nixpkgs/pkgs/development/r-modules/default.nix

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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;
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, rVersion}: "https://bioconductor.org/packages/${rVersion}/bioc/html/${name}.html";
mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/bioc/src/contrib/${name}_${version}.tar.gz" ];
};
deriveBiocAnn = mkDerive {
mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html";
mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ];
};
deriveBiocExp = mkDerive {
mkHomepage = {name, rVersion}: "http://www.bioconductor.org/packages/${name}.html";
mkUrls = {name, version, rVersion}: [ "mirror://bioc/${rVersion}/data/experiment/src/contrib/${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:
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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:
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lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
buildInputs = attrs.buildInputs ++ value;
})
) overrides;
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# 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);
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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 ./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
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packagesWithRDepends = {
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FactoMineR = [ self.car ];
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pander = [ self.codetools ];
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};
packagesWithNativeBuildInputs = {
abn = [ pkgs.gsl_1 ];
adimpro = [ pkgs.imagemagick ];
audio = [ pkgs.portaudio ];
BayesSAE = [ pkgs.gsl_1 ];
BayesVarSel = [ pkgs.gsl_1 ];
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BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
bigGP = [ pkgs.openmpi ];
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bio3d = [ pkgs.zlib ];
BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ];
bnpmr = [ pkgs.gsl_1 ];
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cairoDevice = [ pkgs.gtk2.dev ];
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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 ];
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curl = [ pkgs.curl.dev ];
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devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
diversitree = [ pkgs.gsl_1 pkgs.fftw ];
EMCluster = [ pkgs.liblapack ];
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fftw = [ pkgs.fftw.dev ];
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fftwtools = [ pkgs.fftw.dev ];
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Formula = [ pkgs.gmp ];
geoCount = [ pkgs.gsl_1 ];
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git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
GLAD = [ pkgs.gsl_1 ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
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gmp = [ pkgs.gmp.dev ];
graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ];
h5 = [ pkgs.hdf5-cpp pkgs.which ];
h5vc = [ pkgs.zlib.dev ];
HiCseg = [ pkgs.gsl_1 ];
imager = [ pkgs.x11 ];
iBMQ = [ pkgs.gsl_1 ];
igraph = [ pkgs.gmp ];
JavaGD = [ pkgs.jdk ];
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jpeg = [ pkgs.libjpeg.dev ];
KFKSDS = [ pkgs.gsl_1 ];
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kza = [ pkgs.fftw.dev ];
libamtrack = [ pkgs.gsl_1 ];
mixcat = [ pkgs.gsl_1 ];
mvabund = [ pkgs.gsl_1 ];
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mwaved = [ pkgs.fftw.dev ];
ncdf4 = [ pkgs.netcdf ];
nloptr = [ pkgs.nlopt ];
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openssl = [ pkgs.openssl.dev ];
outbreaker = [ pkgs.gsl_1 ];
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pander = [ pkgs.pandoc pkgs.which ];
pbdMPI = [ pkgs.openmpi ];
pbdNCDF4 = [ pkgs.netcdf ];
pbdPROF = [ pkgs.openmpi ];
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PKI = [ pkgs.openssl.dev ];
png = [ pkgs.libpng.dev ];
2017-01-06 18:25:06 +00:00
PopGenome = [ pkgs.zlib.dev ];
proj4 = [ pkgs.proj ];
qtbase = [ pkgs.qt4 ];
qtpaint = [ pkgs.qt4 ];
R2GUESS = [ pkgs.gsl_1 ];
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R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
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RAppArmor = [ pkgs.libapparmor ];
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rapportools = [ pkgs.which ];
rapport = [ pkgs.which ];
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rbamtools = [ pkgs.zlib.dev ];
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rcdd = [ pkgs.gmp.dev ];
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RcppCNPy = [ pkgs.zlib.dev ];
RcppGSL = [ pkgs.gsl_1 ];
2017-01-06 18:38:00 +00:00
RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.octave ];
RcppZiggurat = [ pkgs.gsl_1 ];
rgdal = [ pkgs.proj pkgs.gdal ];
rgeos = [ pkgs.geos ];
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rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ];
rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
Rglpk = [ pkgs.glpk ];
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RGtk2 = [ pkgs.gtk2.dev ];
rhdf5 = [ pkgs.zlib ];
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Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
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Rhtslib = [ pkgs.zlib.dev ];
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RJaCGH = [ pkgs.zlib.dev ];
rjags = [ pkgs.jags ];
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rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ];
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rmatio = [ pkgs.zlib.dev ];
2017-01-06 19:02:17 +00:00
Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
Rmpi = [ pkgs.openmpi ];
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RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
RODBCext = [ pkgs.libiodbc ];
RODBC = [ pkgs.libiodbc ];
rpg = [ pkgs.postgresql ];
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rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
Rpoppler = [ pkgs.poppler ];
RPostgreSQL = [ pkgs.postgresql ];
RProtoBuf = [ pkgs.protobuf ];
rPython = [ pkgs.python ];
2017-01-06 19:09:43 +00:00
RSclient = [ pkgs.openssl.dev ];
Rserve = [ pkgs.openssl ];
2017-01-06 19:13:30 +00:00
Rssa = [ pkgs.fftw.dev ];
2017-01-06 19:16:49 +00:00
rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
2017-01-06 19:17:42 +00:00
rtiff = [ pkgs.libtiff.dev ];
runjags = [ pkgs.jags ];
2017-01-06 19:22:07 +00:00
RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
rzmq = [ pkgs.zeromq3 ];
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
sdcTable = [ pkgs.gmp pkgs.glpk ];
2017-01-06 15:31:30 +00:00
seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
2017-01-06 19:26:40 +00:00
seqinr = [ pkgs.zlib.dev ];
2017-01-06 19:28:22 +00:00
seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
2017-01-06 19:29:12 +00:00
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
simplexreg = [ pkgs.gsl_1 ];
SOD = [ pkgs.opencl-headers ];
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spate = [ pkgs.fftw.dev ];
sprint = [ pkgs.openmpi ];
ssanv = [ pkgs.proj ];
stsm = [ pkgs.gsl_1 ];
stringi = [ pkgs.icu.dev ];
survSNP = [ pkgs.gsl_1 ];
2017-01-06 18:27:45 +00:00
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
2017-01-06 19:31:16 +00:00
TAQMNGR = [ pkgs.zlib.dev ];
2017-01-06 19:32:48 +00:00
tiff = [ pkgs.libtiff.dev ];
TKF = [ pkgs.gsl_1 ];
2017-01-06 19:37:33 +00:00
tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
topicmodels = [ pkgs.gsl_1 ];
udunits2 = [ pkgs.udunits pkgs.expat ];
V8 = [ pkgs.v8 ];
VBLPCM = [ pkgs.gsl_1 ];
VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
2017-01-06 19:39:10 +00:00
WhopGenome = [ pkgs.zlib.dev ];
2017-01-06 19:39:44 +00:00
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
2017-01-06 19:40:43 +00:00
xml2 = [ pkgs.libxml2.dev ];
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XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
2017-01-06 19:42:00 +00:00
affyPLM = [ pkgs.zlib.dev ];
2017-01-06 19:43:55 +00:00
bamsignals = [ pkgs.zlib.dev ];
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BitSeq = [ pkgs.zlib.dev ];
DiffBind = [ pkgs.zlib ];
ShortRead = [ pkgs.zlib.dev ];
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oligo = [ pkgs.zlib.dev ];
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gmapR = [ pkgs.zlib.dev ];
2017-01-06 19:52:16 +00:00
Rsubread = [ pkgs.zlib.dev ];
XVector = [ pkgs.zlib.dev ];
Rsamtools = [ pkgs.zlib.dev ];
2017-01-06 19:53:12 +00:00
rtracklayer = [ pkgs.zlib.dev ];
2017-01-06 19:47:08 +00:00
affyio = [ pkgs.zlib.dev ];
VariantAnnotation = [ pkgs.zlib.dev ];
2017-01-06 19:54:40 +00:00
snpStats = [ pkgs.zlib.dev ];
gputools = [ pkgs.pcre.dev pkgs.lzma.dev pkgs.zlib.dev pkgs.bzip2.dev pkgs.icu.dev ];
};
packagesWithBuildInputs = {
# sort -t '=' -k 2
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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 pkgs.which ];
RCurl = [ pkgs.curl.dev ];
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 ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
2015-11-24 16:17:54 +00:00
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
rPython = [ pkgs.which ];
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gridGraphics = [ pkgs.which ];
gputools = [ 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 ];
2016-03-25 07:30:20 +00:00
mzR = [ pkgs.netcdf ];
};
packagesRequireingX = [
"accrual"
"ade4TkGUI"
"adehabitat"
"analogue"
"analogueExtra"
"AnalyzeFMRI"
"AnnotLists"
"AnthropMMD"
"aplpack"
"aqfig"
"arf3DS4"
"asbio"
"AtelieR"
"BAT"
"bayesDem"
"BCA"
"BEQI2"
"betapart"
"betaper"
"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"
"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"
"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_steepness"
"RcmdrPlugin_survival"
"RcmdrPlugin_TeachingDemos"
"RcmdrPlugin_temis"
"RcmdrPlugin_UCA"
"recluster"
"relax"
"relimp"
"RenextGUI"
"reportRx"
"reshapeGUI"
"rgl"
"RHRV"
"rich"
"rioja"
"ripa"
"rite"
"RNCEP"
"RQDA"
"RSDA"
"rsgcc"
"RSurvey"
"RunuranGUI"
"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"
"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
"gputools" # requires CUDA runtime
"sprint" # tries to run MPI processes
2015-02-19 20:53:36 +00:00
"pbdMPI" # tries to run MPI processes
];
# Packages which cannot be installed due to lack of dependencies or other reasons.
2015-02-22 16:45:12 +00:00
brokenPackages = [
2017-03-04 20:51:23 +00:00
"acs" # build is broken
"agRee" # depends on broken package BRugs-0.8-6
"aLFQ" # depends on broken package bio3d-2.3-1
"anamiR" # depends on broken package RMySQL-0.10.11
"AneuFinder" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"animation" # build is broken
"anim_plots" # depends on broken package animation-2.4
"annmap" # depends on broken package RMySQL-0.10.9
"apaStyle" # depends on broken package gdtools-0.1.3
"apaTables" # depends on broken package OpenMx-2.7.4
"aptg" # depends on broken package brranching-0.2.0
2017-03-04 20:51:23 +00:00
"ArrayExpressHTS" # build is broken
"arrayQualityMetrics" # build is broken
"auRoc" # depends on broken package OpenMx-2.7.4
"bamsignals" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"BatchQC" # build is broken
"bayesCL" # build is broken
2017-03-04 20:51:23 +00:00
"bayou" # depends on broken package animation-2.4
"bedr" # build is broken
"BETS" # build is broken
"BiGGR" # depends on broken package rsbml-2.30.0
"bio3d" # build is broken
"bioassayR" # depends on broken package ChemmineR-2.24.2
"bioCancer" # depends on broken package covr-2.2.2
2017-03-04 20:51:23 +00:00
"biomformat" # depends on broken package r-rhdf5-2.16.0
"biotools" # depends on broken package rpanel-1.1-3
"birte" # build is broken
"BiSEp" # build is broken
"BLCOP" # depends on broken package Rsymphony-0.1-26
"BMhyd" # depends on broken package animation-2.4
"BNSP" # build is broken
"BPEC" # depends on broken package animation-2.4
"BrailleR" # depends on broken package gridGraphics-0.1-5
"brainGraph" # build is broken
"brranching" # depends on broken package animation-2.4
"brr" # build is broken
"BRugs" # build is broken
"CADStat" # build is broken
"CampaR1" # depends on broken package r-bio3d-2.3-1
"canceR" # build is broken
"CardinalWorkflows" # build is broken
"CARrampsOcl" # depends on broken package OpenCL-0.1-3
"categoryCompare" # depends on broken package RCytoscape-1.21.1
"Causata" # depends on broken package RMySQL-0.10.9
"cdcfluview" # depends on broken package V8-1.2
"CexoR" # depends on broken package Rhtslib-1.6.0
"ChAMP" # depends on broken package goseq-1.26.0
2017-03-04 20:51:23 +00:00
"ChemmineDrugs" # depends on broken package ChemmineR-2.24.2
"ChemmineR" # build is broken
"chinese_misc" # build is broken
"ChIPQC" # depends on broken package r-DiffBind-2.0.9
"ChIPXpress" # build is broken
"ChIPXpressData" # build is broken
"choroplethr" # depends on broken package acs-2.0
"CHRONOS" # build is broken
"cleanEHR" # build is broken
"clickR" # depends on broken package gdtools-0.1.3
"clpAPI" # build is broken
"CNEr" # build is broken
"colormap" # depends on broken package V8-1.2
"colorscience" # build is broken
"compendiumdb" # depends on broken package RMySQL-0.10.9
"CONFESS" # depends on broken package r-flowCore-1.38.2
"CONS" # build is broken
"convevol" # depends on broken package animation-2.4
"CountClust" # build is broken
"CountsEPPM" # build is broken
"COUSCOus" # depends on broken package r-bio3d-2.3-1
"covr" # build is broken
"cplexAPI" # build is broken
"Crossover" # build is broken
"CrypticIBDcheck" # build is broken
"csaw" # build is broken
"ctsem" # depends on broken package OpenMx-2.7.4
"cudaBayesreg" # build is broken
"cytofkit" # depends on broken package flowCore-1.38.2
"CytoML" # depends on broken package flowCore-1.40.6
2017-03-04 20:51:23 +00:00
"daff" # depends on broken package V8-1.2
"dagbag" # build is broken
"dagitty" # depends on broken package V8-1.2
"dagLogo" # depends on broken package MotIV-1.28.0
"DAISIE" # depends on broken package animation-2.4
"DataEntry" # build is broken
2017-03-04 20:51:23 +00:00
"dataMaid" # build is broken
"dataone" # build is broken
"datapack" # build is broken
"dbConnect" # depends on broken package RMySQL-0.10.9
"DBKGrad" # depends on broken package rpanel-1.1-3
"DCM" # build is broken
"DDD" # depends on broken package animation-2.4
"deBInfer" # depends on broken package PBSddesolve-1.12.2
"debrowser" # depends on broken package V8-1.4
2017-03-04 20:51:23 +00:00
"DecisionCurve" # build is broken
"DeepBlueR" # build is broken
2017-03-04 20:51:23 +00:00
"deepSNV" # build is broken
"DEGraph" # depends on broken package RCytoscape-1.21.1
"DEploid" # build is broken
"DiagrammeRsvg" # depends on broken package V8-1.2
"DiffBind" # build is broken
"diffHic" # depends on broken package r-csaw-1.6.1
"DirichletMultinomial" # build is broken
"diveRsity" # build is broken
"DmelSGI" # depends on broken package r-rhdf5-2.16.0
"docxtools" # build is broken
"DOQTL" # depends on broken package r-rhdf5-2.16.0
"DOT" # depends on broken package V8-1.2
"dynr" # build is broken
"ecospat" # depends on broken package MigClim-1.6
"EGAD" # depends on broken package arrayQualityMetrics-3.28.2
"eiR" # depends on broken package ChemmineR-2.24.2
"emg" # build is broken
"envlpaster" # build is broken
"erpR" # depends on broken package rpanel-1.1-3
"euroMix" # build is broken
"evobiR" # depends on broken package animation-2.4
"exifr" # build is broken
"ExperimentHubData" # build is broken
2017-03-04 20:51:23 +00:00
"exprso" # build is broken
"fastR" # build is broken
"fCCAC" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"fdq" # depends on broken package gdtools-0.1.3
"Fgmutils" # depends on broken package gdtools-0.1.3
"flan" # build is broken
"flextable" # depends on broken package gdtools-0.1.4
2017-03-04 20:51:23 +00:00
"flowAI" # depends on broken package r-flowCore-1.38.2
"flowBeads" # depends on broken package r-flowCore-1.38.2
"flowBin" # depends on broken package r-flowCore-1.38.2
"flowCHIC" # depends on broken package r-flowCore-1.38.2
"flowClean" # depends on broken package r-flowCore-1.38.2
"flowClust" # depends on broken package r-flowCore-1.38.2
"flowCore" # build is broken
"flowDensity" # depends on broken package flowCore-1.38.2
"flowDiv" # depends on broken package r-flowCore-1.38.2
"flowFit" # depends on broken package r-flowCore-1.38.2
"flowFitExampleData" # depends on broken package r-flowCore-1.38.2
"flowFP" # depends on broken package r-flowCore-1.38.2
"flowMatch" # depends on broken package r-flowCore-1.38.2
"flowMeans" # depends on broken package r-flowCore-1.38.2
"flowMerge" # depends on broken package r-flowCore-1.38.2
"flowPeaks" # build is broken
"flowPloidy" # depends on broken package flowCore-1.40.6
2017-03-04 20:51:23 +00:00
"flowQB" # depends on broken package r-flowCore-1.38.2
"flowQ" # depends on broken package flowCore-1.38.2
"FlowSOM" # depends on broken package r-flowCore-1.38.2
"flowStats" # depends on broken package r-flowCore-1.38.2
"flowTrans" # depends on broken package r-flowCore-1.38.2
"flowType" # depends on broken package r-flowCore-1.38.2
"flowUtils" # depends on broken package r-flowCore-1.38.2
"flowViz" # depends on broken package r-flowCore-1.38.2
"flowVS" # depends on broken package r-flowCore-1.38.2
"flowWorkspace" # depends on broken package r-flowCore-1.38.2
"fmcsR" # depends on broken package ChemmineR-2.24.2
"fPortfolio" # depends on broken package Rsymphony-0.1-26
"fracprolif" # build is broken
"funModeling" # build is broken
"gahgu133acdf" # build is broken
"gahgu133bcdf" # build is broken
"gahgu133plus2cdf" # build is broken
"gahgu95av2cdf" # build is broken
"gahgu95bcdf" # build is broken
"gahgu95ccdf" # build is broken
"gahgu95dcdf" # build is broken
"gahgu95ecdf" # build is broken
"gamlss_demo" # depends on broken package rpanel-1.1-3
"gazepath" # build is broken
"gdtools" # build is broken
"GENE_E" # depends on broken package r-rhdf5-2.16.0
"GenoGAM" # build is broken
"genomation" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"geojson" # depends on broken package r-protolite-1.5
"geojsonio" # depends on broken package V8-1.2
"geojsonlint" # depends on broken package V8-1.2
"gfcanalysis" # depends on broken package animation-2.4
"gfer" # depends on broken package V8-1.2
"ggcyto" # depends on broken package r-flowCore-1.38.2
"ggghost" # depends on broken package animation-2.4
"ggimage" # depends on broken package gridGraphics-0.1-5
2017-03-04 20:51:23 +00:00
"ggiraph" # depends on broken package gdtools-0.1.3
"ggiraphExtra" # depends on broken package gdtools-0.1.3
"ggseas" # build is broken
"gmapR" # build is broken
2017-03-04 20:51:23 +00:00
"gmatrix" # depends on broken package cudatoolkit-8.0.61
"gMCP" # build is broken
"gmDatabase" # depends on broken package RMySQL-0.10.9
"gmum_r" # build is broken
"googleformr" # build is broken
"goseq" # build is broken
2017-03-04 20:51:23 +00:00
"gpg" # build is broken
"gpuR" # build is broken
"gputools" # depends on broken package cudatoolkit-8.0.61
"GraphPAC" # build is broken
"greengenes13_5MgDb" # build is broken
2017-03-04 20:51:23 +00:00
"gridGraphics" # build is broken
"GSCA" # depends on broken package r-rhdf5-2.16.0
"GUIDE" # depends on broken package rpanel-1.1-3
"gunsales" # build is broken
"h2o" # build is broken
"h5vc" # depends on broken package r-rhdf5-2.16.0
"harrietr" # build is broken
"HDF5Array" # depends on broken package r-rhdf5-2.16.0
"healthyFlowData" # depends on broken package r-flowCore-1.38.2
"hexSticker" # depends on broken package gridGraphics-0.1-5
2017-03-04 20:51:23 +00:00
"HierO" # build is broken
"HilbertVisGUI" # build is broken
"HiPLARM" # build is broken
"hisse" # depends on broken package animation-2.4
"hoardeR" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"homomorpheR" # depends on broken package sodium-0.4
"HTSeqGenie" # depends on broken package gmapR-1.16.0
2017-03-04 20:51:23 +00:00
"HTSSIP" # depends on broken package r-rhdf5-2.16.0
"idm" # depends on broken package animation-2.4
"ifaTools" # depends on broken package OpenMx-2.7.4
"IHW" # depends on broken package r-lpsymphony-1.0.2
"IHWpaper" # depends on broken package r-lpsymphony-1.0.2
"IlluminaHumanMethylation450k_db" # build is broken
"immunoClust" # depends on broken package r-flowCore-1.38.2
"imputeR" # depends on broken package ridge-2.2
2017-03-04 20:51:23 +00:00
"intansv" # build is broken
"interactiveDisplay" # build is broken
"ionicons" # depends on broken package rsvg-1.0
"IONiseR" # depends on broken package r-rhdf5-2.16.0
"ITGM" # depends on broken package gdtools-0.1.3
"jpmesh" # depends on broken package V8-1.2
"js" # depends on broken package V8-1.2
"jsonld" # depends on broken package V8-1.2
"jsonvalidate" # depends on broken package V8-1.2
"KoNLP" # build is broken
"largeList" # build is broken
"largeVis" # build is broken
"lavaan_shiny" # depends on broken package OpenMx-2.7.10
2017-03-04 20:51:23 +00:00
"lawn" # depends on broken package V8-1.2
"LCMCR" # build is broken
"LeArEst" # depends on broken package opencpu-1.6.1
2017-03-04 20:51:23 +00:00
"lefse" # build is broken
"lfe" # build is broken
"lgcp" # depends on broken package rpanel-1.1-3
"Libra" # build is broken
"libsoc" # build is broken
"link2GI" # depends on broken package r-sf-0.3-4
"LinRegInteractive" # depends on broken package rpanel-1.1-3
"liquidSVM" # build is broken
"littler" # build is broken
"LowMACA" # depends on broken package MotIV-1.28.0
"lpsymphony" # build is broken
"lvnet" # depends on broken package OpenMx-2.7.4
"MafDb_1Kgenomes_phase3_hs37d5" # build is broken
"mafs" # build is broken
"magick" # build is broken
"maGUI" # build is broken
"mapr" # depends on broken package V8-1.2
"mar1s" # build is broken
"MatrixRider" # depends on broken package CNEr-1.8.3
"MBESS" # depends on broken package OpenMx-2.7.4
"mBvs" # build is broken
"mcaGUI" # build is broken
"mcPAFit" # build is broken
2017-03-04 20:51:23 +00:00
"mdsr" # depends on broken package RMySQL-0.10.9
"Mediana" # depends on broken package gdtools-0.1.3
"melviewr" # build is broken
"MeSH_Hsa_eg_db" # build is broken
"MeSH_Mmu_eg_db" # build is broken
"meshr" # depends on broken package r-MeSH.Hsa.eg.db-1.6.0
"Metab" # build is broken
"metagear" # build is broken
"MetaIntegrator" # depends on broken package RMySQL-0.10.9
"metaSEM" # depends on broken package OpenMx-2.7.4
"methylKit" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"MigClim" # build is broken
"minimist" # depends on broken package V8-1.2
"miscF" # depends on broken package BRugs-0.8-6
"mixlink" # build is broken
"MLSeq" # build is broken
"mmnet" # build is broken
"MODIStsp" # build is broken
2017-03-04 20:51:23 +00:00
"MonetDBLite" # build is broken
"mongolite" # build is broken
"monogeneaGM" # depends on broken package animation-2.4
"MonoPhy" # depends on broken package animation-2.4
"motifbreakR" # depends on broken package MotIV-1.28.0
"motifStack" # depends on broken package MotIV-1.28.0
"MotIV" # build is broken
"mptools" # depends on broken package animation-2.4
"mrMLM" # build is broken
"mRMRe" # build is broken
"mscstexta4r" # build is broken
"mscsweblm4r" # build is broken
"MSeasyTkGUI" # build is broken
"MSGFgui" # depends on broken package MSGFplus-1.6.2
"MSGFplus" # build is broken
"multiDimBio" # depends on broken package gridGraphics-0.1-5
"multipanelfigure" # depends on broken package gridGraphics-0.1-5
"munsellinterpol" # build is broken
"mutossGUI" # build is broken
"mvMORPH" # depends on broken package animation-2.4
"mvst" # build is broken
"ncdfFlow" # depends on broken package r-flowCore-1.38.2
"NCIgraph" # depends on broken package RCytoscape-1.21.1
"ndjson" # build is broken
"ndtv" # depends on broken package animation-2.4
"NetRep" # depends on broken package r-RhpcBLASctl-0.15-148
"networkBMA" # build is broken
2017-03-04 20:51:23 +00:00
"nlts" # build is broken
"normr" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"NORRRM" # build is broken
"odbc" # build is broken
"officer" # depends on broken package gdtools-0.1.3
"OpenCL" # build is broken
"opencpu" # depends on broken package r-protolite-1.5
"openCyto" # depends on broken package r-flowCore-1.38.2
"OpenMx" # build is broken
"optbdmaeAT" # build is broken
"optBiomarker" # depends on broken package rpanel-1.1-3
"optrcdmaeAT" # build is broken
2017-03-04 20:51:23 +00:00
"ora" # depends on broken package ROracle-1.3-1
"OUwie" # depends on broken package animation-2.4
"PAA" # build is broken
"paleotree" # depends on broken package animation-2.4
"PathoStat" # depends on broken package BatchQC-1.2.1
2017-03-04 20:51:23 +00:00
"PathSelectMP" # build is broken
"PatternClass" # build is broken
"PBD" # depends on broken package animation-2.4
"PBSddesolve" # build is broken
"PBSmapping" # build is broken
"pcadapt" # depends on broken package vcfR-1.4.0
"pcaL1" # build is broken
"pcaPA" # build is broken
"pcrsim" # build is broken
"pdfsearch" # build is broken
"pdftools" # build is broken
"pd_genomewidesnp_6" # build is broken
"permGPU" # build is broken
"PGA" # build is broken
"PGPC" # depends on broken package ChemmineR-2.24.2
"ph2bye" # depends on broken package animation-2.4
"PharmacoGx" # build is broken
2017-03-04 20:51:23 +00:00
"PhyInformR" # depends on broken package animation-2.4
"phylocurve" # depends on broken package animation-2.4
"phyloseq" # depends on broken package r-rhdf5-2.16.0
"PhySortR" # depends on broken package animation-2.4
"phytools" # depends on broken package animation-2.4
"PICS" # build is broken
"PING" # depends on broken package PICS-2.16.0
"plateCore" # depends on broken package r-flowCore-1.38.2
"plfMA" # build is broken
"plink" # build is broken
2017-03-04 20:51:23 +00:00
"podkat" # build is broken
"PottsUtils" # depends on broken package BRugs-0.8-6
"powell" # build is broken
"pqsfinder" # depends on broken package r-flowCore-1.38.2
"prebs" # depends on broken package r-rhdf5-2.16.0
"PREDAsampledata" # depends on broken package gahgu133plus2cdf-2.2.1
"predictionInterval" # depends on broken package OpenMx-2.7.4
"pRoloc" # build is broken
"pRolocGUI" # build is broken
"proteoQC" # build is broken
"protolite" # build is broken
"prototest" # build is broken
"PSAboot" # build is broken
"psbcGroup" # build is broken
"PythonInR" # build is broken
"qcmetrics" # build is broken
"QFRM" # build is broken
"qrqc" # build is broken
"qtbase" # build is broken
"qtpaint" # build is broken
"qtutils" # build is broken
"QUALIFIER" # depends on broken package r-flowCore-1.38.2
"QuartPAC" # build is broken
"QuasR" # build is broken
"QUBIC" # build is broken
"QVM" # build is broken
"raincpc" # build is broken
"rainfreq" # build is broken
"RAM" # depends on broken package animation-2.4
"RamiGO" # depends on broken package RCytoscape-1.21.1
"randomcoloR" # depends on broken package V8-1.2
"randstr" # build is broken
"RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76
"RAppArmor" # build is broken
"raptr" # depends on broken package PBSmapping-2.69.76
"RbioRXN" # depends on broken package ChemmineR-2.24.2
"Rblpapi" # build is broken
"RCAS" # depends on broken package Rhtslib-1.6.0
2017-03-04 20:51:23 +00:00
"Rchemcpp" # depends on broken package ChemmineR-2.24.2
"rchess" # depends on broken package V8-1.2
"RchivalTag" # depends on broken package PBSmapping-2.69.76
2017-03-04 20:51:23 +00:00
"RchyOptimyx" # depends on broken package r-flowCore-1.38.2
"RcmdrPlugin_FuzzyClust" # build is broken
"RcmdrPlugin_PcaRobust" # build is broken
"Rcpi" # depends on broken package ChemmineR-2.24.2
"Rcplex" # build is broken
"RcppAPT" # build is broken
"RcppGetconf" # build is broken
"RcppOctave" # build is broken
"RcppRedis" # build is broken
"rcqp" # build is broken
"rcrypt" # build is broken
"RCytoscape" # build is broken
"rdataretriever" # build is broken
2017-03-04 20:51:23 +00:00
"rDEA" # build is broken
"RDieHarder" # build is broken
"REBayes" # depends on broken package Rmosek-1.2.5.1
"recluster" # depends on broken package animation-2.4
"redland" # build is broken
"remoter" # build is broken
"repijson" # depends on broken package V8-1.2
"replicationInterval" # depends on broken package OpenMx-2.7.4
"ReporteRs" # depends on broken package gdtools-0.1.3
"ReQON" # depends on broken package seqbias-1.20.0
"RforProteomics" # depends on broken package interactiveDisplay-1.10.2
"rgbif" # depends on broken package V8-1.2
"Rgnuplot" # build is broken
"rgp" # build is broken
"rgpui" # depends on broken package rgp-0.4-1
"rgsepd" # depends on broken package goseq-1.26.0
2017-03-04 20:51:23 +00:00
"rhdf5" # build is broken
"RhpcBLASctl" # build is broken
"Rhtslib" # build is broken
2017-03-04 20:51:23 +00:00
"ridge" # build is broken
"rjade" # depends on broken package V8-1.2
"rJPSGCS" # build is broken
"RKEEL" # depends on broken package RKEELjars-1.0.15
"RKEELjars" # build is broken
"Rknots" # depends on broken package r-bio3d-2.3-1
"rLindo" # build is broken
"rlo" # depends on broken package PythonInR-0.1-3
"RMallow" # build is broken
"rmapshaper" # depends on broken package V8-1.2
"rMAT" # build is broken
"Rmosek" # build is broken
"rmumps" # build is broken
2017-03-04 20:51:23 +00:00
"RMySQL" # build is broken
"rnaturalearth" # depends on broken package sf-0.4-1
2017-03-04 20:51:23 +00:00
"RnavGraph" # build is broken
"rnetcarto" # build is broken
"ROI_plugin_clp" # depends on broken package clpAPI-1.2.7
2017-03-04 20:51:23 +00:00
"ROI_plugin_cplex" # depends on broken package Rcplex-0.3-3
"ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-26
"ROracle" # build is broken
"RPA" # depends on broken package r-rhdf5-2.16.0
"RPANDA" # depends on broken package animation-2.4
"rpanel" # build is broken
"rpg" # build is broken
"Rphylopars" # depends on broken package animation-2.4
"Rpoppler" # build is broken
"RQuantLib" # build is broken
"Rsampletrees" # build is broken
2017-03-04 20:51:23 +00:00
"RSAP" # build is broken
"rsbml" # build is broken
"RSCABS" # build is broken
"rscala" # build is broken
"Rsomoclu" # build is broken
"rsparkling" # depends on broken package h2o-3.10.3.6
"rsvg" # build is broken
"Rsymphony" # build is broken
"rtable" # depends on broken package gdtools-0.1.3
"rTANDEM" # build is broken
"Rtextrankr" # build is broken
"rUnemploymentData" # depends on broken package acs-2.0
"rvg" # depends on broken package gdtools-0.1.3
"RVideoPoker" # depends on broken package rpanel-1.1-3
"rzmq" # build is broken
"s2" # build is broken
"sapFinder" # build is broken
"sbrl" # build is broken
"SC3" # depends on broken package scater-1.2.0
2017-03-04 20:51:23 +00:00
"scater" # depends on broken package r-rhdf5-2.16.0
"scran" # depends on broken package r-rhdf5-2.16.0
"SDD" # depends on broken package rpanel-1.1-3
"seasonal" # build is broken
"seasonalview" # build is broken
"Sejong" # build is broken
"SemiCompRisks" # build is broken
"semPlot" # depends on broken package OpenMx-2.7.10
2017-03-04 20:51:23 +00:00
"semtree" # depends on broken package OpenMx-2.7.4
"seqbias" # build is broken
"SeqGrapheR" # build is broken
"seqTools" # build is broken
"sf" # build is broken
"shazam" # build is broken
"shinyTANDEM" # build is broken
"SICtools" # build is broken
"SigTree" # depends on broken package r-rhdf5-2.16.0
"SimInf" # build is broken
"simsalapar" # build is broken
"smapr" # depends on broken package r-rhdf5-2.16.0
"SMITE" # depends on broken package goseq-1.26.0
2017-03-04 20:51:23 +00:00
"SnakeCharmR" # build is broken
"sodium" # build is broken
"soilphysics" # depends on broken package rpanel-1.1-3
"sortinghat" # build is broken
"spdynmod" # depends on broken package animation-2.4
"spocc" # depends on broken package V8-1.2
"spongecake" # build is broken
"srd" # depends on broken package animation-2.4
"SSDM" # build is broken
"stagePop" # depends on broken package PBSddesolve-1.12.2
"Starr" # build is broken
"stream" # depends on broken package animation-2.4
"streamMOA" # depends on broken package animation-2.4
"stremr" # build is broken
"subspaceMOA" # depends on broken package animation-2.4
"svglite" # depends on broken package gdtools-0.1.3
"sybilSBML" # build is broken
"SymTS" # build is broken
2017-03-04 20:51:23 +00:00
"synthACS" # depends on broken package acs-2.0
"tcpl" # depends on broken package RMySQL-0.10.9
"TDA" # build is broken
"TED" # depends on broken package animation-2.4
"tesseract" # build is broken
"texPreview" # depends on broken package magick-0.4
2017-03-04 20:51:23 +00:00
"textreadr" # build is broken
"textTinyR" # build is broken
"TFBSTools" # depends on broken package CNEr-1.8.3
"tilegramsR" # depends on broken package sf-0.4-1
2017-03-04 20:51:23 +00:00
"TKF" # depends on broken package animation-2.4
"tmap" # depends on broken package V8-1.2
"tmaptools" # depends on broken package V8-1.2
"tofsims" # build is broken
"toxboot" # depends on broken package RMySQL-0.10.9
"TransView" # build is broken
"treatSens" # build is broken
2017-03-04 20:51:23 +00:00
"treeplyr" # depends on broken package animation-2.4
"TSMySQL" # depends on broken package RMySQL-0.10.9
"uaparserjs" # depends on broken package V8-1.2
"UBCRM" # build is broken
"uHMM" # build is broken
"umx" # depends on broken package OpenMx-2.7.4
"userfriendlyscience" # depends on broken package OpenMx-2.7.4
"V8" # build is broken
"VariantTools" # depends on broken package gmapR-1.16.0
2017-03-04 20:51:23 +00:00
"VBmix" # build is broken
"vcfR" # build is broken
"vdiffr" # depends on broken package gdtools-0.1.3
"vmsbase" # depends on broken package PBSmapping-2.69.76
"wallace" # depends on broken package V8-1.2
"wand" # build is broken
"WebGestaltR" # depends on broken package PythonInR-0.1-3
2017-03-04 20:51:23 +00:00
"webp" # build is broken
"wordbankr" # depends on broken package RMySQL-0.10.9
"x13binary" # build is broken
"x_ent" # depends on broken package r-protolite-1.5
"xps" # build is broken
"xslt" # build is broken
"zoon" # build is broken
];
otherOverrides = old: new: {
2015-07-22 11:42:23 +00:00
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 $out/library/stringi/libs
'';
});
2015-05-15 11:47:27 +00:00
xml2 = old.xml2.overrideDerivation (attrs: {
preConfigure = ''
export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
patchShebangs configure
'';
2015-05-15 11:47:27 +00:00
});
2017-01-06 16:11:23 +00:00
Cairo = old.Cairo.overrideDerivation (attrs: {
NIX_LDFLAGS = "-lfontconfig";
});
curl = old.curl.overrideDerivation (attrs: {
2015-09-09 18:29:20 +00:00
preConfigure = "patchShebangs configure";
});
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.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 ];
2015-03-19 13:14:28 +00:00
LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
});
RMySQL = old.RMySQL.overrideDerivation (attrs: {
2015-02-19 20:53:36 +00:00
patches = [ ./patches/RMySQL.patch ];
2015-04-01 23:52:38 +00:00
MYSQL_DIR="${pkgs.mysql.lib}";
2015-02-19 20:53:36 +00:00
});
devEMF = old.devEMF.overrideDerivation (attrs: {
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
2017-01-06 16:58:58 +00:00
NIX_LDFLAGS = "-lX11";
});
slfm = old.slfm.overrideDerivation (attrs: {
2015-06-09 16:47:26 +00:00
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
});
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
});
EMCluster = old.EMCluster.overrideDerivation (attrs: {
patches = [ ./patches/EMCluster.patch ];
});
spMC = old.spMC.overrideDerivation (attrs: {
patches = [ ./patches/spMC.patch ];
});
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
patches = [ ./patches/BayesLogit.patch ];
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
});
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
patches = [ ./patches/BayesBridge.patch ];
});
openssl = old.openssl.overrideDerivation (attrs: {
OPENSSL_INCLUDES = "${pkgs.openssl.dev}/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