nixpkgs/pkgs/development/r-modules/default.nix
2015-04-20 17:38:46 +02:00

1104 lines
31 KiB
Nix

/* 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; };
# Package template
#
# some packages, e.g. cncaGUI, require X running while installation,
# so that we use xvfb-run if requireX is true.
derive = lib.makeOverridable ({
name, version, sha256,
depends ? [],
doCheck ? true,
requireX ? false,
broken ? false,
hydraPlatforms ? R.meta.hydraPlatforms
}: buildRPackage {
name = "${name}-${version}";
src = fetchurl {
urls = [
"mirror://cran/src/contrib/${name}_${version}.tar.gz"
"mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
];
inherit sha256;
};
inherit doCheck requireX;
propagatedBuildInputs = depends;
nativeBuildInputs = depends;
meta.homepage = "http://cran.r-project.org/web/packages/${name}/";
meta.platforms = R.meta.platforms;
meta.hydraPlatforms = hydraPlatforms;
meta.broken = broken;
});
# 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 ./cran-packages.nix { inherit self derive; };
# tweaks for the individual packages and "in self" follow
packagesWithRDepends = {
FactoMineR = [ self.car ];
};
packagesWithNativeBuildInputs = {
abn = [ pkgs.gsl ];
adimpro = [ pkgs.imagemagick ];
audio = [ pkgs.portaudio ];
BayesSAE = [ pkgs.gsl ];
BayesVarSel = [ pkgs.gsl ];
BayesXsrc = [ pkgs.readline pkgs.ncurses ];
bigGP = [ pkgs.openmpi ];
bnpmr = [ pkgs.gsl ];
BNSP = [ pkgs.gsl ];
cairoDevice = [ pkgs.gtk2 ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
chebpol = [ pkgs.fftw ];
cit = [ pkgs.gsl ];
curl = [ pkgs.curl pkgs.openldap ];
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 ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
gmp = [ pkgs.gmp ];
graphscan = [ pkgs.gsl ];
gsl = [ pkgs.gsl ];
HiCseg = [ 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 ];
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 ];
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 ];
rgl = [ pkgs.mesa pkgs.x11 ];
Rglpk = [ pkgs.glpk ];
rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
RGtk2 = [ pkgs.gtk2 ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
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 ];
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 = [
"AnalyzeFMRI"
"AnnotLists"
"AnthropMMD"
"AtelieR"
"BAT"
"BCA"
"BEQI2"
"BHMSMAfMRI"
"BioGeoBEARS"
"BiodiversityR"
"CCTpack"
"CommunityCorrelogram"
"ConvergenceConcepts"
"DALY"
"DSpat"
"Deducer"
"DeducerExtras"
"DeducerPlugInExample"
"DeducerPlugInScaling"
"DeducerSpatial"
"DeducerSurvival"
"HomoPolymer"
"MetSizeR"
"DeducerText"
"Demerelate"
"DescTools"
"DivMelt"
"ENiRG"
"EcoVirtual"
"EnQuireR"
"FAiR"
"FD"
"FFD"
"FeedbackTS"
"FreeSortR"
"GGEBiplotGUI"
"GPCSIV"
"GUniFrac"
"Geneland"
"GeoGenetix"
"GeoXp"
"GrammR"
"GrapheR"
"GroupSeq"
"HH"
"HiveR"
"IsotopeR"
"JGR"
"KappaGUI"
"LS2Wstat"
"MAR1"
"MTurkR"
"MareyMap"
"MergeGUI"
"Meth27QC"
"MicroStrategyR"
"MissingDataGUI"
"MplusAutomation"
"OligoSpecificitySystem"
"OpenRepGrid"
"PBSadmb"
"PBSmodelling"
"PCPS"
"PKgraph"
"PopGenReport"
"PredictABEL"
"PrevMap"
"ProbForecastGOP"
"QCAGUI"
"R2STATS"
"RHRV"
"RNCEP"
"RQDA"
"RSDA"
"RSurvey"
"RandomFields"
"Rcmdr"
"RcmdrPlugin_BCA"
"RcmdrPlugin_DoE"
"RcmdrPlugin_EACSPIR"
"RcmdrPlugin_EBM"
"RcmdrPlugin_EZR"
"RcmdrPlugin_EcoVirtual"
"RcmdrPlugin_FactoMineR"
"RcmdrPlugin_HH"
"RcmdrPlugin_IPSUR"
"RcmdrPlugin_KMggplot2"
"RcmdrPlugin_MA"
"RcmdrPlugin_MPAStats"
"RcmdrPlugin_ROC"
"RcmdrPlugin_SCDA"
"RcmdrPlugin_SLC"
"RcmdrPlugin_SM"
"RcmdrPlugin_StatisticalURV"
"RcmdrPlugin_TeachingDemos"
"RcmdrPlugin_UCA"
"RcmdrPlugin_coin"
"RcmdrPlugin_depthTools"
"RcmdrPlugin_doex"
"RcmdrPlugin_epack"
"RcmdrPlugin_lfstat"
"RcmdrPlugin_mosaic"
"RcmdrPlugin_orloca"
"RcmdrPlugin_plotByGroup"
"RcmdrPlugin_pointG"
"RcmdrPlugin_qual"
"RcmdrPlugin_sampling"
"RcmdrPlugin_sos"
"RcmdrPlugin_steepness"
"RcmdrPlugin_survival"
"RcmdrPlugin_temis"
"RenextGUI"
"RunuranGUI"
"SOLOMON"
"SPACECAP"
"SRRS"
"SSDforR"
"STEPCAM"
"SYNCSA"
"Simile"
"SimpleTable"
"StatDA"
"SyNet"
"TDMR"
"TED"
"TIMP"
"TTAinterfaceTrendAnalysis"
"TestScorer"
"VIMGUI"
"VecStatGraphs3D"
"WMCapacity"
"accrual"
"ade4TkGUI"
"adehabitat"
"analogue"
"analogueExtra"
"aplpack"
"aqfig"
"arf3DS4"
"asbio"
"bayesDem"
"betapart"
"betaper"
"bio_infer"
"bipartite"
"biplotbootGUI"
"blender"
"cairoDevice"
"cncaGUI"
"cocorresp"
"confidence"
"constrainedKriging"
"cpa"
"dave"
"debug"
"detrendeR"
"dgmb"
"dpa"
"dynBiplotGUI"
"dynamicGraph"
"eVenn"
"exactLoglinTest"
"fSRM"
"fat2Lpoly"
"fbati"
"feature"
"fgui"
"fisheyeR"
"fit4NM"
"forams"
"forensim"
"fscaret"
"gWidgets2RGtk2"
"gWidgets2tcltk"
"gWidgetsRGtk2"
"gWidgetstcltk"
"gcmr"
"geoR"
"geoRglm"
"geomorph"
"georob"
"gnm"
"gsubfn"
"iBUGS"
"iDynoR"
"ic50"
"in2extRemes"
"iplots"
"isopam"
"likeLTD"
"loe"
"logmult"
"memgene"
"metacom"
"migui"
"miniGUI"
"mixsep"
"mlDNA"
"mpmcorrelogram"
"mritc"
"multgee"
"multibiplotGUI"
"nodiv"
"onemap"
"palaeoSig"
"paleoMAS"
"pbatR"
"pez"
"phylotools"
"picante"
"playwith"
"plotSEMM"
"plsRbeta"
"plsRglm"
"pmg"
"poppr"
"powerpkg"
"prefmod"
"qtbase"
"qtpaint"
"qtutils"
"r4ss"
"rAverage"
"rareNMtests"
"recluster"
"relax"
"relimp"
"reportRx"
"reshapeGUI"
"rgl"
"rich"
"ringscale"
"rioja"
"ripa"
"rite"
"rnbn"
"rsgcc"
"sdcMicroGUI"
"sharpshootR"
"simba"
"soundecology"
"spacodiR"
"spatsurv"
"sqldf"
"statcheck"
"stosim"
"strvalidator"
"stylo"
"svDialogstcltk"
"svIDE"
"svSocket"
"svWidgets"
"tcltk2"
"titan"
"tkrgl"
"tkrplot"
"tmap"
"tspmeta"
"twiddler"
"vcdExtra"
"vegan"
"vegan3d"
"vegclust"
"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 = [
"ACNE" # requires aroma_affymetrix
"Actigraphy" # SDMTools.so: undefined symbol: X
"adaptsmoFMRI" # requires spatstat
"ads" # requires spatstat
"agridat" # requires pcaMethods
"aLFQ" # requires protiq
"AntWeb" # requires leafletR
"aoristic" # requires spatstat
"apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
"aroma_affymetrix" # requires aroma_core
"aroma_cn" # requires PSCBS
"aroma_core" # requires PSCBS
"ArrayBin" # requires SAGx
"babel" # requires edgeR
"BACA" # requires RDAVIDWebService
"BcDiag" # requires fabia
"beadarrayMSV" # requires Biobase, geneplotter, andlimma
"bdvis" # requres taxize
"beadarrayFilter" # requires beadarray
"bigGP" # requires MPI running. HELP WANTED!
"bigpca" # requires NCmisc
"Biograph" # requires mvna
"biotools" # requires rpanel
"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
"BLCOP" # depends on broken fPortfolio
"bmrm" # requires clpAPI
"branchLars" # requires Rgraphviz
"BRugs" # requires OpenBUGS
"calmate" # requires aroma_core
"CARrampsOcl" # depends on OpenCL
"CHAT" # requires DNAcopy
"ChemoSpec" # depends on broken speaq
"Crossover" # fails self-test
"classGraph" # requires graph, and Rgraphviz
"clpAPI" # requires clp
"compendiumdb" # requires Biobase
"CORM" # requires limma
"cplexAPI" # requires CPLEX
"crmn" # requires pcaMethods, and Biobase
"CrypticIBDcheck" # requires rJPSGCS
"cudaBayesreg" # requres Rmath
"curvHDR" # requires flowCore
"D2C" # requires gRbase
"DAAGbio" # requires limma
"daff" # requires V8 to build
"dagbag" # requires Rlapack
"DBKGrad" # requires SDD
"dbmss" # requires spatstat
"DCGL" # requires limma
"dcGOR" # requires dnet
"demi" # requires affy, affxparser, and oligo
"DepthProc" # requires samr
"DiagrammeR" # requires V8 to build
"Digiroo2" # requires spatstat
"dixon" # requires spatstat
"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
"doMPI" # requires MPI running. HELP WANTED!
"dpcR" # requires spatstat
"DSpat" # requires spatstat
"ecespa" # requires spatstat
"ecoengine" # requires leafletR
"ecospat" # requires spatstat
"edgeRun" # requires edgeR
"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
"epoc" # requires graph, and Rgraphviz
"erpR" # requires rpanel
"ETAS" # requires spatstat
"eulerian" # requires graph
"evobiR" # requres taxiz
"evora" # requires qvalue
"ExomeDepth" # requires GenomicRanges, and Rsamtools
"FAMT" # requires impute
"fdrDiscreteNull" # requires edgeR
"FHtest" # requires interval
"flexCWM" # depends on broken mixture
"fPortfolio" # requires rneos
"FunctionalNetworks" # requires breastCancerVDX, and Biobase
"gamlss_demo" # requires rpanel
"GeneticTools" # requires snpStats
"GExMap" # requires Biobase and multtest
"gitter" # requires EBImage
"glmgraph" # test suite says: "undefined symbol: dgemv_"
"gmatrix" # depends on proprietary cudatoolkit
"GOGANPA" # requires WGCNA
"gputools" # depends on proprietary cudatoolkit
"gMCP" # fails self-test
"gRain" # requires gRbase
"gRapHD" # requires graph
"gRbase" # requires RBGL, and graph
"gRc" # requires gRbase
"gridDebug" # requires gridGraphviz
"gridGraphviz" # requires graph, and Rgraphviz
"GriegSmith" # requires spatstat
"gRim" # requires gRbase
"GSAgm" # requires edgeR
"GUIDE" # requires rpanel
"h2o" # tries to download some h2o.jar during its build
"hasseDiagram" # requires Rgraphviz
"hddplot" # requires multtest
"HierO" # requires rneos
"HiPLARM" # requires MAGMA or PLASMA
"hpoPlot" # requires Rgraphviz
"HTSCluster" # requires edgeR
"iFes" # depends on proprietary cudatoolkit
"imputeLCMD" # requires pcaMethods, and impute
"intamapInteractive" # requires spatstat
"interval" # requires Icens
"ionflows" # requires Biostrings
"iRefR" # requires graph, and RBGL
"IsoGene" # requires Biobase, and affy
"isva" # requires qvalue
"jomo" # linking errors
"js" # requires broken V8
"KANT" # requires affy, and Biobase
"ktspair" # requires Biobase
"latticeDensity" # requires spatstat
"leapp" # requires sva
"lefse" # SDMTools.so: undefined symbol: X
"lgcp" # requires rpanel
"LinRegInteractive" # requires Rpanel
"LogisticDx" # requires gRbase
"LOST" # requires pcaMethods
"ltsk" # requires Rlapack and Rblas
"magma" # requires MAGMA
"MAMA" # requires metaMA
"MEET" # requires pcaMethods, and seqLogo
"metabolomics" # depends on broken crmn
"MetaDE" # requires impute, and Biobase
"MetaLandSim" # requires Biobase
"metaMA" # requires limma
"metaMix" # requires MPI running. HELP WANTED!
"mGSZ" # requires Biobase, and limma
"MigClim" # SDMTools.So: Undefined Symbol: X
"minimist" # requires broken V8
"miRtest" # requires globaltest, GlobalAncova, and limma
"mixture" # mixture.so: undefined symbol: dtrmm_
"moduleColor" # requires impute
"msarc" # requires AnnotationDbi
"MSeasy" # requires mzR, and xcms
"MSeasyTkGUI" # requires MSeasyTkGUI
"MSIseq" # requires IRanges
"msSurv" # requires graph
"multiDimBio" # requires pcaMethods
"mutossGUI" # requires mutoss
"mutoss" # requires multtest
"MXM" # depends on broken gRbase
"NBPSeq" # requires qvalue
"NCmisc" # requires BiocInstaller
"netClass" # requires samr
"nettools" # requires WGCNA
"NORRRM" # can't load SDMTools properly
"netweavers" # requires BiocGenerics, Biobase, and limma
"NLPutils" # requires qdap
"NSA" # requires aroma_core
"OpenCL" # FIXME: requires CL/opencl.h
"optBiomarker" # requires rpanel
"ora" # requires ROracle
"orQA" # requires genefilter
"pRF" # requires multtest
"PBSmapping" # fails its test suite for unclear reasons
"PBSddesolve" # fails its test suite for unclear reasons
"PairViz" # requires graph
"PANDA" # requires GO.db
"ParDNAcopy" # requires DNAcopy
"pathClass" # requires affy, and Biobase
"PatternClass" # SDMTools.So: Undefined Symbol: X
"pbdBASE" # requires pbdMPI
"pbdDEMO" # requires pbdMPI
"pbdDMAT" # requires pbdMPI
"pbdSLAP" # requires pbdMPI
"pcaL1" # requires clp
"pcalg" # requires graph, and RBGL
"PCGSE" # requires safe
"PCS" # requires multtest
"PepPrep" # requires biomaRt
"PerfMeas" # requires limma, graph, and RBGL
"permGPU" # requires Biobase
"PhViD" # requires LBE
"pi0" # requires qvalue
"plmDE" # requires limma
"plsRcox" # requires survcomp
"PMA" # requires impute
"pmcgd" # depends on broken mixture
"pmclust" # requires MPI running. HELP WANTED!
"polyCub" # requires spatstat
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
"propOverlap" # requires Biobase
"protiq" # requires graph, and RBGL
"PSCBS" # requires DNAcopy
"pubmed_mineR" # requires SSOAP
"PubMedWordcloud" # requires GOsummaries
"qdap" # requires gender
"qtlnet" # requires pcalg
"qtpaint" # can't find QtCore libraries
"QuACN" # requires graph, RBGL
"QuasiSeq" # requires edgeR
"RADami" # requires Biostrings
"raincpc" # SDMTools.so: undefined symbol: X
"rainfreq" # SDMTools.so: undefined symbol: X
"RAM" # requires Heatplus
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
"RapidPolygonLookup" # depends on broken PBSmapping
"RbioRXN" # requires fmcsR, and KEGGREST
"RcppAPT" # configure script depends on /bin/sh
"RcmdrPlugin_seeg" # requires seeg
"Rcplex" # requires cplexAPI
"RcppRedis" # requires Hiredis
"rDEA" # no such file or directory
"RDieHarder" # requires libdieharder
"reader" # requires NCmisc
"REBayes" # requires Rmosek
"RefFreeEWAS" # requires isva
"retistruct" # depends on broken RImageJROI
"RImageJROI" # requires spatstat
"rjade" # requires V8 to build
"rJPSGCS" # requires chopsticks
"rLindo" # requires LINDO API
"Rmosek" # requires mosek
"RnavGraph" # requires graph, and RBGL
"rneos" # requires XMLRPC
"RNeXML" # requres taxize
"RobLoxBioC" # requires Biobase
"RobLox" # requires Biobase
"RockFab" # requires EBImage
"ROI_plugin_symphony" # depends on broken Rsymphony
"ROracle" # requires OCI
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
"RQuantLib" # requires QuantLib
"RSAP" # requires SAPNWRFCSDK
"rgp" # fails self-test
"rgpui" # depends on broken rgp
"RSeed" # requires RBGL, and graph
"rsig" # requires survcomp
"RSNPset" # requires qvalue
"Rsymphony" # FIXME: requires SYMPHONY
"RVideoPoker" # requires Rpanel
"rysgran" # requires soiltexture
"samr" # requires impute
"saps" # requires piano, and survcomp
"SDD" # requires rpanel
"seeg" # requires spatstat
"selectspm" # depends on broken ecespa
"semiArtificial" # requires RSNNS
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
"sequenza" # requires copynumber
"SGCS" # requires spatstat
"siar" # requires spatstat
"SID" # requires pcalg
"SimRAD" # requires Biostrings, and ShortRead
"SimSeq" # requires edgeR
"siplab" # requires spatstat
"smart" # requires PMA
"snpEnrichment" # requires snpStats
"snplist" # requires biomaRt
"snpStatsWriter" # requires snpStats
"SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
"SOD" # depends on proprietary cudatoolkit
"soilphysics" # requires rpanel
"sparr" # requires spatstat
"spatialsegregation" # requires spatstat
"SpatialVx" # requires spatstat
"speaq" # requires MassSpecWavelet
"spocc" # requires leafletR
"SQDA" # requires limma
"Statomica" # requires Biobase, multtest
"stagePop" # depends on broken PBSddesolve
"SeqGrapheR" # depends on Biostrings
"stpp" # requires spatstat
"structSSI" # requires multtest
"strum" # requires Rgraphviz
"superbiclust" # requires fabia
"surveillance" # requires polyCub
"swamp" # requires impute
"sybilSBML" # requires libSBML
"taxize" # requres bold
"TcGSA" # requires multtest
"topologyGSA" # requires gRbase
"TR8" # requres taxize
"trip" # requires spatstat
"ttScreening" # requires sva, and limma
"V8" # compilation error
"vows" # requires rpanel
"vmsbase" # depends on broken PBSmapping
"WGCNA" # requires impute
"wgsea" # requires snpStats
"WideLM" # depends on proprietary cudatoolkit
"x_ent" # requires opencpu
"zoib" # tarball is invalid on server
"DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest'
"TROM" # misses undeclared dependencies topGO', 'AnnotationDbi', 'GO.db'
"lfe" # fails to compile
"mongolite" # doesn't find OpenSSL
"quanteda" # fails to build
"statar" # depends on broken lfe
"hsdar" # fails to build
];
otherOverrides = old: new: {
curl = old.curl.overrideDerivation (attrs: {
preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include/curl";
});
iFes = old.iFes.overrideDerivation (attrs: {
patches = [ ./patches/iFes.patch ];
CUDA_HOME = "${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${pkgs.atlas}/lib -lf77blas -latlas";
});
qtbase = old.qtbase.overrideDerivation (attrs: {
patches = [ ./patches/qtbase.patch ];
});
Rmpi = old.Rmpi.overrideDerivation (attrs: {
configureFlags = [
"--with-Rmpi-type=OPENMPI"
];
});
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
configureFlags = [
"--with-mpfr-include=${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.atlas}/lib -lf77blas -latlas";
});
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
});
gputools = old.gputools.overrideDerivation (attrs: {
patches = [ ./patches/gputools.patch ];
CUDA_HOME = "${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 ];
});
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'"
];
});
};
in
self