nixpkgs/pkgs/development/r-modules/default.nix
2020-11-27 01:58:30 +01:00

940 lines
27 KiB
Nix

/* This file defines the composition for CRAN (R) packages. */
{ R, pkgs, overrides }:
let
inherit (pkgs) cacert fetchurl stdenv lib;
buildRPackage = pkgs.callPackage ./generic-builder.nix {
inherit R;
inherit (pkgs.darwin.apple_sdk.frameworks) Cocoa Foundation;
inherit (pkgs) gettext gfortran;
};
# Generates package templates given per-repository settings
#
# some packages, e.g. cncaGUI, require X running while installation,
# so that we use xvfb-run if requireX is true.
mkDerive = {mkHomepage, mkUrls}: args:
lib.makeOverridable ({
name, version, sha256,
depends ? [],
doCheck ? true,
requireX ? false,
broken ? false,
hydraPlatforms ? R.meta.hydraPlatforms
}: buildRPackage {
name = "${name}-${version}";
src = fetchurl {
inherit sha256;
urls = mkUrls (args // { inherit name version; });
};
inherit doCheck requireX;
propagatedBuildInputs = depends;
nativeBuildInputs = depends;
meta.homepage = mkHomepage (args // { inherit name; });
meta.platforms = R.meta.platforms;
meta.hydraPlatforms = hydraPlatforms;
meta.broken = broken;
});
# Templates for generating Bioconductor 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" ];
};
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" ];
};
deriveCran = mkDerive {
mkHomepage = {name, snapshot, ...}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
};
# Overrides package definitions with nativeBuildInputs.
# For example,
#
# overrideNativeBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
# });
# }
overrideNativeBuildInputs = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
})
) overrides;
# Overrides package definitions with buildInputs.
# For example,
#
# overrideBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
# });
# }
overrideBuildInputs = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
buildInputs = attrs.buildInputs ++ value;
})
) overrides;
# Overrides package definitions with new R dependencies.
# For example,
#
# overrideRDepends {
# foo = [ self.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
# });
# }
overrideRDepends = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
})
) overrides;
# Overrides package definition requiring X running to install.
# For example,
#
# overrideRequireX [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# requireX = true;
# };
# }
overrideRequireX = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
requireX = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to skip check.
# For example,
#
# overrideSkipCheck [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# doCheck = false;
# };
# }
overrideSkipCheck = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
doCheck = false;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to mark it broken.
# For example,
#
# overrideBroken [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# broken = true;
# };
# }
overrideBroken = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
broken = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
defaultOverrides = old: new:
let old0 = old; in
let
old1 = old0 // (overrideRequireX packagesRequireingX old0);
old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
old3 = old2 // (overrideRDepends packagesWithRDepends old2);
old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
old6 = old5 // (overrideBroken brokenPackages old5);
old = old6;
in old // (otherOverrides old new);
# Recursive override pattern.
# `_self` is a collection of packages;
# `self` is `_self` with overridden packages;
# packages in `_self` may depends on overridden packages.
self = (defaultOverrides _self self) // overrides;
_self = { inherit buildRPackage; } //
import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
import ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } //
import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } //
import ./cran-packages.nix { inherit self; derive = deriveCran; };
# tweaks for the individual packages and "in self" follow
packagesWithRDepends = {
FactoMineR = [ self.car ];
pander = [ self.codetools ];
};
packagesWithNativeBuildInputs = {
adimpro = [ pkgs.imagemagick ];
animation = [ pkgs.which ];
audio = [ pkgs.portaudio ];
BayesSAE = [ pkgs.gsl_1 ];
BayesVarSel = [ pkgs.gsl_1 ];
BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
bigGP = [ pkgs.openmpi ];
bio3d = [ pkgs.zlib ];
BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ];
bnpmr = [ pkgs.gsl_1 ];
cairoDevice = [ pkgs.gtk2.dev ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
Cardinal = [ pkgs.which ];
chebpol = [ pkgs.fftw ];
ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
cit = [ pkgs.gsl_1 ];
curl = [ pkgs.curl.dev ];
data_table = [pkgs.zlib.dev] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
diversitree = [ pkgs.gsl_1 pkgs.fftw ];
EMCluster = [ pkgs.lapack ];
fftw = [ pkgs.fftw.dev ];
fftwtools = [ pkgs.fftw.dev ];
Formula = [ pkgs.gmp ];
gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkgconfig ];
GLAD = [ pkgs.gsl_1 ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
gmp = [ pkgs.gmp.dev ];
graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ];
haven = [ pkgs.libiconv pkgs.zlib.dev ];
h5vc = [ pkgs.zlib.dev ];
HiCseg = [ pkgs.gsl_1 ];
imager = [ pkgs.x11 ];
iBMQ = [ pkgs.gsl_1 ];
igraph = [ pkgs.gmp pkgs.libxml2.dev ];
JavaGD = [ pkgs.jdk ];
jpeg = [ pkgs.libjpeg.dev ];
jqr = [ pkgs.jq.dev ];
KFKSDS = [ pkgs.gsl_1 ];
kza = [ pkgs.fftw.dev ];
magick = [ pkgs.imagemagick.dev ];
ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
mvabund = [ pkgs.gsl_1 ];
mwaved = [ pkgs.fftw.dev ];
ncdf4 = [ pkgs.netcdf ];
nloptr = [ pkgs.nlopt pkgs.pkgconfig ];
odbc = [ pkgs.unixODBC ];
pander = [ pkgs.pandoc pkgs.which ];
pbdMPI = [ pkgs.openmpi ];
pbdNCDF4 = [ pkgs.netcdf ];
pbdPROF = [ pkgs.openmpi ];
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
pdftools = [ pkgs.poppler.dev ];
phytools = [ pkgs.which ];
PKI = [ pkgs.openssl.dev ];
png = [ pkgs.libpng.dev ];
proj4 = [ pkgs.proj ];
protolite = [ pkgs.protobuf ];
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
RAppArmor = [ pkgs.libapparmor ];
rapportools = [ pkgs.which ];
rapport = [ pkgs.which ];
readxl = [ pkgs.libiconv ];
rcdd = [ pkgs.gmp.dev ];
RcppCNPy = [ pkgs.zlib.dev ];
RcppGSL = [ pkgs.gsl_1 ];
RcppZiggurat = [ pkgs.gsl_1 ];
reprex = [ pkgs.which ];
rgdal = [ pkgs.proj.dev pkgs.gdal ];
rgeos = [ pkgs.geos ];
Rglpk = [ pkgs.glpk ];
RGtk2 = [ pkgs.gtk2.dev ];
rhdf5 = [ pkgs.zlib ];
Rhdf5lib = [ pkgs.zlib ];
Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.lzma.dev pkgs.curl.dev ];
rjags = [ pkgs.jags ];
rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ];
rmatio = [ pkgs.zlib.dev ];
Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
Rmpi = [ pkgs.openmpi ];
RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
RODBC = [ pkgs.libiodbc ];
rpanel = [ pkgs.bwidget ];
rpg = [ pkgs.postgresql ];
Rpoppler = [ pkgs.poppler ];
RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
RProtoBuf = [ pkgs.protobuf ];
RSclient = [ pkgs.openssl.dev ];
Rserve = [ pkgs.openssl ];
Rssa = [ pkgs.fftw.dev ];
rtiff = [ pkgs.libtiff.dev ];
runjags = [ pkgs.jags ];
RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
rzmq = [ pkgs.zeromq ];
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
sdcTable = [ pkgs.gmp pkgs.glpk ];
seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
seqinr = [ pkgs.zlib.dev ];
seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
simplexreg = [ pkgs.gsl_1 ];
spate = [ pkgs.fftw.dev ];
ssanv = [ pkgs.proj ];
stsm = [ pkgs.gsl_1 ];
stringi = [ pkgs.icu.dev ];
survSNP = [ pkgs.gsl_1 ];
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
systemfonts = [ pkgs.fontconfig.dev pkgs.freetype.dev ];
TAQMNGR = [ pkgs.zlib.dev ];
tesseract = [ pkgs.tesseract pkgs.leptonica ];
tiff = [ pkgs.libtiff.dev ];
tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
topicmodels = [ pkgs.gsl_1 ];
udunits2 = [ pkgs.udunits pkgs.expat ];
units = [ pkgs.udunits ];
V8 = [ pkgs.v8 ];
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
affyPLM = [ pkgs.zlib.dev ];
bamsignals = [ pkgs.zlib.dev ];
BitSeq = [ pkgs.zlib.dev ];
DiffBind = [ pkgs.zlib ];
ShortRead = [ pkgs.zlib.dev ];
oligo = [ pkgs.zlib.dev ];
gmapR = [ pkgs.zlib.dev ];
Rsubread = [ pkgs.zlib.dev ];
XVector = [ pkgs.zlib.dev ];
Rsamtools = [ pkgs.zlib.dev pkgs.curl.dev ];
rtracklayer = [ pkgs.zlib.dev ];
affyio = [ pkgs.zlib.dev ];
VariantAnnotation = [ pkgs.zlib.dev pkgs.curl.dev ];
snpStats = [ pkgs.zlib.dev ];
};
packagesWithBuildInputs = {
# sort -t '=' -k 2
gam = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
quantreg = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
rmutil = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
robustbase = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
SparseM = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
RMark = [ pkgs.which ];
RPushbullet = [ pkgs.which ];
RcppEigen = [ pkgs.libiconv ];
RCurl = [ pkgs.curl.dev ];
R2SWF = [ pkgs.pkgconfig ];
rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ];
RGtk2 = [ pkgs.pkgconfig ];
RProtoBuf = [ pkgs.pkgconfig ];
Rpoppler = [ pkgs.pkgconfig ];
XML = [ pkgs.pkgconfig ];
cairoDevice = [ pkgs.pkgconfig ];
chebpol = [ pkgs.pkgconfig ];
fftw = [ pkgs.pkgconfig ];
gdtools = [ pkgs.pkgconfig ];
jqr = [ pkgs.jq.lib ];
kza = [ pkgs.pkgconfig ];
magick = [ pkgs.pkgconfig ];
mwaved = [ pkgs.pkgconfig ];
odbc = [ pkgs.pkgconfig ];
openssl = [ pkgs.pkgconfig ];
pdftools = [ pkgs.pkgconfig ];
sf = [ pkgs.pkgconfig pkgs.sqlite.dev pkgs.proj.dev ];
showtext = [ pkgs.pkgconfig ];
spate = [ pkgs.pkgconfig ];
stringi = [ pkgs.pkgconfig ];
sysfonts = [ pkgs.pkgconfig ];
systemfonts = [ pkgs.pkgconfig ];
tesseract = [ pkgs.pkgconfig ];
Cairo = [ pkgs.pkgconfig ];
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
gridGraphics = [ pkgs.which ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
mzR = [ pkgs.netcdf ];
cluster = [ pkgs.libiconv ];
KernSmooth = [ pkgs.libiconv ];
nlme = [ pkgs.libiconv ];
Matrix = [ pkgs.libiconv ];
mgcv = [ pkgs.libiconv ];
minqa = [ pkgs.libiconv ];
igraph = [ pkgs.libiconv ];
ape = [ pkgs.libiconv ];
expm = [ pkgs.libiconv ];
mnormt = [ pkgs.libiconv ];
pan = [ pkgs.libiconv ];
phangorn = [ pkgs.libiconv ];
quadprog = [ pkgs.libiconv ];
randomForest = [ pkgs.libiconv ];
sundialr = [ pkgs.libiconv ];
ucminf = [ pkgs.libiconv ];
glmnet = [ pkgs.libiconv ];
mvtnorm = [ pkgs.libiconv ];
statmod = [ pkgs.libiconv ];
};
packagesRequireingX = [
"accrual"
"ade4TkGUI"
"analogue"
"analogueExtra"
"AnalyzeFMRI"
"AnnotLists"
"AnthropMMD"
"aplpack"
"asbio"
"BAT"
"BCA"
"betapart"
"BiodiversityR"
"bio_infer"
"bipartite"
"biplotbootGUI"
"blender"
"cairoDevice"
"CCTpack"
"cncaGUI"
"cocorresp"
"CommunityCorrelogram"
"confidence"
"constrainedKriging"
"ConvergenceConcepts"
"cpa"
"DALY"
"dave"
"Deducer"
"DeducerPlugInExample"
"DeducerPlugInScaling"
"DeducerSpatial"
"DeducerSurvival"
"DeducerText"
"Demerelate"
"detrendeR"
"dgmb"
"DivMelt"
"dpa"
"DSpat"
"dynamicGraph"
"dynBiplotGUI"
"EasyqpcR"
"EcoVirtual"
"exactLoglinTest"
"fat2Lpoly"
"fbati"
"FD"
"feature"
"FeedbackTS"
"FFD"
"fgui"
"fisheyeR"
"forams"
"forensim"
"FreeSortR"
"fscaret"
"fSRM"
"gcmr"
"geomorph"
"geoR"
"georob"
"GGEBiplotGUI"
"gnm"
"GPCSIV"
"GrapheR"
"GroupSeq"
"gsubfn"
"GUniFrac"
"gWidgets2RGtk2"
"gWidgets2tcltk"
"HH"
"HiveR"
"ic50"
"iDynoR"
"in2extRemes"
"iplots"
"isopam"
"IsotopeR"
"JGR"
"KappaGUI"
"likeLTD"
"logmult"
"LS2Wstat"
"MareyMap"
"memgene"
"metacom"
"Meth27QC"
"migui"
"miniGUI"
"mixsep"
"MplusAutomation"
"mpmcorrelogram"
"mritc"
"multgee"
"multibiplotGUI"
"OligoSpecificitySystem"
"onemap"
"OpenRepGrid"
"paleoMAS"
"pbatR"
"PBSadmb"
"PBSmodelling"
"PCPS"
"pez"
"phylotools"
"picante"
"plotSEMM"
"plsRbeta"
"plsRglm"
"PopGenReport"
"poppr"
"powerpkg"
"PredictABEL"
"prefmod"
"PrevMap"
"ProbForecastGOP"
"r4ss"
"RandomFields"
"rareNMtests"
"rAverage"
"Rcmdr"
"RcmdrPlugin_coin"
"RcmdrPlugin_depthTools"
"RcmdrPlugin_DoE"
"RcmdrPlugin_EACSPIR"
"RcmdrPlugin_EBM"
"RcmdrPlugin_EcoVirtual"
"RcmdrPlugin_EZR"
"RcmdrPlugin_FactoMineR"
"RcmdrPlugin_HH"
"RcmdrPlugin_IPSUR"
"RcmdrPlugin_KMggplot2"
"RcmdrPlugin_lfstat"
"RcmdrPlugin_MA"
"RcmdrPlugin_MPAStats"
"RcmdrPlugin_orloca"
"RcmdrPlugin_plotByGroup"
"RcmdrPlugin_pointG"
"RcmdrPlugin_qual"
"RcmdrPlugin_ROC"
"RcmdrPlugin_sampling"
"RcmdrPlugin_SCDA"
"RcmdrPlugin_SLC"
"RcmdrPlugin_sos"
"RcmdrPlugin_steepness"
"RcmdrPlugin_survival"
"RcmdrPlugin_TeachingDemos"
"RcmdrPlugin_temis"
"RcmdrPlugin_UCA"
"recluster"
"relimp"
"rgl"
"RHRV"
"rich"
"RNCEP"
"RSDA"
"RSurvey"
"simba"
"Simile"
"SimpleTable"
"SOLOMON"
"soundecology"
"spatsurv"
"sqldf"
"SRRS"
"SSDforR"
"statcheck"
"StatDA"
"STEPCAM"
"stosim"
"strvalidator"
"stylo"
"svDialogstcltk"
"svIDE"
"svSocket"
"svWidgets"
"SYNCSA"
"SyNet"
"tcltk2"
"TestScorer"
"TIMP"
"titan"
"tkrgl"
"tkrplot"
"tmap"
"tspmeta"
"TTAinterfaceTrendAnalysis"
"twiddler"
"vcdExtra"
"VecStatGraphs3D"
"vegan"
"vegan3d"
"vegclust"
"x12GUI"
];
packagesToSkipCheck = [
"Rmpi" # tries to run MPI processes
"pbdMPI" # tries to run MPI processes
"data_table" # fails to rename shared library before check
];
# Packages which cannot be installed due to lack of dependencies or other reasons.
brokenPackages = [
];
otherOverrides = old: new: {
stringi = old.stringi.overrideDerivation (attrs: {
postInstall = let
icuName = "icudt52l";
icuSrc = pkgs.fetchzip {
url = "http://static.rexamine.com/packages/${icuName}.zip";
sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj";
stripRoot = false;
};
in ''
${attrs.postInstall or ""}
cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs
'';
});
xml2 = old.xml2.overrideDerivation (attrs: {
preConfigure = ''
export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
patchShebangs configure
'';
});
Cairo = old.Cairo.overrideDerivation (attrs: {
NIX_LDFLAGS = "-lfontconfig";
});
curl = old.curl.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
RcppParallel = old.RcppParallel.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
ggbio = old.ggbio.overrideDerivation (attrs: {
patches = [
(pkgs.fetchpatch {
url = "https://github.com/tengfei/ggbio/commit/b04a9840cf5c0bd0514db2536f2e610bbd364727.patch";
sha256 = "blwtObyIYo1UBWz4nlmcJ8Nyw/n0qwmJrtwFWuoUyMg=";
})
];
});
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
patchPhase = "patchShebangs configure";
});
data_table = old.data_table.overrideDerivation (attrs: {
NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE + " -fopenmp";
patchPhase = "patchShebangs configure";
postInstall = "mv $out/library/data.table/libs/{data.table,datatable}.so";
});
ModelMetrics = old.ModelMetrics.overrideDerivation (attrs: {
NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE
+ lib.optionalString stdenv.isDarwin " -fopenmp";
});
rpf = old.rpf.overrideDerivation (attrs: {
patchPhase = "patchShebangs configure";
});
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
patches = [ ./patches/BayesXsrc.patch ];
});
Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
patches = [ ./patches/Rhdf5lib.patch ];
});
rJava = old.rJava.overrideDerivation (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
JavaGD = old.JavaGD.overrideDerivation (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
jqr = old.jqr.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
pbdZMQ = old.pbdZMQ.overrideDerivation (attrs: {
postPatch = lib.optionalString stdenv.isDarwin ''
for file in R/*.{r,r.in}; do
sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file
done
'';
});
Rmpi = old.Rmpi.overrideDerivation (attrs: {
configureFlags = [
"--with-Rmpi-type=OPENMPI"
];
});
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
configureFlags = [
"--with-mpfr-include=${pkgs.mpfr.dev}/include"
];
});
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
configureFlags = [
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib"
];
});
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
patches = [ ./patches/RAppArmor.patch ];
LIBAPPARMOR_HOME = pkgs.libapparmor;
});
RMySQL = old.RMySQL.overrideDerivation (attrs: {
MYSQL_DIR="${pkgs.libmysqlclient}";
preConfigure = ''
patchShebangs configure
'';
});
devEMF = old.devEMF.overrideDerivation (attrs: {
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
NIX_LDFLAGS = "-lX11";
});
slfm = old.slfm.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
});
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
});
EMCluster = old.EMCluster.overrideDerivation (attrs: {
patches = [ ./patches/EMCluster.patch ];
});
spMC = old.spMC.overrideDerivation (attrs: {
patches = [ ./patches/spMC.patch ];
});
openssl = old.openssl.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
});
websocket = old.websocket.overrideDerivation (attrs: {
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
});
Rserve = old.Rserve.overrideDerivation (attrs: {
patches = [ ./patches/Rserve.patch ];
configureFlags = [
"--with-server" "--with-client"
];
});
nloptr = old.nloptr.overrideDerivation (attrs: {
# Drop bundled nlopt source code. Probably unnecessary, but I want to be
# sure we're using the system library, not this one.
preConfigure = "rm -r src/nlopt_src";
});
V8 = old.V8.overrideDerivation (attrs: {
postPatch = ''
substituteInPlace configure \
--replace " -lv8_libplatform" ""
'';
preConfigure = ''
export INCLUDE_DIR=${pkgs.v8}/include
export LIB_DIR=${pkgs.v8}/lib
patchShebangs configure
'';
});
acs = old.acs.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
gdtools = old.gdtools.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
NIX_LDFLAGS = "-lfontconfig -lfreetype";
});
magick = old.magick.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
protolite = old.protolite.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
rpanel = old.rpanel.overrideDerivation (attrs: {
preConfigure = ''
export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
'';
TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
});
RPostgres = old.RPostgres.overrideDerivation (attrs: {
preConfigure = ''
export INCLUDE_DIR=${pkgs.postgresql}/include
export LIB_DIR=${pkgs.postgresql.lib}/lib
patchShebangs configure
'';
});
OpenMx = old.OpenMx.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
odbc = old.odbc.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
x13binary = old.x13binary.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
geojsonio = old.geojsonio.overrideDerivation (attrs: {
buildInputs = [ cacert ] ++ attrs.buildInputs;
});
rstan = old.rstan.overrideDerivation (attrs: {
NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
});
mongolite = old.mongolite.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include";
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
});
ps = old.ps.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
rlang = old.rlang.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
systemfonts = old.systemfonts.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
littler = old.littler.overrideAttrs (attrs: with pkgs; {
buildInputs = [ pcre lzma 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
'';
});
};
in
self