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What happens if I push all of nixpkgs
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Nix
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This file defines the composition for R packages.
let importJSON = f: builtins.fromJSON (builtins.readFile f);
biocPackagesGenerated = importJSON ./bioc-packages.json; biocAnnotationPackagesGenerated = importJSON ./bioc-annotation-packages.json; biocExperimentPackagesGenerated = importJSON ./bioc-experiment-packages.json; cranPackagesGenerated = importJSON ./cran-packages.json;in
{ R, pkgs, overrides,}:
let inherit (pkgs) cacert fetchurl stdenv lib ;
buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; 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, biocVersion }: "https://www.bioconductor.org/packages/${biocVersion}/data/annotation/html/${name}.html"; mkUrls = { name, version, biocVersion, }: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ]; hydraPlatforms = [ ]; }; deriveBiocExp = mkDerive { mkHomepage = { name, biocVersion }: "https://www.bioconductor.org/packages/${biocVersion}/data/experiment/html/${name}.html"; mkUrls = { name, version, biocVersion, }: [ "mirror://bioc/${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; } // mkPackageSet deriveBioc biocPackagesGenerated // mkPackageSet deriveBiocAnn biocAnnotationPackagesGenerated // mkPackageSet deriveBiocExp biocExperimentPackagesGenerated // mkPackageSet deriveCran cranPackagesGenerated;
# Takes in a generated JSON file's imported contents # and transforms it by swapping each element of the depends array with the dependency's derivation # and passing this new object to the provided derive function mkPackageSet = derive: packagesJSON: lib.mapAttrs ( k: v: derive packagesJSON.extraArgs ( v // { depends = lib.map (name: builtins.getAttr name self) v.depends; } ) ) packagesJSON.packages;
# 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 ]; RQuantLib = [ kupac ]; };
packagesWithRDepends = { spectralGraphTopology = [ self.CVXR ]; FactoMineR = [ self.car ]; pander = [ self.codetools ]; rmsb = [ self.rstantools ]; gastempt = [ self.rstantools ]; interactiveDisplay = [ self.BiocManager ]; disbayes = [ self.rstantools ]; tipsae = [ self.rstantools ]; TriDimRegression = [ self.rstantools ]; bbmix = [ self.rstantools ]; };
packagesWithNativeBuildInputs = { adimpro = [ pkgs.imagemagick ]; animation = [ pkgs.which ]; Apollonius = with pkgs; [ pkg-config gmp.dev mpfr.dev ]; arrow = with pkgs; [ pkg-config cmake ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ intltool ]; alcyon = with pkgs; [ cmake which ]; audio = [ pkgs.portaudio ]; BayesChange = [ pkgs.gsl ]; BayesSAE = [ pkgs.gsl ]; BayesVarSel = [ pkgs.gsl ]; BayesXsrc = with pkgs; [ readline.dev ncurses gsl ]; bioacoustics = [ pkgs.fftw.dev pkgs.cmake ]; bigGP = [ pkgs.mpi ]; bigrquerystorage = with pkgs; [ grpc protobuf which ]; bio3d = [ pkgs.zlib ]; BiocCheck = [ pkgs.which ]; Biostrings = [ pkgs.zlib ]; CellBarcode = [ pkgs.zlib ]; cld3 = [ pkgs.protobuf ]; cpp11qpdf = with pkgs; [ zlib.dev libjpeg ]; bnpmr = [ pkgs.gsl ]; caviarpd = [ pkgs.cargo ]; cairoDevice = [ pkgs.gtk2.dev ]; Cairo = with pkgs; [ libtiff libjpeg cairo.dev xorg.libXt.dev fontconfig.lib ]; Cardinal = [ pkgs.which ]; chebpol = [ pkgs.fftw.dev ]; ChemmineOB = [ pkgs.pkg-config ]; interpolation = [ pkgs.pkg-config ]; clarabel = [ pkgs.cargo ]; curl = [ pkgs.curl.dev ]; CytoML = [ pkgs.libxml2.dev ]; data_table = with pkgs; [ pkg-config zlib.dev ] ++ lib.optional stdenv.hostPlatform.isDarwin pkgs.llvmPackages.openmp; devEMF = with pkgs; [ xorg.libXft.dev ]; DEploid_utils = [ pkgs.zlib.dev ]; diversitree = with pkgs; [ gsl fftw ]; exactextractr = [ pkgs.geos ]; EMCluster = [ pkgs.lapack ]; fangs = with pkgs; [ cargo rustc ]; fastpng = [ pkgs.zlib.dev ]; fcl = with pkgs; [ cargo rustc ]; fftw = [ pkgs.fftw.dev ]; fftwtools = with pkgs; [ fftw.dev pkg-config ]; flint = with pkgs; [ pkg-config gmp.dev mpfr.dev flint3 ]; fingerPro = [ pkgs.gsl ]; Formula = [ pkgs.gmp ]; frailtyMMpen = [ pkgs.gsl ]; gamstransfer = [ pkgs.zlib ]; gdalraster = [ pkgs.pkg-config ]; gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ expat xorg.libXdmcp ]; GeneralizedWendland = [ pkgs.gsl ]; 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 ]; GPBayes = [ pkgs.gsl ]; graphscan = [ pkgs.gsl ]; gsl = [ pkgs.gsl ]; gslnls = [ pkgs.gsl ]; gert = [ pkgs.libgit2 ]; haven = with pkgs; [ zlib.dev ]; hellorust = [ pkgs.cargo ]; hgwrr = [ pkgs.gsl ]; h5vc = with pkgs; [ zlib.dev bzip2.dev xz.dev ]; HiCParser = [ pkgs.zlib ]; yyjsonr = with pkgs; [ zlib.dev ]; RNifti = with pkgs; [ zlib.dev ]; RNiftyReg = with pkgs; [ zlib.dev ]; highs = [ pkgs.which pkgs.cmake ]; crc32c = [ pkgs.which pkgs.cmake ]; cpp11bigwig = with pkgs; [ zlib.dev curl.dev ]; rbedrock = [ pkgs.zlib.dev pkgs.which pkgs.cmake ]; Rigraphlib = [ pkgs.cmake ]; HiCseg = [ pkgs.gsl ]; imager = [ pkgs.xorg.libX11.dev ]; imbibe = [ pkgs.zlib.dev ]; image_CannyEdges = with pkgs; [ fftw.dev libpng.dev ]; iBMQ = [ pkgs.gsl ]; jack = [ pkgs.pkg-config ]; JavaGD = [ pkgs.jdk ]; jpeg = [ pkgs.libjpeg.dev ]; jqr = [ pkgs.jq.dev ]; KFKSDS = [ pkgs.gsl ]; KSgeneral = with pkgs; [ pkg-config ]; kza = [ pkgs.fftw.dev ]; leidenAlg = [ pkgs.gmp.dev ]; Libra = [ pkgs.gsl ]; libstable4u = [ pkgs.gsl ]; heck = [ pkgs.cargo ]; LOMAR = [ pkgs.gmp.dev ]; littler = [ pkgs.libdeflate ]; lpsymphony = with pkgs; [ pkg-config gfortran gettext ]; lwgeom = with pkgs; [ proj geos gdal ]; rsbml = [ pkgs.pkg-config ]; rvg = [ pkgs.libpng.dev ]; MAGEE = [ pkgs.zlib.dev pkgs.bzip2.dev ]; magick = [ pkgs.imagemagick.dev ]; ModelMetrics = lib.optional stdenv.hostPlatform.isDarwin pkgs.llvmPackages.openmp; mvabund = [ pkgs.gsl ]; mcrPioda = [ pkgs.gsl ]; mwaved = [ pkgs.fftw.dev ]; mzR = with pkgs; [ zlib netcdf ]; nanonext = with pkgs; [ mbedtls nng ]; ncdf4 = [ pkgs.netcdf ]; neojags = [ pkgs.jags ]; nloptr = with pkgs; [ nlopt pkg-config ]; n1qn1 = [ pkgs.gfortran ]; odbc = [ pkgs.unixODBC ]; opencv = [ pkgs.pkg-config ]; pak = [ pkgs.curl.dev ]; pander = with pkgs; [ pandoc which ]; pbdMPI = [ pkgs.mpi ]; pbdPROF = [ pkgs.mpi ]; pbdZMQ = [ pkgs.pkg-config ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.which ]; pcaL1 = [ pkgs.pkg-config pkgs.clp ]; pdftools = [ pkgs.poppler.dev ]; PEPBVS = [ pkgs.gsl ]; phytools = [ pkgs.which ]; PKI = [ pkgs.openssl.dev ]; png = [ pkgs.libpng.dev ]; protolite = [ pkgs.protobuf ]; prqlr = with pkgs; [ cargo rustc ]; 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 ]; resultant = with pkgs; [ gmp.dev mpfr.dev pkg-config ]; rgdal = with pkgs; [ proj.dev gdal ]; Rhisat2 = [ pkgs.which pkgs.hostname ]; gdalcubes = [ pkgs.pkg-config ]; 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; [ stripJavaArchivesHook zlib bzip2.dev icu xz.dev zstd.dev pcre.dev jdk libzip libdeflate ]; Rlibeemd = [ pkgs.gsl ]; rmatio = [ pkgs.zlib.dev pkgs.pkg-config ]; Rmpfr = with pkgs; [ gmp mpfr.dev ]; Rmpi = with pkgs; [ mpi.dev prrte.dev ]; RMySQL = with pkgs; [ zlib libmysqlclient openssl.dev ]; RNetCDF = with pkgs; [ netcdf udunits ]; RODBC = [ pkgs.libiodbc ]; rpanel = [ pkgs.tclPackages.bwidget ]; Rpoppler = [ pkgs.poppler ]; RPostgreSQL = with pkgs; [ libpq.pg_config ]; 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 ]; salso = with pkgs; [ cargo rustc ]; ymd = with pkgs; [ cargo rustc ]; arcpbf = with pkgs; [ cargo rustc ]; sdcTable = with pkgs; [ gmp glpk ]; seewave = with pkgs; [ fftw.dev libsndfile.dev ]; seqinr = [ pkgs.zlib.dev ]; smcryptoR = with pkgs; [ cargo rustc which ]; webp = [ pkgs.pkg-config ]; seqminer = with pkgs; [ zlib.dev bzip2 ]; sf = with pkgs; [ gdal proj geos libtiff curl ]; fio = with pkgs; [ cargo rustc ]; strawr = with pkgs; [ curl.dev ]; string2path = [ pkgs.cargo ]; terra = with pkgs; [ gdal proj geos netcdf ]; tok = [ pkgs.cargo ]; rshift = with pkgs; [ cargo rustc ]; arcgisutils = with pkgs; [ cargo rustc ]; arcgisgeocode = with pkgs; [ cargo rustc ]; arcgisplaces = with pkgs; [ pkg-config openssl.dev cargo rustc ]; awdb = [ pkgs.cargo ]; apcf = with pkgs; [ geos ]; SemiCompRisks = [ pkgs.gsl ]; 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 ]; parseLatex = [ 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 ]; TDA = [ pkgs.gmp ]; 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 ]; unigd = [ pkgs.pkg-config ]; vdiffr = [ pkgs.libpng.dev ]; V8 = [ pkgs.nodejs.libv8 ]; XBRL = with pkgs; [ zlib libxml2.dev ]; XLConnect = [ pkgs.jdk ]; xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.perl ]; XML = with pkgs; [ libtool libxml2.dev xmlsec libxslt ]; affyPLM = [ pkgs.zlib.dev ]; BitSeq = [ pkgs.zlib.dev ]; DiffBind = with pkgs; [ zlib.dev xz.dev bzip2.dev ]; 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 bzip2 xz ]; rtracklayer = with pkgs; [ zlib.dev curl.dev ]; affyio = [ pkgs.zlib.dev ]; snpStats = [ pkgs.zlib.dev ]; vcfppR = [ pkgs.curl.dev pkgs.bzip2 pkgs.zlib.dev pkgs.xz ]; 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 ]; RationalMatrix = [ pkgs.pkg-config pkgs.gmp.dev ]; RcppCWB = [ pkgs.pkg-config pkgs.pcre2 ]; redux = [ pkgs.pkg-config ]; s2 = [ pkgs.pkg-config ]; rswipl = with pkgs; [ cmake pkg-config ]; scorematchingad = [ pkgs.cmake ]; rrd = [ pkgs.pkg-config ]; surveyvoi = [ pkgs.pkg-config ]; Rbwa = [ pkgs.zlib.dev ]; tergo = with pkgs; [ cargo rustc ]; gglinedensity = [ pkgs.cargo ]; trackViewer = [ pkgs.zlib.dev ]; themetagenomics = [ pkgs.zlib.dev ]; Rsymphony = [ pkgs.pkg-config ]; 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 ]; qspray = [ pkgs.pkg-config ]; ratioOfQsprays = [ pkgs.pkg-config ]; watcher = with pkgs; [ cmake which ]; symbolicQspray = [ pkgs.pkg-config ]; sphereTessellation = [ pkgs.pkg-config ]; vapour = [ pkgs.pkg-config ]; xdvir = [ pkgs.freetype.dev ]; };
packagesWithBuildInputs = { # sort -t '=' -k 2 adbcpostgresql = with pkgs; [ readline.dev zlib.dev openssl.dev libkrb5.dev openpam libpq ]; asciicast = with pkgs; [ bzip2.dev icu.dev libdeflate xz.dev zlib.dev zstd.dev ]; island = [ pkgs.gsl.dev ]; knowYourCG = with pkgs; [ zlib.dev ncurses.dev ]; svKomodo = [ pkgs.which ]; transmogR = [ pkgs.zlib.dev ]; ulid = [ pkgs.zlib.dev ]; unrtf = with pkgs; [ bzip2.dev icu.dev libdeflate xz.dev zlib.dev zstd.dev ]; nat = [ pkgs.which ]; nat_templatebrains = [ pkgs.which ]; pbdZMQ = [ pkgs.zeromq ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ pkgs.darwin.binutils ]; bigmemory = lib.optionals stdenv.hostPlatform.isLinux [ pkgs.libuuid.dev ]; bayesWatch = [ pkgs.boost.dev ]; clustermq = [ pkgs.pkg-config ]; coga = [ pkgs.gsl.dev ]; mBvs = [ pkgs.gsl.dev ]; rcontroll = [ pkgs.gsl.dev ]; deepSNV = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; epialleleR = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; gdalraster = with pkgs; [ gdal proj.dev sqlite.dev ]; mitoClone2 = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; gpg = [ pkgs.gpgme ]; webp = [ pkgs.libwebp ]; RMark = [ pkgs.which ]; RPushbullet = [ pkgs.which ]; stpphawkes = [ pkgs.gsl ]; registr = with pkgs; [ icu.dev zlib.dev bzip2.dev xz.dev libdeflate ]; RCurl = [ pkgs.curl.dev ]; R2SWF = [ pkgs.pkg-config ]; rDEA = [ pkgs.glpk ]; rgl = with pkgs; [ libGLU libGL xorg.libX11.dev freetype.dev libpng.dev ]; RGtk2 = [ pkgs.pkg-config ]; RProtoBuf = [ pkgs.pkg-config ]; Rpoppler = [ pkgs.pkg-config ]; RPostgres = with pkgs; [ libpq ]; XML = [ pkgs.pkg-config ]; apsimx = [ pkgs.which ]; cairoDevice = [ pkgs.pkg-config ]; chebpol = [ pkgs.pkg-config ]; baseline = [ pkgs.lapack ]; eds = [ pkgs.zlib.dev ]; pgenlibr = [ pkgs.zlib.dev ]; fftw = [ pkgs.pkg-config ]; gdtools = [ pkgs.pkg-config ]; archive = [ pkgs.libarchive ]; gdalcubes = with pkgs; [ proj.dev gdal sqlite.dev netcdf ]; rsbml = [ pkgs.libsbml ]; SuperGauss = [ pkgs.pkg-config pkgs.fftw.dev ]; ravetools = with pkgs; [ pkg-config fftw.dev ]; specklestar = [ pkgs.fftw.dev ]; cartogramR = [ pkgs.fftw.dev ]; jqr = [ pkgs.jq.out ]; kza = [ pkgs.pkg-config ]; igraph = with pkgs; [ gmp libxml2.dev glpk ]; interpolation = [ pkgs.gmp ]; image_textlinedetector = with pkgs; [ pkg-config opencv ]; 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 ]; qckitfastq = [ pkgs.zlib.dev ]; raer = with pkgs; [ zlib.dev xz.dev bzip2.dev ]; RQuantLib = with pkgs; [ quantlib.dev boost.dev ]; 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 ]; excursions = [ pkgs.gsl ]; OpenCL = with pkgs; [ opencl-clhpp ocl-icd ]; gpuMagic = [ pkgs.ocl-icd ]; JMcmprsk = [ pkgs.gsl ]; KSgeneral = [ pkgs.fftw.dev ]; mashr = [ pkgs.gsl ]; hadron = [ pkgs.gsl ]; AMOUNTAIN = [ pkgs.gsl ]; Rsymphony = with pkgs; [ symphony doxygen graphviz subversion cgl clp ]; tcltk2 = with pkgs; [ tcl tk ]; rswipl = with pkgs; [ ncurses.dev libxcrypt zlib.dev ]; GrafGen = [ pkgs.zlib ]; tikzDevice = with pkgs; [ which texliveMedium ]; gridGraphics = [ pkgs.which ]; adimpro = with pkgs; [ which xorg.xdpyinfo ]; tfevents = [ pkgs.protobuf ]; rsvg = [ pkgs.librsvg.dev ]; ssh = with pkgs; [ libssh ]; s2 = with pkgs; [ abseil-cpp openssl.dev ]; ArrayExpressHTS = with pkgs; [ zlib.dev curl.dev which ]; bbl = with pkgs; [ gsl ]; diffHic = with pkgs; [ xz.dev bzip2.dev ]; writexl = with pkgs; [ zlib.dev ]; xslt = with pkgs; [ libxslt libxml2 ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ xz ]; qpdf = with pkgs; [ libjpeg.dev zlib.dev ]; vcfR = with pkgs; [ zlib.dev ]; bio3d = with pkgs; [ zlib.dev ]; arrangements = with pkgs; [ gmp.dev ]; gfilogisreg = [ pkgs.gmp.dev ]; spp = with pkgs; [ zlib.dev ]; bamsignals = with pkgs; [ zlib.dev xz.dev bzip2 ]; Rbowtie = with pkgs; [ zlib.dev ]; gaston = with pkgs; [ zlib.dev ]; csaw = with pkgs; [ zlib.dev xz.dev bzip2.dev curl ]; DirichletMultinomial = with pkgs; [ gsl ]; DiffBind = with pkgs; [ zlib.dev ]; CNEr = with pkgs; [ zlib ]; GMMAT = with pkgs; [ zlib.dev bzip2.dev ]; rmumps = with pkgs; [ zlib.dev ]; HiCDCPlus = [ pkgs.zlib.dev ]; PopGenome = [ pkgs.zlib.dev ]; QuasR = with pkgs; [ zlib.dev xz.dev bzip2.dev ]; Rarr = [ pkgs.zlib.dev ]; Rbowtie2 = [ pkgs.zlib.dev ]; Rfastp = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; maftools = with pkgs; [ zlib.dev bzip2 xz.dev ]; Rmmquant = [ pkgs.zlib.dev ]; SICtools = with pkgs; [ zlib.dev ncurses.dev ]; Signac = [ pkgs.zlib.dev ]; TransView = with pkgs; [ xz.dev bzip2.dev zlib.dev ]; bigsnpr = [ pkgs.zlib.dev ]; zlib = [ pkgs.zlib.dev ]; divest = [ pkgs.zlib.dev ]; hipread = [ pkgs.zlib.dev ]; jack = with pkgs; [ gmp.dev mpfr.dev ]; jackalope = with pkgs; [ zlib.dev xz.dev bzip2.dev ]; largeList = [ pkgs.zlib.dev ]; mappoly = [ pkgs.zlib.dev ]; VariantAnnotation = with pkgs; [ zlib.dev curl.dev bzip2.dev xz.dev ]; matchingMarkets = [ pkgs.zlib.dev ]; methylKit = with pkgs; [ zlib.dev bzip2.dev xz.dev ]; ndjson = [ pkgs.zlib.dev ]; podkat = with pkgs; [ zlib.dev xz.dev bzip2.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 = with pkgs; [ bzip2.dev xz.dev zlib.dev ]; seqTools = [ pkgs.zlib.dev ]; seqbias = with pkgs; [ zlib.dev bzip2.dev xz.dev ]; sparkwarc = [ pkgs.zlib.dev ]; RoBMA = [ pkgs.jags ]; RoBSA = [ pkgs.jags ]; pexm = [ pkgs.jags ]; rGEDI = with pkgs; [ libgeotiff.dev libaec zlib.dev hdf5.dev ]; rawrr = [ pkgs.mono ]; HDF5Array = [ pkgs.zlib.dev ]; FLAMES = with pkgs; [ zlib.dev bzip2.dev xz.dev ]; ncdfFlow = [ pkgs.zlib.dev ]; proj4 = [ pkgs.proj.dev ]; rtmpt = [ pkgs.gsl ]; mixcat = [ pkgs.gsl ]; libstableR = [ pkgs.gsl ]; landsepi = [ pkgs.gsl ]; flan = [ pkgs.gsl ]; econetwork = [ pkgs.gsl ]; crandep = [ pkgs.gsl ]; catSurv = [ pkgs.gsl ]; ccfindR = [ pkgs.gsl ]; screenCounter = [ pkgs.zlib.dev ]; SPARSEMODr = [ pkgs.gsl ]; RKHSMetaMod = [ pkgs.gsl ]; LCMCR = [ pkgs.gsl ]; BNSP = [ pkgs.gsl ]; scModels = [ pkgs.mpfr.dev ]; multibridge = with pkgs; [ pkg-config mpfr.dev ]; RcppCWB = with pkgs; [ pcre.dev glib.dev ]; redux = [ pkgs.hiredis ]; RmecabKo = [ pkgs.mecab ]; markets = [ pkgs.gsl ]; rlas = [ pkgs.boost ]; bgx = [ pkgs.boost ]; PoissonBinomial = [ pkgs.fftw.dev ]; poisbinom = [ pkgs.fftw.dev ]; PoissonMultinomial = [ pkgs.fftw.dev ]; psbcGroup = [ pkgs.gsl.dev ]; rrd = [ pkgs.rrdtool ]; flowWorkspace = [ pkgs.zlib.dev ]; RITCH = [ pkgs.zlib.dev ]; RcppMeCab = [ pkgs.mecab ]; PING = [ pkgs.gsl ]; PROJ = [ pkgs.proj.dev ]; RcppAlgos = [ pkgs.gmp.dev ]; RcppBigIntAlgos = [ pkgs.gmp.dev ]; spaMM = [ pkgs.gsl ]; shrinkTVP = [ pkgs.gsl ]; sbrl = with pkgs; [ gsl gmp.dev ]; surveyvoi = with pkgs; [ gmp.dev mpfr.dev ]; unigd = with pkgs; [ cairo.dev libpng.dev ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ expat xorg.libXdmcp ]; HilbertVisGUI = [ pkgs.gtkmm2.dev ]; textshaping = with pkgs; [ harfbuzz.dev freetype.dev fribidi libpng ]; DropletUtils = [ pkgs.zlib.dev ]; RMariaDB = [ pkgs.libmysqlclient.dev ]; ijtiff = [ pkgs.libtiff ]; ragg = with pkgs; [ freetype.dev libpng.dev libtiff.dev zlib.dev libjpeg.dev bzip2.dev ] ++ lib.optional stdenv.hostPlatform.isDarwin lerc.dev; qqconf = [ pkgs.fftw.dev ]; spFW = [ pkgs.fftw.dev ]; qspray = with pkgs; [ gmp.dev mpfr.dev ]; ratioOfQsprays = with pkgs; [ gmp.dev mpfr.dev ]; symbolicQspray = with pkgs; [ gmp.dev mpfr.dev ]; sphereTessellation = with pkgs; [ gmp.dev mpfr.dev ]; vapour = with pkgs; [ proj.dev gdal ]; MedianaDesigner = [ pkgs.zlib.dev ]; ChemmineOB = with pkgs; [ eigen openbabel ]; DGP4LCF = [ pkgs.lapack pkgs.blas ]; };
packagesRequiringX = [ "analogueExtra" "AnalyzeFMRI" "AnnotLists" "asbio" "BCA" "biplotbootGUI" "cairoDevice" "cncaGUI" "CommunityCorrelogram" "dave" "DeducerPlugInExample" "DeducerPlugInScaling" "DeducerSpatial" "DeducerSurvival" "DeducerText" "Demerelate" "diveR" "dpa" "dynamicGraph" "EasyqpcR" "exactLoglinTest" "fisheyeR" "forams" "forensim" "GGEBiplotGUI" "gsubfn" "gWidgets2RGtk2" "gWidgets2tcltk" "HiveR" "ic50" "iDynoR" "iplots" "likeLTD" "loon" "loon_ggplot" "loon_shiny" "loon_tourr" "Meth27QC" "mixsep" "multibiplotGUI" "OligoSpecificitySystem" "optbdmaeAT" "optrcdmaeAT" "paleoMAS" "RandomFields" "rfviz" "RclusTool" "RcmdrPlugin_coin" "RcmdrPlugin_FuzzyClust" "RcmdrPlugin_IPSUR" "RcmdrPlugin_lfstat" "RcmdrPlugin_PcaRobust" "RcmdrPlugin_plotByGroup" "RcmdrPlugin_pointG" "RcmdrPlugin_sampling" "RcmdrPlugin_SCDA" "RcmdrPlugin_SLC" "RcmdrPlugin_steepness" "rich" "RSurvey" "simba" "SimpleTable" "SOLOMON" "soptdmaeA" "strvalidator" "stylo" "SyNet" "switchboard" "tkImgR" "TTAinterfaceTrendAnalysis" "twiddler" "uHMM" "VecStatGraphs3D" ];
packagesRequiringHome = [ "aroma_affymetrix" "aroma_cn" "aroma_core" "avotrex" "beer" "ceramic" "connections" "covidmx" "csodata" "DiceView" "facmodTS" "gasanalyzer" "margaret" "MSnID" "OmnipathR" "orthGS" "pannotator" "precommit" "protGear" "PCRA" "PSCBS" "iemisc" "red" "repmis" "R_cache" "R_filesets" "RKorAPClient" "R_rsp" "salso" "scholar" "SpatialDecon" "stepR" "styler" "tabs" "teal_code" "TreeTools" "TreeSearch" "ACNE" "APAlyzer" "BAT" "EstMix" "Patterns" "PECA" "Quartet" "ShinyQuickStarter" "TIN" "cfdnakit" "CaDrA" "GNOSIS" "TotalCopheneticIndex" "TreeDist" "biocthis" "calmate" "fgga" "fulltext" "dataverse" "immuneSIM" "mastif" "shinymeta" "shinyobjects" "wppi" "pins" "CoTiMA" "TBRDist" "Rogue" "fixest" "paxtoolsr" "systemPipeShiny" "matlab2r" "GNOSIS" ];
packagesToSkipCheck = [ "MsDataHub" # tries to connect to ExperimentHub "Rmpi" # tries to run MPI processes "ReactomeContentService4R" # tries to connect to Reactome "PhIPData" # tries to download something from a DB "RBioFormats" # tries to download jar during load test "pbdMPI" # tries to run MPI processes "CTdata" # tries to connect to ExperimentHub "rfaRm" # tries to connect to Ebi "data_table" # fails to rename shared library before check "coMethDMR" # tries to connect to ExperimentHub "multiMiR" # tries to connect to DB "snapcount" # tries to connect to snaptron.cs.jhu.edu ];
# Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ "av" "NetLogoR" "valse" "HierO" "HIBAG" "HiveR" "minired" # deprecated on CRAN
# Impure network access during build "waddR" "tiledb" "switchr"
# ExperimentHub dependents, require net access during build "DuoClustering2018" "FieldEffectCrc" "GenomicDistributionsData" "hpar" "HDCytoData" "HMP16SData" "PANTHER_db" "RNAmodR_Data" "SCATEData" "SingleMoleculeFootprintingData" "TabulaMurisData" "benchmarkfdrData2019" "bodymapRat" "clustifyrdatahub" "CTexploreR" "depmap" "emtdata" "metaboliteIDmapping" "msigdb" "muscData" "org_Mxanthus_db" "scpdata" "signatureSearch" "nullrangesData" ];
otherOverrides = old: new: { ACME = old.ACME.overrideAttrs (attrs: { env = (attrs.env or { }) // { # Avoid incompatible pointer type error NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-incompatible-pointer-types"; }; });
vegan3d = old.vegan3d.overrideAttrs (attrs: { RGL_USE_NULL = "true"; });
# it can happen that the major version of arrow-cpp is ahead of the # rPackages.arrow that would be built from CRAN sources; therefore, to avoid # build failures and manual updates of the hash, we use the R source at # the GitHub release state of libarrow (arrow-cpp) in Nixpkgs. This may # not exactly represent the CRAN sources, but because patching of the # CRAN R package is mostly done to meet special CRAN build requirements, # this is a straightforward approach. Example where patching was necessary # -> arrow 14.0.0.2 on CRAN; was lagging behind libarrow release: # https://github.com/apache/arrow/issues/39698 ) arrow = old.arrow.overrideAttrs (attrs: { src = pkgs.arrow-cpp.src; name = "r-arrow-${pkgs.arrow-cpp.version}"; prePatch = "cd r"; postPatch = '' patchShebangs configure ''; buildInputs = attrs.buildInputs ++ [ pkgs.arrow-cpp ]; });
gifski = old.gifski.overrideAttrs (attrs: { cargoDeps = pkgs.rustPlatform.fetchCargoVendor { src = attrs.src; sourceRoot = "gifski/src/myrustlib"; hash = "sha256-yz6M3qDQPfT0HJHyK2wgzgl5sBh7EmdJ5zW8SJkk+wY="; };
cargoRoot = "src/myrustlib";
nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.rustPlatform.cargoSetupHook pkgs.cargo pkgs.rustc ]; });
gmapR = old.gmapR.overrideAttrs (attrs: { env = (attrs.env or { }) // { # Avoid incompatible pointer type error NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-implicit-function-declaration -Wno-incompatible-pointer-types"; }; });
timeless = old.timeless.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; cargoDeps = pkgs.rustPlatform.fetchCargoVendor { src = attrs.src; sourceRoot = "timeless/src/rust"; hash = "sha256-5TV7iCzaaFwROfJNO6pvSUbJBzV+wZlU5+ZK4AMT6X0="; };
cargoRoot = "src/rust";
nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.rustPlatform.cargoSetupHook pkgs.cargo ]; });
arcpbf = old.arcpbf.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
rshift = old.rshift.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
ymd = old.ymd.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
SynExtend = old.SynExtend.overrideAttrs (attrs: { # build might fail due to race condition enableParallelBuilding = false; });
orbweaver = old.orbweaver.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.cargo pkgs.rustc ]; });
xml2 = old.xml2.overrideAttrs (attrs: { preConfigure = '' export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2 patchShebangs configure ''; });
findpython = old.findpython.overrideAttrs (attrs: { postPatch = '' substituteInPlace "R/find_python_cmd.r" \ --replace-fail 'python_cmds[which(python_cmds != "")]' \ 'python_cmds <- c(python_cmds, file.path("${lib.getBin pkgs.python3}", "bin", "python3")) python_cmds[which(python_cmds != "")]' ''; });
fio = old.fio.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
hypeR = old.hypeR.overrideAttrs (attrs: { postPatch = '' substituteInPlace NAMESPACE R/db_msig.R --replace-fail \ "msigdbr_show_species" "msigdbr_species" ''; });
alcyon = old.alcyon.overrideAttrs (attrs: { configureFlags = [ "--enable-force-openmp" ]; });
awdb = old.awdb.overrideAttrs (attrs: { postPatch = '' patchShebangs configure ''; });
clarabel = old.clarabel.overrideAttrs (attrs: { postPatch = '' patchShebangs configure ''; });
cn_farms = old.cn_farms.overrideAttrs (attrs: { postPatch = '' # https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2025/01/08#n2025-01-08 substituteInPlace "src/sparse_farms.c" \ --replace-fail "Calloc" "R_Calloc" \ --replace-fail "Free" "R_Free" ''; });
PICS = old.PICS.overrideAttrs (attrs: { postPatch = '' # https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2025/01/08#n2025-01-08 substituteInPlace "src/segment.c" \ --replace-fail "Calloc" "R_Calloc" ''; });
genoCN = old.genoCN.overrideAttrs (attrs: { postPatch = '' # https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2025/01/08#n2025-01-08 substituteInPlace "src/xCNV.c" \ --replace-fail "Calloc" "R_Calloc" \ --replace-fail "Free" "R_Free" ''; });
trigger = old.trigger.overrideAttrs (attrs: { postPatch = '' # https://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2025/01/08#n2025-01-08 substituteInPlace "src/trigger.c" \ --replace-fail "Calloc" "R_Calloc" \ --replace-fail "Free" "R_Free" ''; });
lwgeom = old.lwgeom.overrideAttrs (attrs: { configureFlags = [ "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" ]; });
sf = old.sf.overrideAttrs (attrs: { configureFlags = [ "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" ]; });
terra = old.terra.overrideAttrs (attrs: { configureFlags = [ "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" ]; });
vapour = old.vapour.overrideAttrs (attrs: { configureFlags = [ "--with-proj-lib=${pkgs.lib.getLib pkgs.proj}/lib" ]; });
rzmq = old.rzmq.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; });
nanoparquet = old.nanoparquet.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
nanonext = old.nanonext.overrideAttrs (attrs: { NIX_LDFLAGS = "-lnng -lmbedtls -lmbedx509 -lmbedcrypto"; });
clustermq = old.clustermq.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; });
Cairo = old.Cairo.overrideAttrs (attrs: { NIX_LDFLAGS = "-lfontconfig"; });
curl = old.curl.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; });
Cyclops = old.Cyclops.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; });
RcppParallel = old.RcppParallel.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; });
Colossus = old.Colossus.overrideAttrs (_: { postPatch = "patchShebangs configure"; });
arcgisutils = old.arcgisutils.overrideAttrs (_: { postPatch = "patchShebangs configure"; });
arcgisgeocode = old.arcgisgeocode.overrideAttrs (_: { postPatch = "patchShebangs configure"; });
gmailr = old.gmailr.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
prqlr = old.prqlr.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
pingr = old.pingr.overrideAttrs (_: { postPatch = "patchShebangs configure"; });
heck = old.heck.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
surtvep = old.surtvep.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
rtiktoken = old.rtiktoken.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.cargo pkgs.rustc ]; });
purrr = old.purrr.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; });
tergo = old.tergo.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; });
luajr = old.luajr.overrideAttrs (attrs: { hardeningDisable = [ "format" ]; postPatch = "patchShebangs configure"; });
RcppArmadillo = old.RcppArmadillo.overrideAttrs (attrs: { patchPhase = "patchShebangs configure"; });
RcppGetconf = old.RcppGetconf.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
SpliceWiz = old.SpliceWiz.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
zoomerjoin = old.zoomerjoin.overrideAttrs (attrs: { nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs; postPatch = "patchShebangs configure"; });
AneuFinder = old.AneuFinder.overrideAttrs (attrs: { postPatch = '' substituteInPlace src/utility.cpp src/densities.cpp src/loghmm.cpp src/scalehmm.cpp \ --replace-fail "Calloc(" "R_Calloc(" \ --replace-fail "Free(" "R_Free(" ''; });
b64 = old.b64.overrideAttrs (attrs: { nativeBuildInputs = with pkgs; [ cargo rustc ] ++ attrs.nativeBuildInputs; postPatch = "patchShebangs configure"; });
graper = old.graper.overrideAttrs (attrs: { postPatch = '' substituteInPlace "src/Makevars" \ --replace-fail "CXX_STD=CXX11" "CXX_STD=CXX14" ''; });
ocf = old.ocf.overrideAttrs (attrs: { postPatch = "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"; });
cisPath = old.cisPath.overrideAttrs (attrs: { hardeningDisable = [ "format" ]; });
HilbertVis = old.HilbertVis.overrideAttrs (attrs: { hardeningDisable = [ "format" ]; });
HilbertVisGUI = old.HilbertVisGUI.overrideAttrs (attrs: { hardeningDisable = [ "format" ]; });
MANOR = old.MANOR.overrideAttrs (attrs: { hardeningDisable = [ "format" ]; });
rGADEM = old.rGADEM.overrideAttrs (attrs: { hardeningDisable = [ "format" ]; });
rsgeo = old.rsgeo.overrideAttrs (attrs: { nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs; postPatch = "patchShebangs configure"; });
instantiate = old.instantiate.overrideAttrs (attrs: { postPatch = "patchShebangs configure"; });
exifr = old.exifr.overrideAttrs (attrs: { postPatch = '' for f in .onLoad .onAttach ; do substituteInPlace R/load_hook.R \ --replace-fail \ "$f <- function(libname, pkgname) {" \ "$f <- function(libname, pkgname) { options( exifr.perlpath = \"${lib.getBin pkgs.perl}/bin/perl\", exifr.exiftoolcommand = \"${lib.getBin pkgs.exiftool}/bin/exiftool\" )" done ''; });
NGCHM = old.NGCHM.overrideAttrs (attrs: { postPatch = '' substituteInPlace "inst/base.config/conf.d/01-server-protocol-scl.R" \ --replace-fail \ "/bin/hostname" "${lib.getBin pkgs.hostname}/bin/hostname" ''; });
metahdep = old.metahdep.overrideAttrs (attrs: { env = (attrs.env or { }) // { # Avoid incompatible pointer type error NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-int-conversion"; }; });
ModelMetrics = old.ModelMetrics.overrideAttrs (attrs: { env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.hostPlatform.isDarwin " -fopenmp"; }; });
rawrr = old.rawrr.overrideAttrs (attrs: { postPatch = '' substituteInPlace "R/zzz.R" "R/dotNetAssembly.R" --replace-warn \ "Sys.which('mono')" "'${lib.getBin pkgs.mono}/bin/mono'"
substituteInPlace "R/dotNetAssembly.R" --replace-warn \ "Sys.which(\"xbuild\")" "\"${lib.getBin pkgs.mono}/bin/xbuild\""
substituteInPlace "R/dotNetAssembly.R" --replace-warn \ "cmd <- ifelse(Sys.which(\"msbuild\") != \"\", \"msbuild\", \"xbuild\")" \ "cmd <- \"${lib.getBin pkgs.mono}/bin/xbuild\""
substituteInPlace "R/rawrr.R" --replace-warn \ "Sys.which(\"mono\")" "\"${lib.getBin pkgs.mono}/bin/mono\"" ''; });
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} substituteInPlace R/zzz.R.in \ --replace-fail ".onLoad <- function(libname, pkgname) {" \ ".onLoad <- function(libname, pkgname) { Sys.setenv(\"JAVA_HOME\" = Sys.getenv(\"JAVA_HOME\", unset = \"${pkgs.jdk}\"))" ''; });
JavaGD = old.JavaGD.overrideAttrs (attrs: { preConfigure = '' export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ export JAVA_HOME=${pkgs.jdk} ''; });
jqr = old.jqr.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
pathfindR = old.pathfindR.overrideAttrs (attrs: { postPatch = '' substituteInPlace "R/zzz.R" \ --replace-fail " check_java_version()" " Sys.setenv(JAVA_HOME = \"${lib.getBin pkgs.jre_minimal}\"); check_java_version()" substituteInPlace "R/active_snw_search.R" \ --replace-fail "system(paste0(\"java" "system(paste0(\"${lib.getBin pkgs.jre_minimal}/bin/java" ''; });
pbdZMQ = old.pbdZMQ.overrideAttrs (attrs: { postPatch = lib.optionalString stdenv.hostPlatform.isDarwin '' for file in R/*.{r,r.in}; do sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.cctools}/bin/\1"#g' $file done ''; });
quarto = old.quarto.overrideAttrs (attrs: { propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.quarto ]; postPatch = '' substituteInPlace "R/quarto.R" \ --replace-fail "Sys.getenv(\"QUARTO_PATH\", unset = NA_character_)" "Sys.getenv(\"QUARTO_PATH\", unset = '${lib.getBin pkgs.quarto}/bin/quarto')" ''; });
Rhisat2 = old.Rhisat2.overrideAttrs (attrs: { enableParallelBuilding = false; });
s2 = old.s2.overrideAttrs (attrs: { preConfigure = '' substituteInPlace "configure" \ --replace-fail "absl_s2" "absl_flags absl_check" ''; });
Rmpi = old.Rmpi.overrideAttrs (attrs: { configureFlags = [ "--with-Rmpi-type=OPENMPI" ]; });
Rmpfr = old.Rmpfr.overrideAttrs (attrs: { configureFlags = [ "--with-mpfr-include=${pkgs.mpfr.dev}/include" ]; });
CNEr = old.CNEr.overrideAttrs (attrs: { patches = [ ./patches/CNEr.patch ]; });
covidsymptom = old.covidsymptom.overrideAttrs (attrs: { preConfigure = "rm R/covidsymptomdata.R"; });
cubature = old.cubature.overrideAttrs (attrs: { enableParallelBuilding = false; });
RVowpalWabbit = old.RVowpalWabbit.overrideAttrs (attrs: { configureFlags = [ "--with-boost=${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${pkgs.xorg.libXft.out}/lib -lXft"; NIX_LDFLAGS = "-lX11"; });
hdf5r = old.hdf5r.overrideAttrs (attrs: { buildInputs = attrs.buildInputs ++ [ new.Rhdf5lib.hdf5 ]; });
slfm = old.slfm.overrideAttrs (attrs: { PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack"; });
SamplerCompare = old.SamplerCompare.overrideAttrs (attrs: { PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack"; });
FLAMES = old.FLAMES.overrideAttrs (attrs: { patches = [ ./patches/FLAMES.patch ]; });
openssl = old.openssl.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; PKGCONFIG_CFLAGS = "-I${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${lib.getLib pkgs.openssl}/lib -lssl -lcrypto"; });
Rserve = old.Rserve.overrideAttrs (attrs: { patches = [ ./patches/Rserve.patch ]; configureFlags = [ "--with-server" "--with-client" ]; });
universalmotif = old.universalmotif.overrideAttrs (attrs: { patches = [ ./patches/universalmotif.patch ]; });
V8 = old.V8.overrideAttrs (attrs: { postPatch = '' substituteInPlace configure \ --replace-fail " -lv8_libplatform" "" # Bypass the test checking if pointer compression is needed substituteInPlace configure \ --replace-fail "./pctest1" "true" '';
preConfigure = '' export INCLUDE_DIR=${pkgs.nodejs.libv8}/include export LIB_DIR=${pkgs.nodejs.libv8}/lib patchShebangs configure '';
R_MAKEVARS_SITE = lib.optionalString (pkgs.stdenv.system == "aarch64-linux") ( pkgs.writeText "Makevars" '' CXX14PICFLAGS = -fPIC '' ); });
acs = old.acs.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
gdtools = old.gdtools.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; NIX_LDFLAGS = "-lfontconfig -lfreetype"; });
magick = old.magick.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
libgeos = old.libgeos.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
protolite = old.protolite.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
rgoslin = old.rgoslin.overrideAttrs (attrs: { enableParallelBuilding = false; });
rpanel = old.rpanel.overrideAttrs (attrs: { preConfigure = '' export TCLLIBPATH="${pkgs.tclPackages.bwidget}/lib/bwidget${pkgs.tclPackages.bwidget.version}" ''; TCLLIBPATH = "${pkgs.tclPackages.bwidget}/lib/bwidget${pkgs.tclPackages.bwidget.version}"; });
networkscaleup = old.networkscaleup.overrideAttrs (attrs: { env = (attrs.env or { }) // { # needed to avoid "log limit exceeded" on Hydra NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes"; };
# consumes a lot of resources in parallel enableParallelBuilding = false; });
OpenMx = old.OpenMx.overrideAttrs (attrs: { env = (attrs.env or { }) // { # needed to avoid "log limit exceeded" on Hydra NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes"; }; preConfigure = '' patchShebangs configure ''; });
odbc = old.odbc.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
x13binary = old.x13binary.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
FlexReg = old.FlexReg.overrideAttrs (attrs: { env = (attrs.env or { }) // { # needed to avoid "log limit exceeded" on Hydra NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -Wno-ignored-attributes"; };
# consumes a lot of resources in parallel enableParallelBuilding = false; });
geojsonio = old.geojsonio.overrideAttrs (attrs: { buildInputs = [ cacert ] ++ attrs.buildInputs; });
float = old.float.overrideAttrs (attrs: { enableParallelBuilding = false; });
redatamx = old.redatamx.overrideAttrs (attrs: { preConfigure = let redatam-core = pkgs.fetchzip { url = "https://redatam-core.s3.us-west-2.amazonaws.com/core-dev/linux/redatamx-core-linux-20241222.zip"; hash = "sha256-CagDpv7v5fj/NgaC5fmYc5UuKuBVlT3gauH2ItVnIIY="; }; in '' mkdir -p ./inst/redengine/ cp ${redatam-core}/lib/libredengine-1.0.0-rc2.so ./inst/redengine/libredengine-1.0.0-rc2.so ''; });
immunotation = let MHC41alleleList = fetchurl { url = "https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list"; hash = "sha256-CRZ+0uHzcq5zK5eONucAChXIXO8tnq5sSEAS80Z7jhg="; };
MHCII40alleleList = fetchurl { url = "https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list"; hash = "sha256-K4Ic2NUs3P4IkvOODwZ0c4Yh8caex5Ih0uO5jXRHp40="; };
# List of valid countries, regions and ethnic groups # The original page is changing a bit every day, but the relevant # content does not. Use archive.org to get a stable snapshot. # It can be updated from time to time, or when the package becomes # deficient. This may be difficult to know. # Update the snapshot date, and add id_ after it, as described here: # https://web.archive.org/web/20130806040521/http://faq.web.archive.org/page-without-wayback-code/ validGeographics = fetchurl { url = "https://web.archive.org/web/20240418194005id_/http://www.allelefrequencies.net/hla6006a.asp"; hash = "sha256-m7Wkmh/cPxeqn94LwoznIh+fcFXskmSGErUYj6kTqak="; }; in old.immunotation.overrideAttrs (attrs: { patches = [ ./patches/immunotation.patch ]; postPatch = '' substituteInPlace "R/external_resources_input.R" --replace-fail \ "nix-NetMHCpan-4.1-allele-list" ${MHC41alleleList}
substituteInPlace "R/external_resources_input.R" --replace-fail \ "nix-NETMHCIIpan-4.0-alleles-name-list" ${MHCII40alleleList}
substituteInPlace "R/AFND_interface.R" --replace-fail \ "nix-valid-geographics" ${validGeographics} ''; });
nearfar = let angrist = fetchurl { url = "https://raw.githubusercontent.com/joerigdon/nearfar/master/angrist.csv"; hash = "sha256-lb+HMHnRGonc26merFGB0B7Vk1Lk+sIJlay+JtQC8m4="; }; in old.nearfar.overrideAttrs (attrs: { postPatch = '' substituteInPlace "R/nearfar.R" --replace-fail \ 'url("https://raw.githubusercontent.com/joerigdon/nearfar/master/angrist.csv")' '"${angrist}"' ''; });
BiocParallel = old.BiocParallel.overrideAttrs (attrs: { env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.hostPlatform.isDarwin " -Wno-error=missing-template-arg-list-after-template-kw"; }; });
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${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz"; });
ChemmineOB = old.ChemmineOB.overrideAttrs (attrs: { # pkg-config knows openbabel-3 without the .0 # Eigen3 is also looked for in the wrong location # pointer was changed in newer version of openbabel: # https://github.com/openbabel/openbabel/commit/305a6fd3183540e4a8ae1d79d10bf1860e6aa373 postPatch = '' substituteInPlace configure \ --replace-fail openbabel-3.0 openbabel-3 substituteInPlace src/Makevars.in \ --replace-fail "-I/usr/include/eigen3" "-I${pkgs.eigen}/include/eigen3" substituteInPlace src/ChemmineOB.cpp \ --replace-fail "obsharedptr<" "std::shared_ptr<" '';
# copied from fastnlo-toolkit: # None of our currently packaged versions of swig are C++17-friendly # Use a workaround from https://github.com/swig/swig/issues/1538 env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = (attrs.env.NIX_CFLAGS_COMPILE or "") + lib.optionalString stdenv.hostPlatform.isDarwin " -D_LIBCPP_ENABLE_CXX17_REMOVED_FEATURES"; }; });
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 zstd.dev ] ++ 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 $out/library/littler/script-tests ''; } );
lpsymphony = old.lpsymphony.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
sodium = old.sodium.overrideAttrs ( attrs: with pkgs; { preConfigure = '' patchShebangs configure ''; nativeBuildInputs = [ pkg-config ] ++ attrs.nativeBuildInputs; buildInputs = [ libsodium.dev ] ++ attrs.buildInputs; } );
keyring = old.keyring.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
Rhtslib = old.Rhtslib.overrideAttrs (attrs: { preConfigure = '' substituteInPlace R/zzz.R --replace-fail "-lcurl" "-L${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-fail \ 'dest_file <- file.path(dest_folder, "h2o.jar")' \ 'dest_file <- file.path("~/.cache/", "h2o.jar")' ''; });
SICtools = old.SICtools.overrideAttrs (attrs: { postPatch = '' substituteInPlace src/Makefile --replace-fail "-lcurses" "-lncurses" ''; hardeningDisable = [ "format" ]; });
Rbwa = old.Rbwa.overrideAttrs (attrs: { # Parallel build cleans up *.o before they can be packed in a library postPatch = '' substituteInPlace src/Makefile --replace-fail \ "all:\$(PROG) ../inst/bwa clean" \ "all:\$(PROG) ../inst/bwa" \ ''; });
ROracle = old.ROracle.overrideAttrs (attrs: { configureFlags = [ "--with-oci-lib=${pkgs.oracle-instantclient.lib}/lib" "--with-oci-inc=${pkgs.oracle-instantclient.dev}/include" ]; });
xslt = old.xslt.overrideAttrs (attrs: { env = (attrs.env or { }) // { NIX_CFLAGS_COMPILE = attrs.env.NIX_CFLAGS_COMPILE + " -fpermissive"; }; });
sparklyr = old.sparklyr.overrideAttrs (attrs: { # Pyspark's spark is full featured and better maintained than pkgs.spark preConfigure = '' if grep "onLoad" R/zzz.R; then echo "onLoad is already present, patch needs to be updated!" exit 1 fi
cat >> R/zzz.R <<EOF .onLoad <- function(...) { Sys.setenv("SPARK_HOME" = Sys.getenv("SPARK_HOME", unset = "${pkgs.python3Packages.pyspark}/${pkgs.python3Packages.python.sitePackages}/pyspark")) Sys.setenv("JAVA_HOME" = Sys.getenv("JAVA_HOME", unset = "${pkgs.jdk}")) } EOF ''; });
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: $(SHLIB) EOF ''; });
RandomFieldsUtils = old.RandomFieldsUtils.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
flowClust = old.flowClust.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
RcppCGAL = old.RcppCGAL.overrideAttrs (_: { postPatch = "patchShebangs configure"; });
httr2 = old.httr2.overrideAttrs (attrs: { preConfigure = "patchShebangs configure"; });
dbarts = old.dbarts.override { platforms = lib.platforms.x86_64 ++ lib.platforms.x86; };
geomorph = old.geomorph.overrideAttrs (attrs: { RGL_USE_NULL = "true"; });
gpuMagic = old.gpuMagic.overrideAttrs (_: { hardeningDisable = [ "format" ]; });
Rdisop = old.Rdisop.overrideAttrs (_: { hardeningDisable = [ "format" ]; });
opencv = let opencvGtk = pkgs.opencv.override (old: { enableGtk2 = true; }); in old.opencv.overrideAttrs (attrs: { buildInputs = attrs.buildInputs ++ [ opencvGtk ]; });
Rhdf5lib = let hdf5 = pkgs.hdf5_1_10; in old.Rhdf5lib.overrideAttrs (attrs: { propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ hdf5.dev pkgs.libaec ]; patches = [ ./patches/Rhdf5lib.patch ]; passthru.hdf5 = hdf5; });
rhdf5filters = old.rhdf5filters.overrideAttrs (attrs: { patches = [ ./patches/rhdf5filters.patch ]; });
rhdf5 = old.rhdf5.overrideAttrs (attrs: { patches = [ ./patches/rhdf5.patch ]; env.NIX_CFLAGS_COMPILE = "-Wno-error=implicit-function-declaration"; });
rmarkdown = old.rmarkdown.overrideAttrs (_: { preConfigure = '' substituteInPlace R/pandoc.R \ --replace-fail '"~/opt/pandoc"' '"~/opt/pandoc", "${pkgs.pandoc}/bin"' ''; });
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"; });
httpuv = old.httpuv.overrideAttrs (_: { preConfigure = '' patchShebangs configure ''; });
oligo = old.oligo.overrideAttrs (_: { hardeningDisable = [ "format" ]; });
tesseract = old.tesseract.overrideAttrs (_: { preConfigure = '' substituteInPlace configure \ --replace-fail 'PKG_CONFIG_NAME="tesseract"' 'PKG_CONFIG_NAME="tesseract lept"' ''; });
ijtiff = old.ijtiff.overrideAttrs (_: { preConfigure = '' patchShebangs configure ''; });
torch = old.torch.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure ''; });
pak = old.pak.overrideAttrs (attrs: { preConfigure = '' patchShebangs configure patchShebangs src/library/curl/configure patchShebangs src/library/keyring/configure patchShebangs src/library/pkgdepends/configure patchShebangs src/library/ps/configure ''; });
pkgdepends = old.pkgdepends.overrideAttrs (attrs: { postPatch = '' patchShebangs configure ''; }); };inself