaGUI" "cocorresp" "CommunityCorrelogram" "confidence" "constrainedKriging" "ConvergenceConcepts" "cpa" "DALY" "dave" "Deducer" "DeducerPlugInExample" "DeducerPlugInScaling" "DeducerSpatial" "DeducerSurvival" "DeducerText" "Demerelate" "detrendeR" "dpa" "dynamicGraph" "dynBiplotGUI" "EasyqpcR" "EcoVirtual" "exactLoglinTest" "fat2Lpoly" "fbati" "FD" "feature" "FeedbackTS" "FFD" "fgui" "fisheyeR" "forams" "forensim" "FreeSortR" "fscaret" "gcmr" "geomorph" "geoR" "georob" "GGEBiplotGUI" "gnm" "GrapheR" "GroupSeq" "gsubfn" "GUniFrac" "gWidgets2RGtk2" "gWidgets2tcltk" "HH" "HiveR" "ic50" "iDynoR" "in2extRemes" "iplots" "isopam" "IsotopeR" "JGR" "KappaGUI" "likeLTD" "logmult" "loon" "LS2Wstat" "MareyMap" "memgene" "metacom" "Meth27QC" "migui" "miniGUI" "mixsep" "MplusAutomation" "mpmcorrelogram" "mritc" "multgee" "multibiplotGUI" "OligoSpecificitySystem" "onemap" "OpenRepGrid" "paleoMAS" "pbatR" "PBSadmb" "PBSmodelling" "PCPS" "pez" "phylotools" "picante" "plotSEMM" "plsRbeta" "plsRglm" "PopGenReport" "poppr" "powerpkg" "PredictABEL" "prefmod" "PrevMap" "r4ss" "RandomFields" "rareNMtests" "rAverage" "RclusTool" "Rcmdr" "RcmdrPlugin_coin" "RcmdrPlugin_depthTools" "RcmdrPlugin_DoE" "RcmdrPlugin_EACSPIR" "RcmdrPlugin_EBM" "RcmdrPlugin_EcoVirtual" "RcmdrPlugin_EZR" "RcmdrPlugin_FactoMineR" "RcmdrPlugin_FuzzyClust" "RcmdrPlugin_HH" "RcmdrPlugin_IPSUR" "RcmdrPlugin_KMggplot2" "RcmdrPlugin_lfstat" "RcmdrPlugin_MA" "RcmdrPlugin_MPAStats" "RcmdrPlugin_orloca" "RcmdrPlugin_PcaRobust" "RcmdrPlugin_plotByGroup" "RcmdrPlugin_pointG" "RcmdrPlugin_ROC" "RcmdrPlugin_sampling" "RcmdrPlugin_SCDA" "RcmdrPlugin_SLC" "RcmdrPlugin_sos" "RcmdrPlugin_steepness" "RcmdrPlugin_survival" "RcmdrPlugin_TeachingDemos" "RcmdrPlugin_temis" "RcmdrPlugin_UCA" "recluster" "relimp" "RHRV" "rich" "RNCEP" "RSDA" "RSurvey" "simba" "Simile" "SimpleTable" "SOLOMON" "soundecology" "spatsurv" "sqldf" "SSDforR" "statcheck" "StatDA" "STEPCAM" "stosim" "strvalidator" "stylo" "svDialogstcltk" "svIDE" "svSocket" "svWidgets" "SYNCSA" "SyNet" "tcltk2" "TestScorer" "TIMP" "tkrplot" "tmap" "tspmeta" "TTAinterfaceTrendAnalysis" "twiddler" "uHMM" "vcdExtra" "VecStatGraphs3D" "vegan" "vegan3d" "vegclust" "x12GUI" ]; packagesRequiringHome = [ "aroma_affymetrix" "aroma_cn" "aroma_core" "csodata" "DiceView" "MSnID" "OmnipathR" "precommit" "PSCBS" "repmis" "R_cache" "R_filesets" "RKorAPClient" "R_rsp" "scholar" "stepR" "styler" "TreeTools" "ACNE" "APAlyzer" "EstMix" "PECA" "Quartet" "ShinyQuickStarter" "TIN" "TotalCopheneticIndex" "TreeDist" "biocthis" "calmate" "fgga" "fulltext" "immuneSIM" "mastif" "shinymeta" "shinyobjects" "wppi" "pins" "CoTiMA" "TBRDist" "Rogue" "fixest" "paxtoolsr" "systemPipeShiny" ]; packagesToSkipCheck = [ "Rmpi" # tries to run MPI processes "pbdMPI" # tries to run MPI processes "data_table" # fails to rename shared library before check ]; # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ "av" "NetLogoR" "valse" "HierO" "HIBAG" "HiveR" # Impure network access during build "waddR" "tiledb" "x13binary" "switchr" # ExperimentHub dependents, require net access during build "DuoClustering2018" "FieldEffectCrc" "GenomicDistributionsData" "HDCytoData" "HMP16SData" "PANTHER_db" "RNAmodR_Data" "SCATEData" "SingleMoleculeFootprintingData" "TabulaMurisData" "benchmarkfdrData2019" "bodymapRat" "clustifyrdatahub" "depmap" "emtdata" "metaboliteIDmapping" "msigdb" "muscData" "org_Mxanthus_db" "scpdata" "nullrangesData" ]; otherOverrides = old: new: { gifski = old.gifski.overrideAttrs (attrs: { cargoDeps = pkgs.rustPlatform.fetchCargoTarball { src = attrs.src; sourceRoot = "gifski/src/myrustlib"; hash = "sha256-vBrTQ+5JZA8554Aasbqw7mbaOfJNQjrOpG00IXAcamI="; }; cargoRoot = "src/myrustlib"; nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.rustPlatform.cargoSetupHook pkgs.cargo pkgs.rustc ]; }); stringi = old.stringi.overrideAttrs (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 $out/library/stringi/libs ''; }); xml2 = old.xml2.overrideAttrs (attrs: { preConfigure = '' export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2 patchShebangs configure ''; }); rzmq = old.rzmq.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); clustermq = old.clustermq.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); Cairo = old.Cairo.overrideAttrs (attrs: { NIX_LDFLAGS = "-lfontconfig"; }); curl = old.curl.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); RcppParallel = old.RcppParallel.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); purrr = old.purrr.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; }); RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; }); data_table = old.data_table.overrideAttrs (attrs: { env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fopenmp"; }; patchPhase = "patchShebangs configure"; }); ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: { env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.isDarwin " -fopenmp"; }; }); rpf = old.rpf.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; }); rJava = old.rJava.overrideAttrs (attrs: { preConfigure = '' export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ export JAVA_HOME=${pkgs.jdk} ''; }); JavaGD = old.JavaGD.overrideAttrs (attrs: { preConfigure = '' export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ export JAVA_HOME=${pkgs.jdk} ''; }); jqr = old.jqr.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); pbdZMQ = old.pbdZMQ.overrideAttrs (attrs: { postPatch = lib.optionalString stdenv.isDarwin '' for file in R/*.{r,r.in}; do sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file done ''; }); quarto = old.quarto.overrideAttrs (attrs: { postPatch = '' substituteInPlace "R/quarto.R" \ --replace "path_env <- Sys.getenv(\"QUARTO_PATH\", unset = NA)" "path_env <- Sys.getenv(\"QUARTO_PATH\", unset = '${lib.getBin pkgs.quarto}/bin/quarto')" ''; }); s2 = old.s2.overrideAttrs (attrs: { PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto"; }); Rmpi = old.Rmpi.overrideAttrs (attrs: { configureFlags = [ "--with-Rmpi-type=OPENMPI" ]; }); Rmpfr = old.Rmpfr.overrideAttrs (attrs: { configureFlags = [ "--with-mpfr-include=${pkgs.mpfr.dev}/include" ]; }); RVowpalWabbit = old.RVowpalWabbit.overrideAttrs (attrs: { configureFlags = [ "--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib" ]; }); RAppArmor = old.RAppArmor.overrideAttrs (attrs: { patches = [ ./patches/RAppArmor.patch ]; LIBAPPARMOR_HOME = pkgs.libapparmor; }); RMySQL = old.RMySQL.overrideAttrs (attrs: { MYSQL_DIR = "${pkgs.libmysqlclient}"; PKGCONFIG_CFLAGS = "-I${pkgs.libmysqlclient.dev}/include/mysql"; NIX_CFLAGS_LINK = "-L${pkgs.libmysqlclient}/lib/mysql -lmysqlclient"; preConfigure = '' patchShebangs configure ''; }); devEMF = old.devEMF.overrideAttrs (attrs: { NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft"; NIX_LDFLAGS = "-lX11"; }); slfm = old.slfm.overrideAttrs (attrs: { PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack"; }); SamplerCompare = old.SamplerCompare.overrideAttrs (attrs: { PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack"; }); spMC = old.spMC.overrideAttrs (attrs: { patches = [ ./patches/spMC.patch ]; }); openssl = old.openssl.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto"; }); websocket = old.websocket.overrideAttrs (attrs: { PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -lssl -lcrypto"; }); Rserve = old.Rserve.overrideAttrs (attrs: { patches = [ ./patches/Rserve.patch ]; configureFlags = [ "--with-server" "--with-client" ]; }); V8 = old.V8.overrideAttrs (attrs: { postPatch = '' substituteInPlace configure \ --replace " -lv8_libplatform" "" ''; preConfigure = '' export INCLUDE_DIR=${pkgs.v8}/include export LIB_DIR=${pkgs.v8}/lib patchShebangs configure ''; R_MAKEVARS_SITE = lib.optionalString (pkgs.stdenv.system == "aarch64-linux") (pkgs.writeText "Makevars" '' CXX14PICFLAGS = -fPIC ''); }); acs = old.acs.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); gdtools = old.gdtools.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; NIX_LDFLAGS = "-lfontconfig -lfreetype"; }); magick = old.magick.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); libgeos = old.libgeos.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); protolite = old.protolite.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); rpanel = old.rpanel.overrideAttrs (attrs: { preConfigure = '' export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}" ''; TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"; }); RPostgres = old.RPostgres.overrideAttrs (attrs: { preConfigure = '' export INCLUDE_DIR=${pkgs.postgresql}/include export LIB_DIR=${pkgs.postgresql.lib}/lib patchShebangs configure ''; }); OpenMx = old.OpenMx.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); odbc = old.odbc.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); x13binary = old.x13binary.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); geojsonio = old.geojsonio.overrideAttrs (attrs: { buildInputs = [ cacert ] ++ attrs.buildInputs; }); rstan = old.rstan.overrideAttrs (attrs: { env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION"; }; }); mongolite = old.mongolite.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include"; PKGCONFIG_LIBS = "-Wl,-rpath,${lib.getLib pkgs.openssl}/lib -L${lib.getLib pkgs.openssl}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz"; }); ps = old.ps.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); rlang = old.rlang.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); systemfonts = old.systemfonts.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; }); littler = old.littler.overrideAttrs (attrs: with pkgs; { buildInputs = [ pcre xz zlib bzip2 icu which ] ++ attrs.buildInputs; postInstall = '' install -d $out/bin $out/share/man/man1 ln -s ../library/littler/bin/r $out/bin/r ln -s ../library/littler/bin/r $out/bin/lr ln -s ../../../library/littler/man-page/r.1 $out/share/man/man1 # these won't run without special provisions, so better remove them rm -r $out/library/littler/script-tests ''; }); lpsymphony = old.lpsymphony.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); sodium = old.sodium.overrideAttrs (attrs: with pkgs; { preConfigure = '' patchShebangs configure ''; nativeBuildInputs = [ pkg-config ] ++ attrs.nativeBuildInputs; buildInputs = [ libsodium.dev ] ++ attrs.buildInputs; }); keyring = old.keyring.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); Rhtslib = old.Rhtslib.overrideAttrs (attrs: { preConfigure = '' substituteInPlace R/zzz.R --replace "-lcurl" "-L${pkgs.curl.out}/lib -lcurl" ''; }); h2o = old.h2o.overrideAttrs (attrs: { preConfigure = '' # prevent download of jar file during install and postpone to first use sed -i '/downloadJar()/d' R/zzz.R # during runtime the package directory is not writable as it's in the # nix store, so store the jar in the user's cache directory instead substituteInPlace R/connection.R --replace \ 'dest_file <- file.path(dest_folder, "h2o.jar")' \ 'dest_file <- file.path("~/.cache/", "h2o.jar")' ''; }); SICtools = old.SICtools.overrideAttrs (attrs: { preConfigure = '' substituteInPlace src/Makefile --replace "-lcurses" "-lncurses" ''; }); arrow = old.arrow.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); ROracle = old.ROracle.overrideAttrs (attrs: { configureFlags = [ "--with-oci-lib=${pkgs.oracle-instantclient.lib}/lib" "--with-oci-inc=${pkgs.oracle-instantclient.dev}/include" ]; }); sparklyr = old.sparklyr.overrideAttrs (attrs: { # Pyspark's spark is full featured and better maintained than pkgs.spark preConfigure = '' substituteInPlace R/zzz.R \ --replace ".onLoad <- function(...) {" \ ".onLoad <- function(...) { Sys.setenv(\"SPARK_HOME\" = Sys.getenv(\"SPARK_HOME\", unset = \"${pkgs.python3Packages.pyspark}/lib/${pkgs.python3Packages.python.libPrefix}/site-packages/pyspark\")) Sys.setenv(\"JAVA_HOME\" = Sys.getenv(\"JAVA_HOME\", unset = \"${pkgs.jdk}\"))" ''; }); proj4 = old.proj4.overrideAttrs (attrs: { preConfigure = '' substituteInPlace configure \ --replace "-lsqlite3" "-L${lib.makeLibraryPath [ pkgs.sqlite ]} -lsqlite3" ''; }); rrd = old.rrd.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); ChIPXpress = old.ChIPXpress.override { hydraPlatforms = []; }; rgl = old.rgl.overrideAttrs (attrs: { RGL_USE_NULL = "true"; }); Rrdrand = old.Rrdrand.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; }; symengine = old.symengine.overrideAttrs (_: { preConfigure = '' rm configure cat > src/Makevars << EOF PKG_LIBS=-lsymengine all: $(SHLIB) EOF ''; }); RandomFieldsUtils = old.RandomFieldsUtils.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; }; flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; }; geomorph = old.geomorph.overrideAttrs (attrs: { RGL_USE_NULL = "true"; }); Rhdf5lib = let hdf5 = pkgs.hdf5_1_10.overrideAttrs (attrs: {configureFlags = attrs.configureFlags ++ ["--enable-cxx"];}); in old.Rhdf5lib.overrideAttrs (attrs: { propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ hdf5.dev pkgs.libaec ]; patches = [ ./patches/Rhdf5lib.patch ]; passthru.hdf5 = hdf5; }); rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: { propagatedBuildInputs = with pkgs; attrs.propagatedBuildInputs ++ [ (hdf5-blosc.override {hdf5 = self.Rhdf5lib.hdf5;}) ]; patches = [ ./patches/rhdf5filters.patch ]; }); rhdf5= old.rhdf5.overrideAttrs (attrs: { patches = [ ./patches/rhdf5.patch ]; }); redland = old.redland.overrideAttrs (_: { PKGCONFIG_CFLAGS="-I${pkgs.redland}/include -I${pkgs.librdf_raptor2}/include/raptor2 -I${pkgs.librdf_rasqal}/include/rasqal"; PKGCONFIG_LIBS="-L${pkgs.redland}/lib -L${pkgs.librdf_raptor2}/lib -L${pkgs.librdf_rasqal}/lib -lrdf -lraptor2 -lrasqal"; }); textshaping = old.textshaping.overrideAttrs (attrs: { env.NIX_LDFLAGS = "-lfribidi -lharfbuzz"; }); torch = old.torch.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; }); }; in self