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nixpkgs/pkgs/development/r-modules/default.nix
Peter Simons bb42c215e2 R: improve support for CRAN and Bioconductor package sets 
- Update the instructions for re-generating each of the package set files.
 - Provide test-evaluation.nix expression to verify that the package sets evaluates.
 - Update list of known broken packages.
2015-06-17 23:19:56 +02:00

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/* This file defines the composition for CRAN (R) packages. */
{ R, pkgs, overrides }:
let
inherit (pkgs) fetchurl stdenv lib;
buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; };
# 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}: 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 { inherit name version; };
};
inherit doCheck requireX;
propagatedBuildInputs = depends;
nativeBuildInputs = depends;
meta.homepage = mkHomepage 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: "http://cran.r-project.org/web/packages/${name}/";
mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ];
};
deriveCran = mkDerive {
mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html";
mkUrls = {name, version}: [
"mirror://cran/src/contrib/${name}_${version}.tar.gz"
"mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
];
};
# Overrides package definitions with nativeBuildInputs.
# For example,
#
# overrideNativeBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
# });
# }
overrideNativeBuildInputs = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
})
) overrides;
# Overrides package definitions with buildInputs.
# For example,
#
# overrideBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
# });
# }
overrideBuildInputs = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
buildInputs = attrs.buildInputs ++ value;
})
) overrides;
# Overrides package definitions with new R dependencies.
# For example,
#
# overrideRDepends {
# foo = [ self.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
# });
# }
overrideRDepends = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
})
) overrides;
# Overrides package definition requiring X running to install.
# For example,
#
# overrideRequireX [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# requireX = true;
# };
# }
overrideRequireX = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
requireX = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to skip check.
# For example,
#
# overrideSkipCheck [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# doCheck = false;
# };
# }
overrideSkipCheck = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
doCheck = false;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to mark it broken.
# For example,
#
# overrideBroken [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# broken = true;
# };
# }
overrideBroken = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
broken = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
defaultOverrides = old: new:
let old0 = old; in
let
old1 = old0 // (overrideRequireX packagesRequireingX old0);
old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
old3 = old2 // (overrideRDepends packagesWithRDepends old2);
old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
old6 = old5 // (overrideBroken brokenPackages old5);
old = old6;
in old // (otherOverrides old new);
# Recursive override pattern.
# `_self` is a collection of packages;
# `self` is `_self` with overridden packages;
# packages in `_self` may depends on overridden packages.
self = (defaultOverrides _self self) // overrides;
_self = import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
import ./cran-packages.nix { inherit self; derive = deriveCran; };
# tweaks for the individual packages and "in self" follow
packagesWithRDepends = {
FactoMineR = [ self.car ];
pander = [ self.codetools ];
};
packagesWithNativeBuildInputs = {
abn = [ pkgs.gsl ];
adimpro = [ pkgs.imagemagick ];
audio = [ pkgs.portaudio ];
BayesSAE = [ pkgs.gsl ];
BayesVarSel = [ pkgs.gsl ];
BayesXsrc = [ pkgs.readline pkgs.ncurses ];
bigGP = [ pkgs.openmpi ];
BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ];
bnpmr = [ pkgs.gsl ];
BNSP = [ pkgs.gsl ];
cairoDevice = [ pkgs.gtk2 ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
Cardinal = [ pkgs.which ];
CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
chebpol = [ pkgs.fftw ];
ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
cit = [ pkgs.gsl ];
curl = [ pkgs.curl ];
devEMF = [ pkgs.xlibs.libXft ];
diversitree = [ pkgs.gsl pkgs.fftw ];
EMCluster = [ pkgs.liblapack ];
fftw = [ pkgs.fftw ];
fftwtools = [ pkgs.fftw ];
Formula = [ pkgs.gmp ];
geoCount = [ pkgs.gsl ];
git2r = [ pkgs.zlib pkgs.openssl ];
GLAD = [ pkgs.gsl ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
gmp = [ pkgs.gmp ];
graphscan = [ pkgs.gsl ];
gsl = [ pkgs.gsl ];
HiCseg = [ pkgs.gsl ];
iBMQ = [ pkgs.gsl ];
igraph = [ pkgs.gmp ];
JavaGD = [ pkgs.jdk ];
jpeg = [ pkgs.libjpeg ];
KFKSDS = [ pkgs.gsl ];
kza = [ pkgs.fftw ];
libamtrack = [ pkgs.gsl ];
mixcat = [ pkgs.gsl ];
mvabund = [ pkgs.gsl ];
mwaved = [ pkgs.fftw ];
ncdf4 = [ pkgs.netcdf ];
ncdf = [ pkgs.netcdf ];
nloptr = [ pkgs.nlopt ];
openssl = [ pkgs.openssl ];
outbreaker = [ pkgs.gsl ];
pander = [ pkgs.pandoc pkgs.which ];
pbdMPI = [ pkgs.openmpi ];
pbdNCDF4 = [ pkgs.netcdf ];
pbdPROF = [ pkgs.openmpi ];
PKI = [ pkgs.openssl ];
png = [ pkgs.libpng ];
PopGenome = [ pkgs.zlib ];
proj4 = [ pkgs.proj ];
qtbase = [ pkgs.qt4 ];
qtpaint = [ pkgs.qt4 ];
R2GUESS = [ pkgs.gsl ];
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
RAppArmor = [ pkgs.libapparmor ];
rapportools = [ pkgs.which ];
rapport = [ pkgs.which ];
rbamtools = [ pkgs.zlib ];
RCA = [ pkgs.gmp ];
rcdd = [ pkgs.gmp ];
RcppCNPy = [ pkgs.zlib ];
RcppGSL = [ pkgs.gsl ];
RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
RcppZiggurat = [ pkgs.gsl ];
rgdal = [ pkgs.proj pkgs.gdal ];
rgeos = [ pkgs.geos ];
rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
rgl = [ pkgs.mesa pkgs.x11 ];
Rglpk = [ pkgs.glpk ];
RGtk2 = [ pkgs.gtk2 ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
Rhtslib = [ pkgs.zlib ];
ridge = [ pkgs.gsl ];
RJaCGH = [ pkgs.zlib ];
rjags = [ pkgs.jags ];
rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl ];
rmatio = [ pkgs.zlib ];
Rmpfr = [ pkgs.gmp pkgs.mpfr ];
Rmpi = [ pkgs.openmpi ];
RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
RODBCext = [ pkgs.libiodbc ];
RODBC = [ pkgs.libiodbc ];
rpg = [ pkgs.postgresql ];
rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
Rpoppler = [ pkgs.poppler ];
RPostgreSQL = [ pkgs.postgresql ];
RProtoBuf = [ pkgs.protobuf ];
rpud = [ pkgs.linuxPackages.nvidia_x11 ];
rPython = [ pkgs.python ];
RSclient = [ pkgs.openssl ];
Rserve = [ pkgs.openssl ];
Rssa = [ pkgs.fftw ];
rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
rtiff = [ pkgs.libtiff ];
runjags = [ pkgs.jags ];
RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
rzmq = [ pkgs.zeromq3 ];
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
sdcTable = [ pkgs.gmp pkgs.glpk ];
seewave = [ pkgs.fftw pkgs.libsndfile ];
SemiCompRisks = [ pkgs.gsl ];
seqinr = [ pkgs.zlib ];
seqminer = [ pkgs.zlib pkgs.bzip2 ];
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
simplexreg = [ pkgs.gsl ];
SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
spate = [ pkgs.fftw ];
sprint = [ pkgs.openmpi ];
ssanv = [ pkgs.proj ];
stsm = [ pkgs.gsl ];
survSNP = [ pkgs.gsl ];
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
TAQMNGR = [ pkgs.zlib ];
tiff = [ pkgs.libtiff ];
TKF = [ pkgs.gsl ];
tkrplot = [ pkgs.xlibs.libX11 ];
topicmodels = [ pkgs.gsl ];
udunits2 = [ pkgs.udunits pkgs.expat ];
V8 = [ pkgs.v8 ];
VBLPCM = [ pkgs.gsl ];
VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
WhopGenome = [ pkgs.zlib ];
XBRL = [ pkgs.zlib pkgs.libxml2 ];
xml2 = [ pkgs.libxml2 ];
XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
};
packagesWithBuildInputs = {
# sort -t '=' -k 2
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_nblast = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
RMark = [ pkgs.which ];
RPushbullet = [ pkgs.which ];
qtpaint = [ pkgs.cmake ];
qtbase = [ pkgs.cmake pkgs.perl ];
gmatrix = [ pkgs.cudatoolkit ];
WideLM = [ pkgs.cudatoolkit ];
RCurl = [ pkgs.curl ];
R2SWF = [ pkgs.pkgconfig ];
rggobi = [ pkgs.pkgconfig ];
RGtk2 = [ pkgs.pkgconfig ];
RProtoBuf = [ pkgs.pkgconfig ];
Rpoppler = [ pkgs.pkgconfig ];
VBmix = [ pkgs.pkgconfig ];
XML = [ pkgs.pkgconfig ];
cairoDevice = [ pkgs.pkgconfig ];
chebpol = [ pkgs.pkgconfig ];
fftw = [ pkgs.pkgconfig ];
geoCount = [ pkgs.pkgconfig ];
kza = [ pkgs.pkgconfig ];
mwaved = [ pkgs.pkgconfig ];
showtext = [ pkgs.pkgconfig ];
spate = [ pkgs.pkgconfig ];
stringi = [ pkgs.pkgconfig ];
sysfonts = [ pkgs.pkgconfig ];
Cairo = [ pkgs.pkgconfig ];
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
qtutils = [ pkgs.qt4 ];
ecoretriever = [ pkgs.which ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.which pkgs.texLive ];
rPython = [ pkgs.which ];
CARramps = [ pkgs.which pkgs.cudatoolkit ];
gridGraphics = [ pkgs.which ];
gputools = [ pkgs.which pkgs.cudatoolkit ];
rpud = [ pkgs.which pkgs.cudatoolkit ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
};
packagesRequireingX = [
"accrual"
"ade4TkGUI"
"adehabitat"
"analogue"
"analogueExtra"
"AnalyzeFMRI"
"AnnotLists"
"AnthropMMD"
"aplpack"
"aqfig"
"arf3DS4"
"asbio"
"AtelieR"
"BAT"
"bayesDem"
"BCA"
"BEQI2"
"betapart"
"betaper"
"BHMSMAfMRI"
"BiodiversityR"
"BioGeoBEARS"
"bio_infer"
"bipartite"
"biplotbootGUI"
"blender"
"cairoDevice"
"CCTpack"
"cncaGUI"
"cocorresp"
"CommunityCorrelogram"
"confidence"
"constrainedKriging"
"ConvergenceConcepts"
"cpa"
"DALY"
"dave"
"debug"
"Deducer"
"DeducerExtras"
"DeducerPlugInExample"
"DeducerPlugInScaling"
"DeducerSpatial"
"DeducerSurvival"
"DeducerText"
"Demerelate"
"DescTools"
"detrendeR"
"dgmb"
"DivMelt"
"dpa"
"DSpat"
"dynamicGraph"
"dynBiplotGUI"
"EasyqpcR"
"EcoVirtual"
"ENiRG"
"EnQuireR"
"eVenn"
"exactLoglinTest"
"FAiR"
"fat2Lpoly"
"fbati"
"FD"
"feature"
"FeedbackTS"
"FFD"
"fgui"
"fisheyeR"
"fit4NM"
"forams"
"forensim"
"FreeSortR"
"fscaret"
"fSRM"
"gcmr"
"Geneland"
"GeoGenetix"
"geomorph"
"geoR"
"geoRglm"
"georob"
"GeoXp"
"GGEBiplotGUI"
"gnm"
"GPCSIV"
"GrammR"
"GrapheR"
"GroupSeq"
"gsubfn"
"GUniFrac"
"gWidgets2RGtk2"
"gWidgets2tcltk"
"gWidgetsRGtk2"
"gWidgetstcltk"
"HH"
"HiveR"
"HomoPolymer"
"iBUGS"
"ic50"
"iDynoR"
"in2extRemes"
"iplots"
"isopam"
"IsotopeR"
"JGR"
"KappaGUI"
"likeLTD"
"loe"
"logmult"
"LS2Wstat"
"MAR1"
"MareyMap"
"memgene"
"MergeGUI"
"metacom"
"Meth27QC"
"MetSizeR"
"MicroStrategyR"
"migui"
"miniGUI"
"MissingDataGUI"
"mixsep"
"mlDNA"
"MplusAutomation"
"mpmcorrelogram"
"mritc"
"MTurkR"
"multgee"
"multibiplotGUI"
"nodiv"
"OligoSpecificitySystem"
"onemap"
"OpenRepGrid"
"palaeoSig"
"paleoMAS"
"pbatR"
"PBSadmb"
"PBSmodelling"
"PCPS"
"pez"
"phylotools"
"picante"
"PKgraph"
"playwith"
"plotSEMM"
"plsRbeta"
"plsRglm"
"pmg"
"PopGenReport"
"poppr"
"powerpkg"
"PredictABEL"
"prefmod"
"PrevMap"
"ProbForecastGOP"
"QCAGUI"
"qtbase"
"qtpaint"
"qtutils"
"R2STATS"
"r4ss"
"RandomFields"
"rareNMtests"
"rAverage"
"Rcmdr"
"RcmdrPlugin_BCA"
"RcmdrPlugin_coin"
"RcmdrPlugin_depthTools"
"RcmdrPlugin_DoE"
"RcmdrPlugin_doex"
"RcmdrPlugin_EACSPIR"
"RcmdrPlugin_EBM"
"RcmdrPlugin_EcoVirtual"
"RcmdrPlugin_epack"
"RcmdrPlugin_EZR"
"RcmdrPlugin_FactoMineR"
"RcmdrPlugin_HH"
"RcmdrPlugin_IPSUR"
"RcmdrPlugin_KMggplot2"
"RcmdrPlugin_lfstat"
"RcmdrPlugin_MA"
"RcmdrPlugin_mosaic"
"RcmdrPlugin_MPAStats"
"RcmdrPlugin_orloca"
"RcmdrPlugin_plotByGroup"
"RcmdrPlugin_pointG"
"RcmdrPlugin_qual"
"RcmdrPlugin_ROC"
"RcmdrPlugin_sampling"
"RcmdrPlugin_SCDA"
"RcmdrPlugin_SLC"
"RcmdrPlugin_SM"
"RcmdrPlugin_sos"
"RcmdrPlugin_StatisticalURV"
"RcmdrPlugin_steepness"
"RcmdrPlugin_survival"
"RcmdrPlugin_TeachingDemos"
"RcmdrPlugin_temis"
"RcmdrPlugin_UCA"
"recluster"
"relax"
"relimp"
"RenextGUI"
"reportRx"
"reshapeGUI"
"rgl"
"RHRV"
"rich"
"ringscale"
"rioja"
"ripa"
"rite"
"rnbn"
"RNCEP"
"RQDA"
"RSDA"
"rsgcc"
"RSurvey"
"RunuranGUI"
"sdcMicroGUI"
"sharpshootR"
"simba"
"Simile"
"SimpleTable"
"SOLOMON"
"soundecology"
"SPACECAP"
"spacodiR"
"spatsurv"
"sqldf"
"SRRS"
"SSDforR"
"statcheck"
"StatDA"
"STEPCAM"
"stosim"
"strvalidator"
"stylo"
"svDialogstcltk"
"svIDE"
"svSocket"
"svWidgets"
"SYNCSA"
"SyNet"
"tcltk2"
"TDMR"
"TED"
"TestScorer"
"TIMP"
"titan"
"tkrgl"
"tkrplot"
"tmap"
"tspmeta"
"TTAinterfaceTrendAnalysis"
"twiddler"
"vcdExtra"
"VecStatGraphs3D"
"vegan"
"vegan3d"
"vegclust"
"VIMGUI"
"WMCapacity"
"x12GUI"
"xergm"
];
packagesToSkipCheck = [
"Rmpi" # tries to run MPI processes
"gmatrix" # requires CUDA runtime
"sprint" # tries to run MPI processes
"pbdMPI" # tries to run MPI processes
];
# Packages which cannot be installed due to lack of dependencies or other reasons.
brokenPackages = [
"a4Base" # depends on broken package annaffy-1.41.1
"a4" # depends on broken package annaffy-1.41.1
"a4Reporting" # depends on broken package annaffy-1.41.1
"abd" # depends on broken package nlopt-2.4.2
"adabag" # depends on broken package nlopt-2.4.2
"ADaCGH2" # depends on broken package tilingArray-1.47.0
"adSplit" # build is broken
"AER" # depends on broken package nlopt-2.4.2
"afex" # depends on broken package nlopt-2.4.2
"affyContam" # depends on broken package affyio-1.37.0
"affycoretools" # depends on broken package affyio-1.37.0
"affy" # depends on broken package affyio-1.37.0
"AffyExpress" # depends on broken package affyio-1.37.0
"affyILM" # depends on broken package affyio-1.37.0
"affyio" # build is broken
"affylmGUI" # depends on broken package affyio-1.37.0
"affyPara" # depends on broken package affyio-1.37.0
"affypdnn" # depends on broken package affyio-1.37.0
"affyPLM" # depends on broken package affyio-1.37.0
"affyQCReport" # depends on broken package affyio-1.37.0
"AffyRNADegradation" # depends on broken package affyio-1.37.0
"AffyTiling" # depends on broken package affyio-1.37.0
"AgiMicroRna" # depends on broken package affyio-1.37.0
"agRee" # depends on broken package nlopt-2.4.2
"aLFQ" # depends on broken package nlopt-2.4.2
"alr3" # depends on broken package nlopt-2.4.2
"alr4" # depends on broken package nlopt-2.4.2
"altcdfenvs" # depends on broken package affyio-1.37.0
"anacor" # depends on broken package nlopt-2.4.2
"annaffy" # build is broken
"AnnotationForge" # Build Is Broken
"AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0
"aods3" # depends on broken package nlopt-2.4.2
"apComplex" # build is broken
"apt" # depends on broken package nlopt-2.4.2
"ArfimaMLM" # depends on broken package nlopt-2.4.2
"arm" # depends on broken package nlopt-2.4.2
"ArrayExpress" # depends on broken package affyio-1.37.0
"arrayMvout" # depends on broken package affyio-1.37.0
"arrayQualityMetrics" # depends on broken package affyio-1.37.0
"ArrayTools" # depends on broken package affyio-1.37.0
"ArrayTV" # depends on broken package affyio-1.37.0
"ARRmNormalization" # Build Is Broken
"ARTool" # depends on broken package nlopt-2.4.2
"attract" # depends on broken package AnnotationForge-1.11.3
"BACA" # depends on broken package Category-2.35.1
"BAGS" # build is broken
"bartMachine" # depends on broken package nlopt-2.4.2
"bayesDem" # depends on broken package nlopt-2.4.2
"bayesLife" # depends on broken package nlopt-2.4.2
"bayesPop" # depends on broken package nlopt-2.4.2
"Bayesthresh" # depends on broken package nlopt-2.4.2
"BBRecapture" # depends on broken package nlopt-2.4.2
"BCA" # depends on broken package nlopt-2.4.2
"bgmm" # depends on broken package nlopt-2.4.2
"bgx" # depends on broken package affyio-1.37.0
"BIFIEsurvey" # depends on broken package nlopt-2.4.2
"BiGGR" # depends on broken package rsbml-2.27.0
"BiodiversityR" # depends on broken package nlopt-2.4.2
"birte" # build is broken
"BiSEp" # depends on broken package GOSemSim-1.27.3
"blmeco" # depends on broken package nlopt-2.4.2
"blme" # depends on broken package nlopt-2.4.2
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"imageHTS" # depends on broken package Category-2.35.1
"immunoClust" # build is broken
"imputeR" # depends on broken package nlopt-2.4.2
"in2extRemes" # depends on broken package nlopt-2.4.2
"incReg" # depends on broken package nlopt-2.4.2
"inferference" # depends on broken package nlopt-2.4.2
"influence_ME" # depends on broken package nlopt-2.4.2
"inSilicoMerging" # build is broken
"interactiveDisplayBase" # build is broken
"interactiveDisplay" # depends on broken package Category-2.35.1
"IsingFit" # depends on broken package nlopt-2.4.2
"IsoGene" # depends on broken package affyio-1.37.0
"IsoGeneGUI" # depends on broken package affyio-1.37.0
"ITALICS" # depends on broken package oligo-1.33.0
"IVAS" # depends on broken package nlopt-2.4.2
"ivpack" # depends on broken package nlopt-2.4.2
"JAGUAR" # depends on broken package nlopt-2.4.2
"joda" # depends on broken package nlopt-2.4.2
"jomo" # build is broken
"KANT" # depends on broken package affyio-1.37.0
"keggorthology" # build is broken
"learnstats" # depends on broken package nlopt-2.4.2
"lessR" # depends on broken package nlopt-2.4.2
"lfe" # build is broken
"limmaGUI" # depends on broken package affyio-1.37.0
"LiquidAssociation" # build is broken
"lmdme" # build is broken
"lme4" # depends on broken package nlopt-2.4.2
"LMERConvenienceFunctions" # depends on broken package nlopt-2.4.2
"lmerTest" # depends on broken package nlopt-2.4.2
"LMGene" # depends on broken package affyio-1.37.0
"lmSupport" # depends on broken package nlopt-2.4.2
"LogisticDx" # depends on broken package nlopt-2.4.2
"logitT" # depends on broken package affyio-1.37.0
"longpower" # depends on broken package nlopt-2.4.2
"lumi" # depends on broken package affyio-1.37.0
"LVSmiRNA" # depends on broken package affyio-1.37.0
"MAIT" # depends on broken package nlopt-2.4.2
"makecdfenv" # depends on broken package affyio-1.37.0
"mAPKL" # build is broken
"maPredictDSC" # depends on broken package nlopt-2.4.2
"marked" # depends on broken package nlopt-2.4.2
"maskBAD" # depends on broken package affyio-1.37.0
"MatrixRider" # depends on broken package DirichletMultinomial-1.11.1
"MaxPro" # depends on broken package nlopt-2.4.2
"mbest" # depends on broken package nlopt-2.4.2
"mBPCR" # depends on broken package affyio-1.37.0
"MCRestimate" # build is broken
"mdgsa" # build is broken
"meboot" # depends on broken package nlopt-2.4.2
"MEDME" # depends on broken package nlopt-2.4.2
"MEMSS" # depends on broken package nlopt-2.4.2
"meshr" # depends on broken package Category-2.35.1
"metagear" # build is broken
"metaplus" # depends on broken package nlopt-2.4.2
"metaseqR" # depends on broken package affyio-1.37.0
"Metatron" # depends on broken package nlopt-2.4.2
"methyAnalysis" # depends on broken package affyio-1.37.0
"miceadds" # depends on broken package nlopt-2.4.2
"micEconAids" # depends on broken package nlopt-2.4.2
"micEconCES" # depends on broken package nlopt-2.4.2
"micEconSNQP" # depends on broken package nlopt-2.4.2
"mi" # depends on broken package nlopt-2.4.2
"migui" # depends on broken package nlopt-2.4.2
"MineICA" # depends on broken package AnnotationForge-1.11.3
"MinimumDistance" # depends on broken package affyio-1.37.0
"missMDA" # depends on broken package nlopt-2.4.2
"mitoODE" # build is broken
"mixAK" # depends on broken package nlopt-2.4.2
"mixlm" # depends on broken package nlopt-2.4.2
"MixMAP" # depends on broken package nlopt-2.4.2
"mlmRev" # depends on broken package nlopt-2.4.2
"MLP" # depends on broken package affyio-1.37.0
"MLSeq" # depends on broken package nlopt-2.4.2
"mlVAR" # depends on broken package nlopt-2.4.2
"MMDiff" # depends on broken package AnnotationForge-1.11.3
"MmPalateMiRNA" # depends on broken package affyio-1.37.0
"mongolite" # build is broken
"monocle" # build is broken
"mosaic" # depends on broken package nlopt-2.4.2
"MSGFgui" # depends on broken package MSGFplus-1.3.0
"MSGFplus" # Build Is Broken
"msmsEDA" # depends on broken package affyio-1.37.0
"msmsTests" # depends on broken package affyio-1.37.0
"MSnbase" # depends on broken package affyio-1.37.0
"MSnID" # depends on broken package affyio-1.37.0
"MSstats" # depends on broken package nlopt-2.4.2
"multiDimBio" # depends on broken package nlopt-2.4.2
"MultiRR" # depends on broken package nlopt-2.4.2
"muma" # depends on broken package nlopt-2.4.2
"mutossGUI" # build is broken
"mvGST" # depends on broken package AnnotationForge-1.11.3
"mvinfluence" # depends on broken package nlopt-2.4.2
"mzR" # build is broken
"NanoStringQCPro" # build is broken
"nCal" # depends on broken package nlopt-2.4.2
"ncdfFlow" # build is broken
"NCIgraph" # depends on broken package RCytoscape-1.19.0
"netbenchmark" # build is broken
"NHPoisson" # depends on broken package nlopt-2.4.2
"nloptr" # depends on broken package nlopt-2.4.2
"nondetects" # depends on broken package affyio-1.37.0
"nonrandom" # depends on broken package nlopt-2.4.2
"NormqPCR" # depends on broken package affyio-1.37.0
"NORRRM" # build is broken
"npIntFactRep" # depends on broken package nlopt-2.4.2
"oligoClasses" # depends on broken package affyio-1.37.0
"oligo" # depends on broken package affyio-1.37.0
"OmicsMarkeR" # depends on broken package nlopt-2.4.2
"oneChannelGUI" # depends on broken package affyio-1.37.0
"OpenCL" # build is broken
"openCyto" # depends on broken package ncdfFlow-2.15.2
"OpenMx" # build is broken
"OperaMate" # depends on broken package Category-2.35.1
"ordBTL" # depends on broken package nlopt-2.4.2
"OUwie" # depends on broken package nlopt-2.4.2
"PADOG" # build is broken
"pamm" # depends on broken package nlopt-2.4.2
"PANDA" # build is broken
"panelAR" # depends on broken package nlopt-2.4.2
"panp" # depends on broken package affyio-1.37.0
"papeR" # depends on broken package nlopt-2.4.2
"parboost" # depends on broken package nlopt-2.4.2
"parma" # depends on broken package nlopt-2.4.2
"pathClass" # depends on broken package affyio-1.37.0
"pathRender" # build is broken
"PatternClass" # build is broken
"Pbase" # depends on broken package affyio-1.37.0
"pbdSLAP" # build is broken
"PBImisc" # depends on broken package nlopt-2.4.2
"pbkrtest" # depends on broken package nlopt-2.4.2
"PBSddesolve" # build is broken
"PBSmapping" # build is broken
"PCpheno" # depends on broken package Category-2.35.1
"pdInfoBuilder" # depends on broken package affyio-1.37.0
"pdmclass" # build is broken
"PECA" # depends on broken package affyio-1.37.0
"pedigreemm" # depends on broken package nlopt-2.4.2
"pedometrics" # depends on broken package nlopt-2.4.2
"pequod" # depends on broken package nlopt-2.4.2
"PGSEA" # depends on broken package annaffy-1.41.1
"phenoDist" # depends on broken package Category-2.35.1
"phenoTest" # depends on broken package Category-2.35.1
"PhenStat" # depends on broken package nlopt-2.4.2
"phia" # depends on broken package nlopt-2.4.2
"phylocurve" # depends on broken package nlopt-2.4.2
"phyloTop" # depends on broken package nlopt-2.4.2
"plateCore" # depends on broken package ncdfFlow-2.15.2
"plier" # depends on broken package affyio-1.37.0
"plsRbeta" # depends on broken package nlopt-2.4.2
"plsRcox" # depends on broken package nlopt-2.4.2
"plsRglm" # depends on broken package nlopt-2.4.2
"plw" # depends on broken package affyio-1.37.0
"pmm" # depends on broken package nlopt-2.4.2
"polytomous" # depends on broken package nlopt-2.4.2
"pomp" # depends on broken package nlopt-2.4.2
"ppiPre" # depends on broken package GOSemSim-1.27.3
"ppiStats" # depends on broken package Category-2.35.1
"prebs" # depends on broken package affyio-1.37.0
"predictmeans" # depends on broken package nlopt-2.4.2
"prLogistic" # depends on broken package nlopt-2.4.2
"ProCoNA" # depends on broken package AnnotationForge-1.11.3
"pRoloc" # depends on broken package nlopt-2.4.2
"pRolocGUI" # depends on broken package nlopt-2.4.2
"proteoQC" # depends on broken package affyio-1.37.0
"PSAboot" # depends on broken package nlopt-2.4.2
"puma" # depends on broken package affyio-1.37.0
"pvac" # depends on broken package affyio-1.37.0
"pvca" # depends on broken package nlopt-2.4.2
"pwOmics" # depends on broken package interactiveDisplayBase-1.7.0
"qcmetrics" # build is broken
"qgraph" # depends on broken package nlopt-2.4.2
"qpcrNorm" # depends on broken package affyio-1.37.0
"qtlnet" # depends on broken package nlopt-2.4.2
"QUALIFIER" # depends on broken package ncdfFlow-2.15.2
"quantification" # depends on broken package nlopt-2.4.2
"R2STATS" # depends on broken package nlopt-2.4.2
"radiant" # depends on broken package nlopt-2.4.2
"raincpc" # build is broken
"rainfreq" # build is broken
"RamiGO" # depends on broken package RCytoscape-1.19.0
"rasclass" # depends on broken package nlopt-2.4.2
"RbioRXN" # depends on broken package ChemmineR-2.21.7
"Rchemcpp" # depends on broken package ChemmineR-2.21.7
"Rcmdr" # depends on broken package nlopt-2.4.2
"RcmdrMisc" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_BCA" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_coin" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_depthTools" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_DoE" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_doex" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_EACSPIR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_IPSUR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_KMggplot2" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_lfstat" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_MA" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_mosaic" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_MPAStats" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_NMBU" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_orloca" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_plotByGroup" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_pointG" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_qual" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_RMTCJags" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_ROC" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_sampling" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_SCDA" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_seeg" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_SLC" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_SM" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_sos" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_StatisticalURV" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_steepness" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_survival" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_TeachingDemos" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_temis" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_UCA" # depends on broken package nlopt-2.4.2
"Rcpi" # depends on broken package ChemmineR-2.21.7
"RcppOctave" # build is broken
"RcppRedis" # build is broken
"RCytoscape" # Build Is Broken
"RDAVIDWebService" # depends on broken package Category-2.35.1
"rdd" # depends on broken package nlopt-2.4.2
"RDieHarder" # build is broken
"ReactomePA" # depends on broken package GOSemSim-1.27.3
"ReadqPCR" # depends on broken package affyio-1.37.0
"referenceIntervals" # depends on broken package nlopt-2.4.2
"RefNet" # depends on broken package interactiveDisplayBase-1.7.0
"RefPlus" # depends on broken package affyio-1.37.0
"refund" # depends on broken package nlopt-2.4.2
"Repitools" # depends on broken package affyio-1.37.0
"ReportingTools" # depends on broken package Category-2.35.1
"REST" # depends on broken package nlopt-2.4.2
"rgp" # build is broken
"rgsepd" # depends on broken package goseq-1.21.1
"rhdf5" # build is broken
"rHVDM" # depends on broken package affyio-1.37.0
"Ringo" # depends on broken package affyio-1.37.0
"Risa" # depends on broken package affyio-1.37.0
"rMAT" # build is broken
"rmgarch" # depends on broken package nlopt-2.4.2
"rminer" # depends on broken package nlopt-2.4.2
"RmiR" # Build Is Broken
"Rmosek" # build is broken
"RNAinteract" # depends on broken package Category-2.35.1
"RNAither" # depends on broken package nlopt-2.4.2
"RnavGraph" # build is broken
"Rnits" # depends on broken package affyio-1.37.0
"RobLoxBioC" # depends on broken package affyio-1.37.0
"robustlmm" # depends on broken package nlopt-2.4.2
"rockchalk" # depends on broken package nlopt-2.4.2
"rols" # build is broken
"RPA" # depends on broken package affyio-1.37.0
"rpanel" # build is broken
"rpubchem" # depends on broken package nlopt-2.4.2
"RQuantLib" # build is broken
"rr" # depends on broken package nlopt-2.4.2
"RSAP" # build is broken
"rsbml" # build is broken
"rscala" # build is broken
"RSDA" # depends on broken package nlopt-2.4.2
"Rsubread" # Build Is Broken
"Rsymphony" # build is broken
"rTANDEM" # build is broken
"RTN" # depends on broken package nlopt-2.4.2
"rugarch" # depends on broken package nlopt-2.4.2
"RUVcorr" # build is broken
"RUVnormalize" # Build Is Broken
"RVAideMemoire" # depends on broken package nlopt-2.4.2
"RVFam" # depends on broken package nlopt-2.4.2
"ryouready" # depends on broken package nlopt-2.4.2
"sampleSelection" # depends on broken package nlopt-2.4.2
"SCAN_UPC" # depends on broken package affyio-1.37.0
"ScISI" # depends on broken package apComplex-2.35.0
"sdcMicro" # depends on broken package nlopt-2.4.2
"sdcMicroGUI" # depends on broken package nlopt-2.4.2
"seeg" # depends on broken package nlopt-2.4.2
"sem" # depends on broken package nlopt-2.4.2
"semdiag" # depends on broken package nlopt-2.4.2
"SemDist" # Build Is Broken
"semGOF" # depends on broken package nlopt-2.4.2
"semPlot" # depends on broken package nlopt-2.4.2
"SensoMineR" # depends on broken package nlopt-2.4.2
"SEPA" # depends on broken package topGO-2.21.0
"seqTools" # build is broken
"SimBindProfiles" # depends on broken package affyio-1.37.0
"simpleaffy" # depends on broken package affyio-1.37.0
"sirt" # depends on broken package nlopt-2.4.2
"sjPlot" # depends on broken package nlopt-2.4.2
"skewr" # depends on broken package affyio-1.37.0
"SLGI" # depends on broken package apComplex-2.35.0
"SNAGEE" # build is broken
"snapCGH" # depends on broken package tilingArray-1.47.0
"snm" # depends on broken package nlopt-2.4.2
"SNPchip" # depends on broken package affyio-1.37.0
"snpEnrichment" # depends on broken package snpStats-1.19.0
"snpStats" # build is broken
"snpStatsWriter" # depends on broken package snpStats-1.19.0
"SOD" # depends on broken package cudatoolkit-5.5.22
"spacom" # depends on broken package nlopt-2.4.2
"specificity" # depends on broken package nlopt-2.4.2
"sscore" # depends on broken package affyio-1.37.0
"ssmrob" # depends on broken package nlopt-2.4.2
"staRank" # depends on broken package Category-2.35.1
"Starr" # depends on broken package affyio-1.37.0
"STATegRa" # depends on broken package affyio-1.37.0
"stcm" # depends on broken package nlopt-2.4.2
"stepp" # depends on broken package nlopt-2.4.2
"stringgaussnet" # build is broken
"Surrogate" # depends on broken package nlopt-2.4.2
"synapter" # depends on broken package affyio-1.37.0
"systemfit" # depends on broken package nlopt-2.4.2
"systemPipeR" # depends on broken package AnnotationForge-1.11.3
"TcGSA" # depends on broken package nlopt-2.4.2
"TDMR" # depends on broken package nlopt-2.4.2
"TFBSTools" # depends on broken package DirichletMultinomial-1.11.1
"tigerstats" # depends on broken package nlopt-2.4.2
"tilingArray" # depends on broken package affyio-1.37.0
"topGO" # build is broken
"tRanslatome" # depends on broken package GOSemSim-1.27.3
"TriMatch" # depends on broken package nlopt-2.4.2
"TROM" # depends on broken package topGO-2.21.0
"TurboNorm" # depends on broken package affyio-1.37.0
"unifiedWMWqPCR" # depends on broken package affyio-1.37.0
"userfriendlyscience" # depends on broken package nlopt-2.4.2
"V8" # build is broken
"VanillaICE" # depends on broken package affyio-1.37.0
"VIM" # depends on broken package nlopt-2.4.2
"VIMGUI" # depends on broken package nlopt-2.4.2
"vows" # depends on broken package nlopt-2.4.2
"vsn" # depends on broken package affyio-1.37.0
"vtpnet" # depends on broken package interactiveDisplayBase-1.7.0
"wateRmelon" # depends on broken package affyio-1.37.0
"waveTiling" # depends on broken package affyio-1.37.0
"webbioc" # depends on broken package affyio-1.37.0
"wfe" # depends on broken package nlopt-2.4.2
"WGCNA" # build is broken
"wgsea" # depends on broken package snpStats-1.19.0
"WideLM" # depends on broken package cudatoolkit-5.5.22
"xergm" # depends on broken package nlopt-2.4.2
"xps" # build is broken
"yaqcaffy" # depends on broken package affyio-1.37.0
"ZeligMultilevel" # depends on broken package nlopt-2.4.2
"zetadiv" # depends on broken package nlopt-2.4.2
];
otherOverrides = old: new: {
xml2 = old.xml2.overrideDerivation (attrs: {
preConfigure = "export LIBXML_INCDIR=${pkgs.libxml2}/include/libxml2";
});
curl = old.curl.overrideDerivation (attrs: {
preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include";
});
iFes = old.iFes.overrideDerivation (attrs: {
patches = [ ./patches/iFes.patch ];
CUDA_HOME = "${pkgs.cudatoolkit}";
});
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
patchPhase = "patchShebangs configure";
});
rpf = old.rpf.overrideDerivation (attrs: {
patchPhase = "patchShebangs configure";
});
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
patches = [ ./patches/BayesXsrc.patch ];
});
rJava = old.rJava.overrideDerivation (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
JavaGD = old.JavaGD.overrideDerivation (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
Mposterior = old.Mposterior.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
});
qtbase = old.qtbase.overrideDerivation (attrs: {
patches = [ ./patches/qtbase.patch ];
});
Rmpi = old.Rmpi.overrideDerivation (attrs: {
configureFlags = [
"--with-Rmpi-type=OPENMPI"
];
});
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
configureFlags = [
"--with-mpfr-include=${pkgs.mpfr}/include"
];
});
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
configureFlags = [
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
];
});
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
patches = [ ./patches/RAppArmor.patch ];
LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
});
RMySQL = old.RMySQL.overrideDerivation (attrs: {
patches = [ ./patches/RMySQL.patch ];
MYSQL_DIR="${pkgs.mysql.lib}";
});
devEMF = old.devEMF.overrideDerivation (attrs: {
NIX_CFLAGS_LINK = "-L${pkgs.xlibs.libXft}/lib -lXft";
});
slfm = old.slfm.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
});
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
});
gputools = old.gputools.overrideDerivation (attrs: {
patches = [ ./patches/gputools.patch ];
CUDA_HOME = "${pkgs.cudatoolkit}";
});
# It seems that we cannot override meta attributes with overrideDerivation.
CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
patches = [ ./patches/CARramps.patch ];
configureFlags = [
"--with-cuda-home=${pkgs.cudatoolkit}"
];
});
gmatrix = old.gmatrix.overrideDerivation (attrs: {
patches = [ ./patches/gmatrix.patch ];
CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
R_INC_PATH = "${pkgs.R}/lib/R/include";
CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include";
});
# It seems that we cannot override meta attributes with overrideDerivation.
rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
patches = [ ./patches/rpud.patch ];
CUDA_HOME = "${pkgs.cudatoolkit}";
});
WideLM = old.WideLM.overrideDerivation (attrs: {
patches = [ ./patches/WideLM.patch ];
configureFlags = [
"--with-cuda-home=${pkgs.cudatoolkit}"
];
});
EMCluster = old.EMCluster.overrideDerivation (attrs: {
patches = [ ./patches/EMCluster.patch ];
});
spMC = old.spMC.overrideDerivation (attrs: {
patches = [ ./patches/spMC.patch ];
});
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
patches = [ ./patches/BayesLogit.patch ];
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
});
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
patches = [ ./patches/BayesBridge.patch ];
});
openssl = old.openssl.overrideDerivation (attrs: {
OPENSSL_INCLUDES = "${pkgs.openssl}/include";
});
Rserve = old.Rserve.overrideDerivation (attrs: {
patches = [ ./patches/Rserve.patch ];
configureFlags = [
"--with-server" "--with-client"
];
});
nloptr = old.nloptr.overrideDerivation (attrs: {
configureFlags = [
"--with-nlopt-cflags=-I${pkgs.nlopt}/include"
"--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
];
});
V8 = old.V8.overrideDerivation (attrs: {
preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
});
};
in
self
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