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nixpkgs/pkgs/development/r-modules/default.nix
Andreas Herrmann cf3a2e99ad r-modules: edgeR is broken due to broken url
2016-09-27 17:47:16 +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;
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:
# XXX: not ideal ("2.2" would match "2.22") but sufficient
assert (!(args ? rVersion) || lib.hasPrefix args.rVersion (lib.getVersion R));
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, CRAN and IRkernel 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" ];
};
deriveIRkernel = mkDerive {
mkHomepage = {name}: "https://irkernel.github.io/";
mkUrls = {name, version}: [ "http://irkernel.github.io/src/contrib/${name}_${version}.tar.gz" ];
};
# Overrides package definitions with nativeBuildInputs.
# For example,
#
# overrideNativeBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
# });
# }
overrideNativeBuildInputs = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
})
) overrides;
# Overrides package definitions with buildInputs.
# For example,
#
# overrideBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
# });
# }
overrideBuildInputs = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
buildInputs = attrs.buildInputs ++ value;
})
) overrides;
# Overrides package definitions with new R dependencies.
# For example,
#
# overrideRDepends {
# foo = [ self.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
# });
# }
overrideRDepends = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
})
) overrides;
# Overrides package definition requiring X running to install.
# For example,
#
# overrideRequireX [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# requireX = true;
# };
# }
overrideRequireX = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
requireX = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to skip check.
# For example,
#
# overrideSkipCheck [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# doCheck = false;
# };
# }
overrideSkipCheck = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
doCheck = false;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to mark it broken.
# For example,
#
# overrideBroken [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# broken = true;
# };
# }
overrideBroken = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
broken = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
defaultOverrides = old: new:
let old0 = old; in
let
old1 = old0 // (overrideRequireX packagesRequireingX old0);
old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
old3 = old2 // (overrideRDepends packagesWithRDepends old2);
old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
old6 = old5 // (overrideBroken brokenPackages old5);
old = old6;
in old // (otherOverrides old new);
# Recursive override pattern.
# `_self` is a collection of packages;
# `self` is `_self` with overridden packages;
# packages in `_self` may depends on overridden packages.
self = (defaultOverrides _self self) // overrides;
_self = 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; } //
import ./irkernel-packages.nix { inherit self; derive = deriveIRkernel; };
# tweaks for the individual packages and "in self" follow
packagesWithRDepends = {
FactoMineR = [ self.car ];
pander = [ self.codetools ];
};
packagesWithNativeBuildInputs = {
abn = [ pkgs.gsl_1 ];
adimpro = [ pkgs.imagemagick ];
audio = [ pkgs.portaudio ];
BayesSAE = [ pkgs.gsl_1 ];
BayesVarSel = [ pkgs.gsl_1 ];
BayesXsrc = [ pkgs.readline pkgs.ncurses ];
bigGP = [ pkgs.openmpi ];
BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ];
bnpmr = [ pkgs.gsl_1 ];
BNSP = [ pkgs.gsl_1 ];
cairoDevice = [ pkgs.gtk2 ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
Cardinal = [ pkgs.which ];
chebpol = [ pkgs.fftw ];
ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
cit = [ pkgs.gsl_1 ];
curl = [ pkgs.curl.dev ];
devEMF = [ pkgs.xorg.libXft ];
diversitree = [ pkgs.gsl_1 pkgs.fftw ];
EMCluster = [ pkgs.liblapack ];
fftw = [ pkgs.fftw ];
fftwtools = [ pkgs.fftw ];
Formula = [ pkgs.gmp ];
geoCount = [ pkgs.gsl_1 ];
git2r = [ pkgs.zlib pkgs.openssl ];
GLAD = [ pkgs.gsl_1 ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
gmp = [ pkgs.gmp ];
graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ];
h5 = [ pkgs.hdf5-cpp pkgs.which ];
h5vc = [ pkgs.zlib.dev ];
HiCseg = [ pkgs.gsl_1 ];
iBMQ = [ pkgs.gsl_1 ];
igraph = [ pkgs.gmp ];
JavaGD = [ pkgs.jdk ];
jpeg = [ pkgs.libjpeg ];
KFKSDS = [ pkgs.gsl_1 ];
kza = [ pkgs.fftw ];
libamtrack = [ pkgs.gsl_1 ];
mixcat = [ pkgs.gsl_1 ];
mvabund = [ pkgs.gsl_1 ];
mwaved = [ pkgs.fftw ];
ncdf4 = [ pkgs.netcdf ];
nloptr = [ pkgs.nlopt ];
openssl = [ pkgs.openssl.dev ];
outbreaker = [ pkgs.gsl_1 ];
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_1 ];
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
RAppArmor = [ pkgs.libapparmor ];
rapportools = [ pkgs.which ];
rapport = [ pkgs.which ];
rbamtools = [ pkgs.zlib ];
rcdd = [ pkgs.gmp ];
RcppCNPy = [ pkgs.zlib ];
RcppGSL = [ pkgs.gsl_1 ];
RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
RcppZiggurat = [ pkgs.gsl_1 ];
rgdal = [ pkgs.proj pkgs.gdal ];
rgeos = [ pkgs.geos ];
rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
Rglpk = [ pkgs.glpk ];
RGtk2 = [ pkgs.gtk2 ];
rhdf5 = [ pkgs.zlib ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
Rhtslib = [ pkgs.zlib ];
RJaCGH = [ pkgs.zlib ];
rjags = [ pkgs.jags ];
rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ];
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 ];
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 ];
seqinr = [ pkgs.zlib ];
seqminer = [ pkgs.zlib pkgs.bzip2 ];
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
simplexreg = [ pkgs.gsl_1 ];
SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
spate = [ pkgs.fftw ];
sprint = [ pkgs.openmpi ];
ssanv = [ pkgs.proj ];
stsm = [ pkgs.gsl_1 ];
stringi = [ pkgs.icu.dev ];
survSNP = [ pkgs.gsl_1 ];
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
TAQMNGR = [ pkgs.zlib ];
tiff = [ pkgs.libtiff ];
TKF = [ pkgs.gsl_1 ];
tkrplot = [ pkgs.xorg.libX11 ];
topicmodels = [ pkgs.gsl_1 ];
udunits2 = [ pkgs.udunits pkgs.expat ];
V8 = [ pkgs.v8 ];
VBLPCM = [ pkgs.gsl_1 ];
VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
WhopGenome = [ pkgs.zlib ];
XBRL = [ pkgs.zlib pkgs.libxml2 ];
xml2 = [ pkgs.libxml2 ];
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
affyPLM = [ pkgs.zlib ];
bamsignals = [ pkgs.zlib ];
BitSeq = [ pkgs.zlib ];
DiffBind = [ pkgs.zlib ];
ShortRead = [ pkgs.zlib.dev ];
oligo = [ pkgs.zlib ];
gmapR = [ pkgs.zlib ];
Rsubread = [ pkgs.zlib ];
XVector = [ pkgs.zlib.dev ];
Rsamtools = [ pkgs.zlib.dev ];
rtracklayer = [ pkgs.zlib ];
affyio = [ pkgs.zlib ];
VariantAnnotation = [ pkgs.zlib ];
snpStats = [ pkgs.zlib ];
};
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 ];
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 ];
ecoretriever = [ pkgs.which ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
rPython = [ pkgs.which ];
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 ];
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"
"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"
"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"
"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 = [
"TED" # depends on broken package animation
"streamMOA" # depends on broken package animation
"stream" # depends on broken package animation
"spdynmod" # depends on broken package animation
"treeplyr" # depends on broken package animation
"recluster" # depends on broken package animation
"geomorph" # depends on broken package animation
"phytools" # depends on broken package animation
"animation" # broken build
"srd" # broken build
"paleotree" # broken build
"ndtv" # broken build
"mvMORPH" # broken build
"mptools" # broken build
"monogeneaGM" # broken build
"molaR" # broken build
"idm" # broken build
"hisse" # broken build
"gfcanalysis" # broken build
"evolqg" # broken build
"evobiR" # broken build
"convevol" # broken build
"bayou" # broken build
"anim_plots" # broken build
"TKF" # broken build
"Rphylopars" # broken build
"RAM" # broken build
"PhySortR" # broken build
"MonoPhy" # broken build
"Momocs" # broken build
"Evomorph" # broken build
"PBD" # depends on broken package DDD
"DDD" # broken build
"BMhyd" # broken build
"rscala" # broken build
"rgpui" # depends on broken package rgp
"rgp" # broken build
"qcmetrics" # broken build
"lfe" # broken build
"interactiveDisplay" # depends on broken package interactiveDisplayBase
"RefNet" # depends on broken package interactiveDisplayBase
"pwOmics" # depends on broken package interactiveDisplayBase
"grasp2db" # depends on broken package interactiveDisplayBase
"EnsDb_Rnorvegicus_v79" # depends on broken package interactiveDisplayBase
"EnsDb_Rnorvegicus_v75" # depends on broken package interactiveDisplayBase
"EnsDb_Mmusculus_v79" # depends on broken package interactiveDisplayBase
"EnsDb_Mmusculus_v75" # depends on broken package interactiveDisplayBase
"EnsDb_Hsapiens_v79" # depends on broken package interactiveDisplayBase
"EnsDb_Hsapiens_v75" # depends on broken package interactiveDisplayBase
"ensembldb" # depends on broken package interactiveDisplayBase
"AnnotationHubData" # depends on broken package interactiveDisplayBase
"AnnotationHub" # depends on broken package interactiveDisplayBase
"interactiveDisplayBase" # broken build
"h2o" # broken build
"funModeling" # broken build
"brr" # broken build
"bedr" # broken build
"Sabermetrics" # broken build
"RKEEL" # depends on broken package RKEELjars
"RKEELjars" # broken build
"RapidPolygonLookup" # depends on broken package PBSmapping
"PBSmapping" # broken build
"stagePop" # depends on broken package PBSddesolve
"PBSddesolve" # broken build
"Metab" # broken build
"Crossover" # broken build
"CardinalWorkflows" # broken build
"spoccutils" # depends on broken package spocc
"mapr" # depends on broken package spocc
"vmsbase" # broken build
"vcfR" # broken build
"strataG" # broken build
"SSDM" # broken build
"SimInf" # broken build
"shazam" # broken build
"rsvg" # broken build
"Rothermel" # broken build
"rfPermute" # broken build
"redland" # broken build
"RAppArmor" # broken build
"permGPU" # broken build
"pdftools" # broken build
"OceanView" # broken build
"MSeasyTkGUI" # broken build
"mrMLM" # broken build
"MonetDBLite" # broken build
"MixGHD" # broken build
"LCMCR" # broken build
"hunspell" # broken build
"googleformr" # broken build
"ggseas" # depends on broken package x13binary
"seasonal" # depends on broken package x13binary
"gunsales" # depends on broken package x13binary
"x13binary" # broken build
"fds" # broken build
"exifr" # broken build
"rite" # depends on broken package euroMix
"MBCB" # depends on broken package euroMix
"forensim" # depends on broken package euroMix
"dynBiplotGUI" # depends on broken package euroMix
"cncaGUI" # depends on broken package euroMix
"biplotbootGUI" # depends on broken package euroMix
"AnthropMMD" # depends on broken package euroMix
"ilc" # depends on broken package demography
"demography" # broken build
"webbioc" # depends on broken package limma
"davidTiling" # depends on broken package limma
"tilingArray" # depends on broken package limma
"NAPPA" # depends on broken package limma
"NanoStringNorm" # depends on broken package limma
"synapterdata" # depends on broken package limma
"synapter" # depends on broken package limma
"RforProteomics" # depends on broken package limma
"pRolocdata" # depends on broken package limma
"ProCoNA" # depends on broken package limma
"Pbase" # depends on broken package limma
"MSnID" # depends on broken package limma
"msmsEDA" # depends on broken package limma
"MSnbase" # depends on broken package limma
"staRank" # depends on broken package limma
"phenoDist" # depends on broken package limma
"imageHTS" # depends on broken package limma
"Mulder2012" # depends on broken package limma
"HTSanalyzeR" # depends on broken package limma
"gespeR" # depends on broken package limma
"cellHTS2" # depends on broken package limma
"affyPara" # depends on broken package limma
"vsn" # depends on broken package limma
"ttScreening" # depends on broken package limma
"metaX" # depends on broken package limma
"SSPA" # depends on broken package limma
"SQDA" # depends on broken package limma
"ADaCGH2" # depends on broken package limma
"snapCGH" # depends on broken package limma
"Shrinkage" # depends on broken package limma
"SafeQuant" # depends on broken package limma
"RTopper" # depends on broken package limma
"RTCGAToolbox" # depends on broken package limma
"RPPanalyzer" # depends on broken package limma
"Rnits" # depends on broken package limma
"RNAinteractMAPK" # depends on broken package limma
"RNAinteract" # depends on broken package limma
"SimBindProfiles" # depends on broken package limma
"ccTutorial" # depends on broken package limma
"Ringo" # depends on broken package limma
"rCGH" # depends on broken package limma
"qusage" # depends on broken package limma
"qpcrNorm" # depends on broken package limma
"prot2D" # depends on broken package limma
"polyester" # depends on broken package limma
"plmDE" # depends on broken package limma
"phenoTest" # depends on broken package limma
"RANKS" # depends on broken package limma
"PerfMeas" # depends on broken package limma
"pepStat" # depends on broken package limma
"PECA" # depends on broken package limma
"PADOG" # depends on broken package limma
"OGSA" # depends on broken package limma
"nethet" # depends on broken package limma
"lpNet" # depends on broken package limma
"nem" # depends on broken package limma
"monocle" # depends on broken package limma
"MmPalateMiRNA" # depends on broken package limma
"miRtest" # depends on broken package limma
"miRLAB" # depends on broken package limma
"mGSZ" # depends on broken package limma
"MAMA" # depends on broken package limma
"metaMA" # depends on broken package limma
"msd16s" # depends on broken package limma
"metagenomeSeq" # depends on broken package limma
"metabolomics" # depends on broken package limma
"maSigPro" # depends on broken package limma
"timecourse" # depends on broken package limma
"stepNorm" # depends on broken package limma
"RBM" # depends on broken package limma
"saps" # depends on broken package limma
"PharmacoGx" # depends on broken package limma
"piano" # depends on broken package limma
"OLINgui" # depends on broken package limma
"OLIN" # depends on broken package limma
"nnNorm" # depends on broken package limma
"ListerEtAlBSseq" # depends on broken package limma
"compEpiTools" # depends on broken package limma
"methylPipe" # depends on broken package limma
"dyebiasexamples" # depends on broken package limma
"dyebias" # depends on broken package limma
"CluMix" # depends on broken package limma
"HCsnip" # depends on broken package limma
"sigaR" # depends on broken package limma
"plrs" # depends on broken package limma
"CGHregions" # depends on broken package limma
"QDNAseq_mm10" # depends on broken package limma
"QDNAseq_hg19" # depends on broken package limma
"QDNAseq" # depends on broken package limma
"GeneBreak" # depends on broken package limma
"focalCall" # depends on broken package limma
"CGHnormaliter" # depends on broken package limma
"CGHcall" # depends on broken package limma
"CGHbase" # depends on broken package limma
"beta7" # depends on broken package limma
"marray" # depends on broken package limma
"LVSmiRNA" # depends on broken package limma
"lmdme" # depends on broken package limma
"limmaGUI" # depends on broken package limma
"InPAS" # depends on broken package limma
"iChip" # depends on broken package limma
"unifiedWMWqPCR" # depends on broken package limma
"nondetects" # depends on broken package limma
"HTqPCR" # depends on broken package limma
"HD2013SGI" # depends on broken package limma
"vtpnet" # depends on broken package limma
"gwascat" # depends on broken package limma
"gQTLstats" # depends on broken package limma
"GOsummaries" # depends on broken package limma
"yri1kgv" # depends on broken package limma
"hmyriB36" # depends on broken package limma
"cheung2010" # depends on broken package limma
"GGtools" # depends on broken package limma
"GGdata" # depends on broken package limma
"encoDnaseI" # depends on broken package limma
"dsQTL" # depends on broken package limma
"ceuhm3" # depends on broken package limma
"ceu1kgv" # depends on broken package limma
"ceu1kg" # depends on broken package limma
"GGBase" # depends on broken package limma
"GeneSelector" # depends on broken package limma
"GeneSelectMMD" # depends on broken package limma
"gCMAPWeb" # depends on broken package limma
"gCMAP" # depends on broken package limma
"flowBin" # depends on broken package limma
"Fletcher2013a" # depends on broken package limma
"FEM" # depends on broken package limma
"explorase" # depends on broken package limma
"ExiMiR" # depends on broken package limma
"tweeDEseq" # depends on broken package limma
"tRanslatome" # depends on broken package limma
"ToPASeq" # depends on broken package limma
"timeSeq" # depends on broken package limma
"TCGAbiolinks" # depends on broken package limma
"TCC" # depends on broken package limma
"systemPipeR" # depends on broken package limma
"STATegRa" # depends on broken package limma
"ssizeRNA" # depends on broken package limma
"RUVSeq" # depends on broken package limma
"RnaSeqSampleSizeData" # depends on broken package limma
"RnaSeqSampleSize" # depends on broken package limma
"rnaSeqMap" # depends on broken package limma
"ReportingTools" # depends on broken package limma
"QuasiSeq" # depends on broken package limma
"PROPER" # depends on broken package limma
"myTAI" # depends on broken package limma
"msmsTests" # depends on broken package limma
"methylMnM" # depends on broken package limma
"metaseqR" # depends on broken package limma
"MEDIPS" # depends on broken package limma
"manta" # depends on broken package limma
"HTSFilter" # depends on broken package limma
"HTSCluster" # depends on broken package limma
"GSAgm" # depends on broken package limma
"fdrDiscreteNull" # depends on broken package limma
"erccdashboard" # depends on broken package limma
"EnrichmentBrowser" # depends on broken package limma
"edgeRun" # depends on broken package limma
"EDDA" # depends on broken package limma
"RnaSeqTutorial" # depends on broken package limma
"easyRNASeq" # depends on broken package limma
"DEGreport" # depends on broken package limma
"Imetagene" # depends on broken package limma
"metagene" # depends on broken package limma
"DBChIP" # depends on broken package limma
"babel" # depends on broken package limma
"apmsWAPP" # depends on broken package limma
"ampliQueso" # depends on broken package limma
"edgeR" # depends on broken package limma
"MMDiff" # depends on broken package limma
"ChIPQC" # depends on broken package limma
"DiffBind" # depends on broken package limma
"DCGL" # depends on broken package limma
"Prostar" # depends on broken package limma
"DAPAR" # depends on broken package limma
"DAAGbio" # depends on broken package limma
"csaw" # depends on broken package limma
"cp4p" # depends on broken package limma
"coRNAi" # depends on broken package limma
"Cormotif" # depends on broken package limma
"CORM" # depends on broken package limma
"TurboNorm" # depends on broken package limma
"maigesPack" # depends on broken package limma
"convert" # depends on broken package limma
"compcodeR" # depends on broken package limma
"codelink" # depends on broken package limma
"clippda" # depends on broken package limma
"REDseq" # depends on broken package limma
"GUIDEseq" # depends on broken package limma
"ggtut" # depends on broken package limma
"FunciSNP" # depends on broken package limma
"ChIPpeakAnno" # depends on broken package limma
"ChIPComp" # depends on broken package limma
"ChimpHumanBrainData" # depends on broken package limma
"charmData" # depends on broken package limma
"charm" # depends on broken package limma
"cghMCR" # depends on broken package limma
"CCl4" # depends on broken package limma
"casper" # depends on broken package limma
"CancerMutationAnalysis" # depends on broken package limma
"CALIB" # depends on broken package limma
"quantro" # depends on broken package limma
"RnBeads" # depends on broken package limma
"mvoutData" # depends on broken package limma
"MineICA" # depends on broken package limma
"methyAnalysis" # depends on broken package limma
"MAQCsubsetILM" # depends on broken package limma
"MAQCsubset" # depends on broken package limma
"lumiRatIDMapping" # depends on broken package limma
"lumiMouseIDMapping" # depends on broken package limma
"lumiHumanIDMapping" # depends on broken package limma
"lumiBarnes" # depends on broken package limma
"iCheck" # depends on broken package limma
"ffpeExampleData" # depends on broken package limma
"arrayMvout" # depends on broken package limma
"lumi" # depends on broken package limma
"ffpe" # depends on broken package limma
"methylumi" # depends on broken package limma
"shinyMethyl" # depends on broken package limma
"MethylAidData" # depends on broken package limma
"MethylAid" # depends on broken package limma
"IlluminaHumanMethylation450kmanifest" # depends on broken package limma
"skewr" # depends on broken package limma
"wateRmelon" # depends on broken package limma
"missMethyl" # depends on broken package limma
"minfiData" # depends on broken package limma
"IlluminaHumanMethylation450kanno_ilmn12_hg19" # depends on broken package limma
"IlluminaHumanMethylation27kmanifest" # depends on broken package limma
"FlowSorted_DLPFC_450k" # depends on broken package limma
"FlowSorted_Blood_450k" # depends on broken package limma
"ENmix" # depends on broken package limma
"ELMER" # depends on broken package limma
"MEAL" # depends on broken package limma
"DMRcate" # depends on broken package limma
"CopyNumber450kData" # depends on broken package limma
"CopyNumber450k" # depends on broken package limma
"conumee" # depends on broken package limma
"ChAMP" # depends on broken package limma
"minfi" # depends on broken package limma
"regionReport" # depends on broken package limma
"derfinderPlot" # depends on broken package limma
"derfinder" # depends on broken package limma
"bumphunter" # depends on broken package limma
"birta" # depends on broken package limma
"betr" # depends on broken package limma
"beadarrayMSV" # depends on broken package limma
"RobLoxBioC" # depends on broken package limma
"maGUI" # depends on broken package limma
"epigenomix" # depends on broken package limma
"blima" # depends on broken package limma
"BeadArrayUseCases" # depends on broken package limma
"beadarrayFilter" # depends on broken package limma
"beadarrayExampleData" # depends on broken package limma
"beadarray" # depends on broken package limma
"ballgown" # depends on broken package limma
"attract" # depends on broken package limma
"ArrayTools" # depends on broken package limma
"arrayQuality" # depends on broken package limma
"DrugVsDisease" # depends on broken package limma
"ArrayExpress" # depends on broken package limma
"oneChannelGUI" # depends on broken package limma
"affylmGUI" # depends on broken package limma
"AffyExpress" # depends on broken package limma
"AgiMicroRna" # depends on broken package limma
"affycoretools" # depends on broken package limma
"ABSSeq" # depends on broken package limma
"a4" # depends on broken package limma
"a4Base" # depends on broken package limma
"limma" # broken build
"TransView" # broken build
"Starr" # broken build
"SICtools" # broken build
"ReQON" # depends on broken package seqbias
"seqbias" # broken build
"Repitools" # broken build
"QuasR" # broken build
"qrqc" # broken build
"ProteomicsAnnotationHubData" # broken build
"podkat" # broken build
"PING" # depends on broken package PICS
"PICS" # broken build
"mcaGUI" # broken build
"deepSNV" # broken build
"motifbreakR" # depends on broken package MotIV
"LowMACA" # depends on broken package MotIV
"dagLogo" # depends on broken package MotIV
"motifStack" # depends on broken package MotIV
"MotIV" # broken build
"CNEr" # broken build
"canceR" # broken build
"BubbleTree" # broken build
"arrayQualityMetrics" # broken build
"ArrayExpressHTS" # broken build
"TargetSearchData" # depends on broken package TargetSearch
"TargetSearch" # broken build
"ptw" # depends on broken package nloptr
"gpuR" # broken build
"erma" # broken build
"MBmca" # depends on broken package chipPCR
"dpcR" # depends on broken package chipPCR
"chipPCR" # broken build
"alsace" # broken build
"rrlda" # depends on broken package VIM
"qrfactor" # depends on broken package VIM
"MVN" # depends on broken package VIM
"mvoutlier" # depends on broken package VIM
"robCompositions" # depends on broken package VIM
"DiagrammeRsvg" # depends on broken package V8
"dagitty" # depends on broken package V8
"remoter" # depends on broken package sodium
"Fletcher2013b" # depends on broken package RTN
"apaStyle" # depends on broken package ReporteRs
"categoryCompare" # depends on broken package RCytoscape
"preseqR" # depends on broken package polynom
"permutations" # depends on broken package partitions
"GLMMRR" # depends on broken package lme4
"replicationInterval" # depends on broken package lme4
"GWASdata" # depends on broken package GWASTools
"EnsemblePCReg" # depends on broken package EnsembleBase
"EnsembleCV" # depends on broken package EnsembleBase
"cpgen" # depends on broken package pedigreemm
"mitml" # depends on broken package jomo
"IlluminaHumanMethylation450k_db" # broken build
"gahgu95ecdf" # broken build
"gahgu95dcdf" # broken build
"gahgu95ccdf" # broken build
"gahgu95bcdf" # broken build
"gahgu95av2cdf" # broken build
"PREDAsampledata" # depends on broken package gahgu133plus2cdf
"gahgu133plus2cdf" # broken build
"gahgu133bcdf" # broken build
"gahgu133acdf" # broken build
"annmap" # depends on broken package RMySQL
"choroplethr" # depends on broken package acs
"acs" # broken build
"spray" # depends on broken package partitions
"CNVrd2" # broken build
"proteoQC" # depends on broken package rTANDEM
"PGA" # depends on broken package rTANDEM
"MBESS" # depends on broken package OpenMx
"DOQTL" # depends on broken package rhdf5
"DmelSGI" # depends on broken package rhdf5
"flowDiv" # depends on broken package ncdfFlow
"ChemmineDrugs" # depends on broken package ChemmineR
"stpm" # depends on broken package nloptr
"sjmisc" # depends on broken package nloptr
"rstanarm" # depends on broken package nloptr
"glmmsr" # depends on broken package nloptr
"FDboost" # depends on broken package nloptr
"faraway" # depends on broken package nloptr
"interplot" # depends on broken package nloptr
"VSE" # depends on broken package car
"VARSEDIG" # depends on broken package car
"translateSPSS2R" # depends on broken package car
"tadaatoolbox" # depends on broken package car
"lavaan_shiny" # depends on broken package car
"RcmdrPlugin_GWRM" # depends on broken package car
"TextoMineR" # depends on broken package car
"pcaBootPlot" # depends on broken package car
"ClustGeo" # depends on broken package car
"preproviz" # depends on broken package car
"hsdar" # depends on broken package car
"DecisionCurve" # depends on broken package car
"CONDOP" # depends on broken package car
"EnsemblePenReg" # depends on broken package car
"EnsembleBase" # depends on broken package car
"fullfact" # depends on broken package car
"clusterSEs" # depends on broken package car
"ggiraph" # depends on broken package gdtools
"rvg" # depends on broken package gdtools
"ggpmisc" # depends on broken package polynom
"mlt_docreg" # depends on broken package polynom
"mlt" # depends on broken package polynom
"basefun" # depends on broken package polynom
"rtable" # depends on broken package ReporteRs
"Mediana" # depends on broken package ReporteRs
"ReporteRs" # broken build
"abd" # depends on broken package nlopt
"adabag" # depends on broken package nlopt
"adhoc" # broken build
"AER" # depends on broken package nlopt
"afex" # depends on broken package nlopt
"agRee" # depends on broken package nlopt
"aLFQ" # depends on broken package nlopt
"algstat" # broken build
"alr3" # depends on broken package nlopt
"alr4" # depends on broken package nlopt
"alsace" # depends on broken nloptr
"anacor" # depends on broken package nlopt
"aods3" # depends on broken package nlopt
"apaTables" # depends on broken package car
"apt" # depends on broken package nlopt
"ArfimaMLM" # depends on broken package nlopt
"arm" # depends on broken package nlopt
"ART" # depends on broken package car
"ARTool" # depends on broken package nlopt
"AssetPricing" # broken build
"AtelieR" # broken build
"auRoc" # depends on broken package MBESS
"AutoModel" # depends on broken package car
"bamdit" # broken build
"bapred" # depends on broken package lme4
"bartMachine" # depends on broken package nlopt
"bayesDem" # depends on broken package nlopt
"bayesLife" # depends on broken package nlopt
"BayesMed" # broken build
"bayesmix" # broken build
"bayesPop" # depends on broken package nlopt
"Bayesthresh" # depends on broken package nlopt
"BaySIC" # broken build
"BBRecapture" # depends on broken package nlopt
"BCA" # depends on broken package nlopt
"bdynsys" # depends on broken package car
"BEST" # broken build
"bgmm" # depends on broken package nlopt
"BIFIEsurvey" # depends on broken package nlopt
"BiGGR" # depends on broken package rsbml
"bioassayR" # broken build
"BiodiversityR" # depends on broken package nlopt
"biotools" # depends on broken package rpanel
"birte" # build is broken
"BLCOP" # depends on broken package Rsymphony
"blmeco" # depends on broken package nlopt
"blme" # depends on broken package nlopt
"bmd" # depends on broken package nlopt
"bmem" # depends on broken package nlopt
"bmeta" # depends on broken package R2jags
"bootnet" # depends on broken package nlopt
"boral" # broken build
"BradleyTerry2" # depends on broken package nlopt
"BrailleR" # broken build
"brainGraph" # build is broken
"brms" # build is broken
"BRugs" # build is broken
"BTSPAS" # broken build
"CADFtest" # depends on broken package nlopt
"cAIC4" # depends on broken package nlopt
"candisc" # depends on broken package nlopt
"carcass" # depends on broken package nlopt
"car" # depends on broken package nlopt
"caret" # depends on broken package nlopt
"caretEnsemble" # depends on broken package nlopt
"CARrampsOcl" # depends on broken package OpenCL
"Causata" # broken build
"CCpop" # depends on broken package nlopt
"CCTpack" # broken build
"ChainLadder" # depends on broken package nlopt
"ChemmineR" # Build Is Broken
"chipenrich" # build is broken
"chipPCR" # depends on broken nloptr
"classify" # broken build
"climwin" # depends on broken package nlopt
"CLME" # depends on broken package nlopt
"clpAPI" # build is broken
"clusterPower" # depends on broken package nlopt
"clusterSEs" # depends on broken AER
"ClustGeo" # depends on broken FactoMineR
"CNORfuzzy" # depends on broken package nlopt
"CNVPanelizer" # depends on broken cn.mops
"COHCAP" # build is broken
"colorscience" # broken build
"compendiumdb" # broken build
"conformal" # depends on broken package nlopt
"corHMM" # depends on broken package nlopt
"CosmoPhotoz" # depends on broken package nlopt
"covmat" # depends on broken package VIM
"cplexAPI" # build is broken
"cquad" # depends on broken package car
"CrypticIBDcheck" # depends on broken package nlopt
"ctsem" # depends on broken package OpenMx
"cudaBayesreg" # build is broken
"daff" # depends on broken package V8
"dagbag" # build is broken
"DAMisc" # depends on broken package nlopt
"datafsm" # depends on broken package caret
"dbConnect" # broken build
"DBKGrad" # depends on broken package rpanel
#"dcmle" # broken build
"ddst" # broken build
"Deducer" # depends on broken package nlopt
"DeducerExtras" # depends on broken package nlopt
"DeducerPlugInExample" # depends on broken package nlopt
"DeducerPlugInScaling" # depends on broken package nlopt
"DeducerSpatial" # depends on broken package nlopt
"DeducerSurvival" # depends on broken package nlopt
"DeducerText" # depends on broken package nlopt
"DEGraph" # depends on broken package RCytoscape
"destiny" # depends on broken package VIM
"DiagTest3Grp" # depends on broken package nlopt
"diffHic" # depends on broken package edgeR
"difR" # depends on broken package nlopt
"DirichletMultinomial" # Build Is Broken
"DistatisR" # depends on broken package nlopt
"diveRsity" # depends on broken package nlopt
"DJL" # depends on broken package car
"dpa" # depends on broken package nlopt
"dpcR" # depends on broken nloptr
"drc" # depends on broken package nlopt
"drfit" # depends on broken package nlopt
"drsmooth" # depends on broken package nlopt
"dynlm" # depends on broken package nlopt
"easyanova" # depends on broken package nlopt
"ecd" # depends on broken package polynom
"edge" # depends on broken package nlopt
"edgeR" # broken url
"eeptools" # depends on broken package nlopt
"EffectLiteR" # depends on broken package nlopt
"effects" # depends on broken package nlopt
"eiR" # depends on broken package ChemmineR
"EMA" # depends on broken package nlopt
"embryogrowth" # broken build
"emg" # broken build
"EnQuireR" # depends on broken package nlopt
"episplineDensity" # depends on broken package nlopt
"epr" # depends on broken package nlopt
"erer" # depends on broken package nlopt
"erma" # depends on broken GenomicFiles
"erpR" # depends on broken package rpanel
"ESKNN" # depends on broken package caret
"euroMix" # build is broken
"extRemes" # depends on broken package nlopt
"ez" # depends on broken package nlopt
"ezec" # depends on broken package drc
"facopy" # depends on broken package nlopt
"FactoMineR" # depends on broken package nlopt
"Factoshiny" # depends on broken package nlopt
"faoutlier" # depends on broken package nlopt
"fastR" # depends on broken package nlopt
"FDRreg" # depends on broken package nlopt
"fishmethods" # depends on broken package lme4
"flipflop" # broken build
"flowDensity" # depends on broken package nlopt
"flowPeaks" # build is broken
"flowQ" # build is broken
"flowStats" # depends on broken package ncdfFlow
"flowVS" # depends on broken package ncdfFlow
"flowWorkspace" # depends on broken package ncdfFlow
"fmcsR" # depends on broken package ChemmineR
"fPortfolio" # depends on broken package Rsymphony
"fracprolif" # broken build
"FreeSortR" # broken build
"freqweights" # depends on broken package nlopt
"frmqa" # broken build
"FSA" # depends on broken package car
"fscaret" # depends on broken package nlopt
"funcy" # depends on broken package car
"fxregime" # depends on broken package nlopt
"gamclass" # depends on broken package nlopt
"gamlss_demo" # depends on broken package rpanel
"gamm4" # depends on broken package nlopt
"gaussquad" # broken build
"gcmr" # depends on broken package nlopt
"GDAtools" # depends on broken package nlopt
"gdtools" # broken build
"GENESIS" # broken build
"genridge" # depends on broken package nlopt
"geojsonio" # depends on broken package V8
"GEWIST" # depends on broken package nlopt
"ggtree" # broken build
"gimme" # depends on broken package nlopt
"gmatrix" # depends on broken package cudatoolkit
"gMCP" # build is broken
"gmum_r" # broken build
"Goslate" # depends on broken package PythonInR
"GPC" # broken build
"gplm" # depends on broken package nlopt
"gpuR" # depends on GPU-specific header files
"gputools" # depends on broken package cudatoolkit
"granova" # depends on broken package nlopt
"graphicalVAR" # depends on broken package nlopt
"GraphPAC" # broken build
"gridGraphics" # build is broken
"GSCA" # depends on broken package rhdf5
"GUIDE" # depends on broken package rpanel
"GWAF" # depends on broken package nlopt
"GWASTools" # broken build
"hbsae" # depends on broken package nlopt
"heplots" # depends on broken package nlopt
"HiDimMaxStable" # broken build
"HierO" # Build Is Broken
"HilbertVisGUI" # Build Is Broken
"HiPLARM" # Build Is Broken
"HistDAWass" # depends on broken package nlopt
"HLMdiag" # depends on broken package nlopt
"homomorpheR" # broken build
"hpcwld" # broken build
"hwwntest" # broken build
"HydeNet" # broken build
"hysteresis" # depends on broken package nlopt
"IATscores" # depends on broken package nlopt
"ibd" # depends on broken package nlopt
"iccbeta" # depends on broken package nlopt
"iClick" # depends on broken package rugarch
"ifaTools" # depends on broken package OpenMx
"imager" # broken build
"immunoClust" # build is broken
"in2extRemes" # depends on broken package nlopt
"inferference" # depends on broken package nlopt
"influence_ME" # depends on broken package nlopt
"inSilicoMerging" # build is broken
"INSPEcT" # depends on broken GenomicFeatures
"interplot" # depends on broken arm
"IsingFit" # depends on broken package nlopt
"ITEMAN" # depends on broken package car
"iteRates" # broken build
"iterpc" # broken build
"IUPS" # broken build
"IVAS" # depends on broken package nlopt
"ivpack" # depends on broken package nlopt
"jagsUI" # broken build
"JAGUAR" # depends on broken package nlopt
"joda" # depends on broken package nlopt
"jomo" # build is broken
"js" # depends on broken package V8
"KoNLP" # broken build
"kzft" # broken build
"LaplaceDeconv" # depends on broken package orthopolynom
"lawn" # depends on broken package V8
"ldamatch" # broken build
"learnstats" # depends on broken package nlopt
"lefse" # build is broken
"lessR" # depends on broken package nlopt
"lgcp" # depends on broken package rpanel
"Libra" # broken build
"LinRegInteractive" # depends on broken package rpanel
"lira" # broken build
"littler" # broken build
"lme4" # depends on broken package nlopt
"LMERConvenienceFunctions" # depends on broken package nlopt
"lmerTest" # depends on broken package nlopt
"lmSupport" # depends on broken package nlopt
"LOGIT" # depends on broken package caret
"longpower" # depends on broken package nlopt
"LPTime" # broken build
"MAIT" # depends on broken package nlopt
"mAPKL" # build is broken
"maPredictDSC" # depends on broken package nlopt
"mar1s" # broken build
"marked" # depends on broken package nlopt
"matchingMarkets" # broken build
"MatrixRider" # depends on broken package DirichletMultinomial
"MaxPro" # depends on broken package nlopt
"mbest" # depends on broken package nlopt
"MBmca" # depends on broken nloptr
"mBvs" # build is broken
"meboot" # depends on broken package nlopt
"medflex" # depends on broken package car
"mediation" # depends on broken package lme4
"MEDME" # depends on broken package nlopt
"MEMSS" # depends on broken package nlopt
"merTools" # depends on broken package arm
"meta4diag" # broken build
"metagear" # build is broken
"metaheur" # depends on broken package preprocomb
"metamisc" # broken build
"metaplus" # depends on broken package nlopt
"metaSEM" # depends on broken package OpenMx
"Metatron" # depends on broken package nlopt
"miceadds" # depends on broken package nlopt
"micEconAids" # depends on broken package nlopt
"micEconCES" # depends on broken package nlopt
"micEconSNQP" # depends on broken package nlopt
"mi" # depends on broken package nlopt
"MigClim" # Build Is Broken
"migui" # depends on broken package nlopt
"minimist" # depends on broken package V8
"missMDA" # depends on broken package nlopt
"mitoODE" # build is broken
"mixAK" # depends on broken package nlopt
"MixedPoisson" # broken build
"mixlm" # depends on broken package nlopt
"MixMAP" # depends on broken package nlopt
"mlma" # depends on broken package lme4
"mlmRev" # depends on broken package nlopt
"MLSeq" # depends on broken package nlopt
"mlVAR" # depends on broken package nlopt
"MM" # broken build
"mongolite" # build is broken
"mosaic" # depends on broken package nlopt
"mpoly" # broken build
"mRMRe" # broken build
"msa" # broken build
"MSGFgui" # depends on broken package MSGFplus
"MSGFplus" # Build Is Broken
"MSstats" # depends on broken package nlopt
"MultiRR" # depends on broken package nlopt
"muma" # depends on broken package nlopt
"munsellinterpol" # broken build
"mutossGUI" # build is broken
"mvinfluence" # depends on broken package nlopt
"MXM" # broken build
"NanoStringDiff" # broken build
"NanoStringQCPro" # build is broken
"nCal" # depends on broken package nlopt
"ncdfFlow" # build is broken
"NCIgraph" # depends on broken package RCytoscape
"NHPoisson" # depends on broken package nlopt
"nloptr" # depends on broken package nlopt
"nlsem" # broken build
"nlts" # broken build
"nonrandom" # depends on broken package nlopt
"NORRRM" # build is broken
"npIntFactRep" # depends on broken package nlopt
"NSM3" # broken build
"omics" # depends on broken package lme4
"OmicsMarkeR" # depends on broken package nlopt
"OPDOE" # broken build
"OpenCL" # build is broken
"openCyto" # depends on broken package ncdfFlow
"OpenMx" # build is broken
"optBiomarker" # depends on broken package rpanel
"ora" # depends on broken package ROracle
"ordBTL" # depends on broken package nlopt
"ordPens" # depends on broken package lme4
"orthopolynom" # broken build
"OUwie" # depends on broken package nlopt
"oz" # broken build
"PAA" # broken build
"pamm" # depends on broken package nlopt
"panelAR" # depends on broken package nlopt
"papeR" # depends on broken package nlopt
"parboost" # depends on broken package nlopt
"parma" # depends on broken package nlopt
"partitions" # broken build
"PatternClass" # build is broken
"PBImisc" # depends on broken package nlopt
"pcaBootPlot" # depends on broken FactoMineR
"pcaL1" # build is broken
"pcnetmeta" # broken build
"PDQutils" # broken build
"pedigreemm" # depends on broken package nlopt
"pequod" # depends on broken package nlopt
"pglm" # depends on broken package car
"PhenStat" # depends on broken package nlopt
"phia" # depends on broken package nlopt
"phylocurve" # depends on broken package nlopt
"piecewiseSEM" # depends on broken package lme4
"plateCore" # depends on broken package ncdfFlow
"plfMA" # broken build
"plm" # depends on broken package car
"plsRbeta" # depends on broken package nlopt
"plsRcox" # depends on broken package nlopt
"plsRglm" # depends on broken package nlopt
"pmm" # depends on broken package nlopt
"polynom" # broken build
"pomp" # depends on broken package nlopt
"predictmeans" # depends on broken package nlopt
"preprocomb" # depends on broken package caret
"prevalence" # broken build
"prLogistic" # depends on broken package nlopt
"pRoloc" # depends on broken package nlopt
"pRolocGUI" # depends on broken package nlopt
"PSAboot" # depends on broken package nlopt
"ptw" # depends on broken nloptr
"PurBayes" # broken build
"pvca" # depends on broken package nlopt
"PythonInR" # broken build
"QFRM" # broken build
"qgraph" # depends on broken package nlopt
"qtbase" # build is broken
"qtlnet" # depends on broken package nlopt
"qtpaint" # depends on broken package qtbase
"qtutils" # depends on broken package qtbase
"QUALIFIER" # depends on broken package ncdfFlow
"quantification" # depends on broken package nlopt
"QuartPAC" # broken build
"R2jags" # broken build
"R2STATS" # depends on broken package nlopt
"rain" # broken build
"raincpc" # build is broken
"rainfreq" # build is broken
"RamiGO" # depends on broken package RCytoscape
"RareVariantVis" # depends on broken VariantAnnotation
"rasclass" # depends on broken package nlopt
"rationalfun" # broken build
"RBerkeley" # broken build
"RbioRXN" # depends on broken package ChemmineR
"Rblpapi" # broken build
"Rchemcpp" # depends on broken package ChemmineR
"rchess" # depends on broken package V8
"Rchoice" # depends on broken package car
"Rcmdr" # depends on broken package nlopt
"RcmdrMisc" # depends on broken package nlopt
"RcmdrPlugin_BCA" # depends on broken package nlopt
"RcmdrPlugin_coin" # depends on broken package nlopt
"RcmdrPlugin_depthTools" # depends on broken package nlopt
"RcmdrPlugin_DoE" # depends on broken package nlopt
"RcmdrPlugin_doex" # depends on broken package nlopt
"RcmdrPlugin_EACSPIR" # depends on broken package nlopt
"RcmdrPlugin_EBM" # depends on broken package nlopt
"RcmdrPlugin_EcoVirtual" # depends on broken package nlopt
"RcmdrPlugin_epack" # depends on broken package nlopt
"RcmdrPlugin_Export" # depends on broken package Rcmdr
"RcmdrPlugin_EZR" # depends on broken package nlopt
"RcmdrPlugin_FactoMineR" # depends on broken package nlopt
"RcmdrPlugin_HH" # depends on broken package nlopt
"RcmdrPlugin_IPSUR" # depends on broken package nlopt
"RcmdrPlugin_KMggplot2" # depends on broken package nlopt
"RcmdrPlugin_lfstat" # depends on broken package nlopt
"RcmdrPlugin_MA" # depends on broken package nlopt
"RcmdrPlugin_mosaic" # depends on broken package nlopt
"RcmdrPlugin_MPAStats" # depends on broken package nlopt
"RcmdrPlugin_NMBU" # depends on broken package nlopt
"RcmdrPlugin_orloca" # depends on broken package nlopt
"RcmdrPlugin_plotByGroup" # depends on broken package nlopt
"RcmdrPlugin_pointG" # depends on broken package nlopt
"RcmdrPlugin_qual" # depends on broken package nlopt
"RcmdrPlugin_RMTCJags" # depends on broken package nlopt
"RcmdrPlugin_ROC" # depends on broken package nlopt
"RcmdrPlugin_sampling" # depends on broken package nlopt
"RcmdrPlugin_SCDA" # depends on broken package nlopt
"RcmdrPlugin_seeg" # depends on broken package nlopt
"RcmdrPlugin_SLC" # depends on broken package nlopt
"RcmdrPlugin_SM" # depends on broken package nlopt
"RcmdrPlugin_sos" # depends on broken package nlopt
"RcmdrPlugin_steepness" # depends on broken package nlopt
"RcmdrPlugin_survival" # depends on broken package nlopt
"RcmdrPlugin_TeachingDemos" # depends on broken package nlopt
"RcmdrPlugin_temis" # depends on broken package nlopt
"RcmdrPlugin_UCA" # depends on broken package nlopt
"Rcpi" # depends on broken package ChemmineR
"Rcplex" # Build Is Broken
"RcppAPT" # Build Is Broken
"RcppRedis" # build is broken
"rcrypt" # broken build
"RCytoscape" # Build Is Broken
"rdd" # depends on broken package nlopt
"rddtools" # depends on broken package AER
"rDEA" # build is broken
"RDieHarder" # build is broken
"REBayes" # depends on broken package Rmosek
"referenceIntervals" # depends on broken package nlopt
"refund" # depends on broken package nlopt
"refund_shiny" # depends on broken package refund
"REndo" # depends on broken package AER
"repijson" # depends on broken package V8
"REST" # depends on broken package nlopt
"rgbif" # depends on broken package V8
"Rgnuplot" # broken build
"rjade" # depends on broken package V8
"rJPSGCS" # build is broken
"rLindo" # build is broken
"RLRsim" # depends on broken package lme4
"RMallow" # broken build
"rMAT" # build is broken
"rmgarch" # depends on broken package nlopt
"rminer" # depends on broken package nlopt
"Rmosek" # build is broken
"RMySQL" # broken build
"RNAither" # depends on broken package nlopt
"RnavGraph" # build is broken
"rnetcarto" # broken build
"robustlmm" # depends on broken package nlopt
"rockchalk" # depends on broken package nlopt
"ROI_plugin_symphony" # depends on broken package Rsymphony
"rols" # build is broken
"ROracle" # Build Is Broken
"rpanel" # build is broken
"Rpoppler" # broken build
"rpubchem" # depends on broken package nlopt
"RQuantLib" # build is broken
"rr" # depends on broken package nlopt
"RRreg" # depends on broken package lme4
"RSAP" # build is broken
"rsbml" # build is broken
"RSDA" # depends on broken package nlopt
"Rsomoclu" # broken build
"RStoolbox" # depends on broken package caret
"Rsymphony" # build is broken
"rTableICC" # broken build
"rTANDEM" # build is broken
"RTN" # depends on broken package nlopt
"rugarch" # depends on broken package nlopt
"rUnemploymentData" # broken build
"RVAideMemoire" # depends on broken package nlopt
"RVFam" # depends on broken package nlopt
"RVideoPoker" # depends on broken package rpanel
"RWebServices" # broken build
"ryouready" # depends on broken package nlopt
"sadists" # broken build
"sampleSelection" # depends on broken package nlopt
"sapFinder" # depends on broken package rTANDEM
"sdcMicro" # depends on broken package nlopt
"sdcMicroGUI" # depends on broken package nlopt
"SDD" # depends on broken package rpanel
"seeg" # depends on broken package nlopt
"Sejong" # broken build
"sem" # depends on broken package nlopt
"semdiag" # depends on broken package nlopt
"semGOF" # depends on broken package nlopt
"semPlot" # depends on broken package nlopt
"SensMixed" # depends on broken package lme4
"SensoMineR" # depends on broken package nlopt
"seqCNA" # build is broken
"SeqFeatR" # broken build
"SeqGrapheR" # Build Is Broken
"seqHMM" # depends on broken package nloptr
"seqTools" # build is broken
"SharpeR" # broken build
"shinyTANDEM" # depends on broken package rTANDEM
"SIBER" # broken build
"simPop" # depends on broken package VIM
"simr" # depends on broken package lme4
"SJava" # broken build
"sjPlot" # depends on broken package nlopt
"smacof" # broken build
"SNAGEE" # build is broken
"snm" # depends on broken package nlopt
"SOD" # depends on broken package cudatoolkit
"sodium" # broken build
"soilphysics" # depends on broken package rpanel
"sortinghat" # broken build
"SoyNAM" # depends on broken package lme4
"spacom" # depends on broken package nlopt
"SparseLearner" # depends on broken package qgraph
"specificity" # depends on broken package nlopt
"specmine" # depends on broken package caret
"splm" # depends on broken package car
"spocc" # depends on broken package V8
"spoccutils" # depends on broken spocc
"ssmrob" # depends on broken package nlopt
"StatMethRank" # broken build
"stepp" # depends on broken package nlopt
"stringgaussnet" # build is broken
"Surrogate" # depends on broken package nlopt
"svglite" # depends on broken package gdtools
"sybilSBML" # build is broken
"systemfit" # depends on broken package nlopt
"TcGSA" # depends on broken package nlopt
"TDMR" # depends on broken package nlopt
"TextoMineR" # depends on broken package FactoMineR
"TFBSTools" # depends on broken package DirichletMultinomial
"tigerstats" # depends on broken package nlopt
"TLBC" # depends on broken package caret
"tmle" # broken build
"tnam" # depends on broken package lme4
"tolBasis" # depends on broken package polynom
"translateSPSS2R" # depends on broken car
"TriMatch" # depends on broken package nlopt
"TSMySQL" # broken build
"tsoutliers" # broken build
"UBCRM" # broken build
"umx" # depends on broken package OpenMx
"uniftest" # broken build
"untb" # broken build
"userfriendlyscience" # depends on broken package nlopt
"V8" # build is broken
"varComp" # depends on broken package lme4
"varian" # build is broken
"variancePartition" # depends on broken package lme4
"VBmix" # broken build
"VIM" # depends on broken package nlopt
"VIMGUI" # depends on broken package nlopt
"vows" # depends on broken package nlopt
"webp" # build is broken
"wfe" # depends on broken package nlopt
"wordbankr" # depends on broken package RMySQL
"xergm" # depends on broken package nlopt
"xps" # build is broken
"ZeligChoice" # depends on broken package AER
"Zelig" # depends on broken package AER
"zetadiv" # depends on broken package nlopt
"zoib" # broken build
];
otherOverrides = old: new: {
stringi = old.stringi.overrideDerivation (attrs: {
postInstall = let
icuName = "icudt52l";
icuSrc = pkgs.fetchzip {
url = "http://static.rexamine.com/packages/${icuName}.zip";
sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj";
stripRoot = false;
};
in ''
${attrs.postInstall or ""}
cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs
'';
});
xml2 = old.xml2.overrideDerivation (attrs: {
preConfigure = ''
export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
patchShebangs configure
'';
});
curl = old.curl.overrideDerivation (attrs: {
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 ];
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${pkgs.xorg.libXft.out}/lib -lXft";
});
slfm = old.slfm.overrideDerivation (attrs: {
PKG_LIBS = "-L${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}";
});
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 = "${pkgs.cudatoolkit}/include";
});
EMCluster = old.EMCluster.overrideDerivation (attrs: {
patches = [ ./patches/EMCluster.patch ];
});
spMC = old.spMC.overrideDerivation (attrs: {
patches = [ ./patches/spMC.patch ];
});
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
patches = [ ./patches/BayesLogit.patch ];
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
});
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
patches = [ ./patches/BayesBridge.patch ];
});
openssl = old.openssl.overrideDerivation (attrs: {
OPENSSL_INCLUDES = "${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
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