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nixpkgs/pkgs/development/r-modules/default.nix
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Merge staging-next into staging
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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.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; } //
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 = {
adbcpostgresql = [ pkgs.postgresql ];
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 ];
audio = [ pkgs.portaudio ];
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 ];
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 ];
diversitree = with pkgs; [ gsl fftw ];
exactextractr = [ pkgs.geos ];
EMCluster = [ pkgs.lapack ];
fangs = [ pkgs.cargo ];
fcl = [ pkgs.cargo ];
fftw = [ pkgs.fftw.dev ];
fftwtools = with pkgs; [ fftw.dev pkg-config ];
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 ];
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 ];
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 ];
rbedrock = [ pkgs.zlib.dev pkgs.which 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 ];
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 ];
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 ];
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; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip libdeflate ];
Rlibeemd = [ pkgs.gsl ];
rmatio = [ pkgs.zlib.dev pkgs.pkg-config ];
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 ];
RPostgres = with pkgs; [ postgresql ];
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 ];
salso = [ pkgs.cargo ];
ymd = [ pkgs.cargo ];
arcpbf = [ pkgs.cargo ];
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 ];
strawr = with pkgs; [ curl.dev ];
string2path = [ pkgs.cargo ];
terra = with pkgs; [ gdal proj geos ];
tok = [ pkgs.cargo ];
rshift = [ pkgs.cargo ];
arcgisutils = with pkgs; [ cargo rustc ];
arcgisgeocode = with pkgs; [ cargo rustc ];
arcgisplaces = with pkgs; [ pkg-config openssl.dev cargo rustc ];
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 ];
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 ];
rswipl = with pkgs; [ cmake pkg-config ];
rrd = [ pkgs.pkg-config ];
surveyvoi = [ pkgs.pkg-config ];
Rbwa = [ pkgs.zlib.dev ];
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 ];
symbolicQspray = [ pkgs.pkg-config ];
sphereTessellation = [ pkgs.pkg-config ];
vapour = [ pkgs.pkg-config ];
};
packagesWithBuildInputs = {
# sort -t '=' -k 2
asciicast = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev libdeflate ];
island = [ pkgs.gsl.dev ];
svKomodo = [ pkgs.which ];
ulid = [ pkgs.zlib.dev ];
unrtf = with pkgs; [ xz.dev bzip2.dev zlib.dev icu.dev libdeflate ];
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 ];
XML = [ pkgs.pkg-config ];
apsimx = [ pkgs.which ];
cairoDevice = [ pkgs.pkg-config ];
chebpol = [ pkgs.pkg-config ];
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];
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 ];
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 = [ pkgs.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 ];
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 ];
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 ];
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 = [ pkgs.eigen ];
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"
"precommit"
"protGear"
"PCRA"
"PSCBS"
"iemisc"
"repmis"
"R_cache"
"R_filesets"
"RKorAPClient"
"R_rsp"
"salso"
"scholar"
"SpatialDecon"
"stepR"
"styler"
"teal_code"
"TreeTools"
"TreeSearch"
"ACNE"
"APAlyzer"
"EstMix"
"Patterns"
"PECA"
"Quartet"
"ShinyQuickStarter"
"TIN"
"cfdnakit"
"CaDrA"
"GNOSIS"
"TotalCopheneticIndex"
"TreeDist"
"biocthis"
"calmate"
"fgga"
"fulltext"
"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"
# Impure network access during build
"waddR"
"tiledb"
"x13binary"
"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: {
# 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 )
vegan3d = old.vegan3d.overrideAttrs (attrs: {
RGL_USE_NULL = "true";
});
arrow = old.arrow.overrideAttrs (attrs: {
src = pkgs.arrow-cpp.src;
name = "r-arrow-${pkgs.arrow-cpp.version}";
prePatch = "cd r";
postPatch = ''
patchShebangs configure
'';
buildInputs = attrs.buildInputs ++ [
pkgs.arrow-cpp
];
});
gifski = old.gifski.overrideAttrs (attrs: {
cargoDeps = pkgs.rustPlatform.fetchCargoTarball {
src = attrs.src;
sourceRoot = "gifski/src/myrustlib";
hash = "sha256-e6nuiQU22GiO2I+bu0muyICGrdkCLSZUDHDz2mM2hz0=";
};
cargoRoot = "src/myrustlib";
nativeBuildInputs = attrs.nativeBuildInputs ++ [
pkgs.rustPlatform.cargoSetupHook
pkgs.cargo
pkgs.rustc
];
});
timeless = old.timeless.overrideAttrs (attrs: {
cargoDeps = pkgs.rustPlatform.fetchCargoTarball {
src = attrs.src;
sourceRoot = "timeless/src/rust";
hash = "sha256-n0/52CV3NzWe7T3N6VoaURMxWrnqeYaUMPKkUy+LRQs=";
};
cargoRoot = "src/rust";
nativeBuildInputs = attrs.nativeBuildInputs ++ [
pkgs.rustPlatform.cargoSetupHook
pkgs.cargo
];
});
stringi = old.stringi.overrideAttrs (attrs: {
postInstall = let
icuName = "icudt52l";
icuSrc = pkgs.fetchzip {
url = "http://static.rexamine.com/packages/${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
'';
});
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";
});
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";
});
gmailr = old.gmailr.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
heck = old.heck.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
surtvep = old.surtvep.overrideAttrs (attrs: {
postPatch = "patchShebangs configure";
});
purrr = old.purrr.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";
});
b64 = old.b64.overrideAttrs (attrs: {
nativeBuildInputs = [ pkgs.cargo ] ++ attrs.nativeBuildInputs;
postPatch = "patchShebangs configure";
});
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"
'';
});
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}
'';
});
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: {
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"
];
});
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="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
'';
TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.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;
});
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: {
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;
});
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}"'
'';
});
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${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
});
ChemmineOB = let
# R package doesn't compile with the latest (unstable) version.
# Override from nixpkgs-23.11
openbabel3 = pkgs.openbabel.overrideAttrs (attrs: {
version = "3.1.1";
src = pkgs.fetchFromGitHub {
owner = "openbabel";
repo = "openbabel";
rev = "openbabel-${lib.replaceStrings ["."] ["-"] attrs.version}";
sha256 = "sha256-wQpgdfCyBAoh4pmj9j7wPTlMtraJ62w/EShxi/olVMY=";
};
});
in
old.ChemmineOB.overrideAttrs (attrs: {
# pkg-config knows openbabel-3 without the .0
# Eigen3 is also looked for in the wrong location
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"
'';
buildInputs = attrs.buildInputs ++ [openbabel3];
});
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: {
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 = ''
substituteInPlace R/zzz.R \
--replace ".onLoad <- function(...) {" \
".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 = \"${pkgs.jdk}\"))"
'';
});
proj4 = old.proj4.overrideAttrs (attrs: {
preConfigure = ''
substituteInPlace configure \
--replace "-lsqlite3" "-L${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; };
RcppCGAL = old.RcppCGAL.overrideAttrs (_: {
postPatch = "patchShebangs configure";
});
SharedObject = old.SharedObject.overrideAttrs (attrs: {
# backport PR resolving build issues: https://github.com/Jiefei-Wang/SharedObject/pull/17
patches = let inherit (pkgs) fetchpatch; in [
(fetchpatch {
url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/50c4b2964649d7f5a14d843bd7089ab62650fcd3.patch";
sha256 = "sha256-zn535IeOYRvyQ2yxgoGEq2wccrl9xdu9nREmy7sV+PQ=";
})
(fetchpatch {
url = "https://github.com/Jiefei-Wang/SharedObject/pull/17/commits/bf096a39858e9210cbe246d4b136905d4cfbfaf4.patch";
sha256 = "sha256-Z+BZOkFnLgIBiVuPsAHp7bMXzADcvuHV4hILdmLvd+k=";
})
];
});
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.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: {
patches = [ ./patches/rhdf5filters.patch ];
});
rhdf5= old.rhdf5.overrideAttrs (attrs: {
patches = [ ./patches/rhdf5.patch ];
});
rmarkdown = old.rmarkdown.overrideAttrs (_: {
preConfigure = ''
substituteInPlace R/pandoc.R \
--replace '"~/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 '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/pkgdepends/configure
patchShebangs src/library/ps/configure
'';
});
pkgdepends = old.pkgdepends.overrideAttrs (attrs: {
postPatch = ''
patchShebangs configure
'';
});
};
in
self
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