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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;
};
# 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}_${version}.tar.gz" ];
};
deriveCran = mkDerive {
mkHomepage = {name, snapshot}: "http://mran.revolutionanalytics.com/snapshot/${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 ./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 ];
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 ];
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 ];
ncdf = [ pkgs.netcdf ];
nloptr = [ pkgs.nlopt ];
openssl = [ pkgs.openssl ];
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 ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
Rhtslib = [ pkgs.zlib ];
ridge = [ pkgs.gsl_1 ];
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 ];
SemiCompRisks = [ pkgs.gsl_1 ];
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 ];
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 pkgs.xmlsec pkgs.libxslt ];
};
packagesWithBuildInputs = {
# sort -t '=' -k 2
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_nblast = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
RMark = [ pkgs.which ];
RPushbullet = [ pkgs.which ];
qtpaint = [ pkgs.cmake ];
qtbase = [ pkgs.cmake pkgs.perl ];
gmatrix = [ pkgs.cudatoolkit ];
RCurl = [ pkgs.curl ];
R2SWF = [ pkgs.pkgconfig ];
rggobi = [ pkgs.pkgconfig ];
RGtk2 = [ pkgs.pkgconfig ];
RProtoBuf = [ pkgs.pkgconfig ];
Rpoppler = [ pkgs.pkgconfig ];
VBmix = [ pkgs.pkgconfig ];
XML = [ pkgs.pkgconfig ];
cairoDevice = [ pkgs.pkgconfig ];
chebpol = [ pkgs.pkgconfig ];
fftw = [ pkgs.pkgconfig ];
geoCount = [ pkgs.pkgconfig ];
kza = [ pkgs.pkgconfig ];
mwaved = [ pkgs.pkgconfig ];
showtext = [ pkgs.pkgconfig ];
spate = [ pkgs.pkgconfig ];
stringi = [ pkgs.pkgconfig ];
sysfonts = [ pkgs.pkgconfig ];
Cairo = [ pkgs.pkgconfig ];
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
qtutils = [ pkgs.qt4 ];
ecoretriever = [ pkgs.which ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.which pkgs.texlive.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 ];
};
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 = [
"a4Base" # depends on broken package annaffy-1.41.1
"a4Classif" # broken build
"a4Core" # broken build
"a4" # depends on broken package annaffy-1.41.1
"a4Preproc" # broken build
"a4Reporting" # depends on broken package annaffy-1.41.1
"ABAEnrichment" # broken build
"ABarray" # broken build
"abd" # depends on broken package nlopt-2.4.2
"aCGH" # broken build
"ACME" # broken build
"Actigraphy" # Build Is Broken
"adabag" # depends on broken package nlopt-2.4.2
"ADaCGH2" # depends on broken package tilingArray-1.47.0
"adhoc" # broken build
"adSplit" # build is broken
"AER" # depends on broken package nlopt-2.4.2
"afex" # depends on broken package nlopt-2.4.2
"AffyCompatible" # broken build
"affycomp" # broken build
"affyContam" # depends on broken package affyio-1.37.0
"affycoretools" # depends on broken package affyio-1.37.0
"affy" # depends on broken package affyio-1.37.0
"AffyExpress" # depends on broken package affyio-1.37.0
"affyILM" # depends on broken package affyio-1.37.0
"affyio" # build is broken
"affylmGUI" # depends on broken package affyio-1.37.0
"affyPara" # depends on broken package affyio-1.37.0
"affypdnn" # depends on broken package affyio-1.37.0
"affyPLM" # depends on broken package affyio-1.37.0
"affyQCReport" # depends on broken package affyio-1.37.0
"AffyRNADegradation" # depends on broken package affyio-1.37.0
"AffyTiling" # depends on broken package affyio-1.37.0
"AGDEX" # broken build
"AgiMicroRna" # depends on broken package affyio-1.37.0
"agRee" # depends on broken package nlopt-2.4.2
"AIMS" # broken build
"ALDEx2" # broken build
"aLFQ" # depends on broken package nlopt-2.4.2
"algstat" # broken build
"AllelicImbalance" # depends on broken package Rsamtools-1.21.8
"alr3" # depends on broken package nlopt-2.4.2
"alr4" # depends on broken package nlopt-2.4.2
"alsace" # depends on broken nloptr-1.0.4
"altcdfenvs" # depends on broken package affyio-1.37.0
"ampliQueso" # depends on broken package Rsamtools-1.21.8
"anacor" # depends on broken package nlopt-2.4.2
"AnalysisPageServer" # broken build
"animation" # broken build
"anim_plots" # broken build
"annaffy" # build is broken
"annmap" # depends on broken package Rsamtools-1.21.8
"annotate" # broken build
"AnnotationDbi" # broken build
"AnnotationForge" # Build Is Broken
"AnnotationFuncs" # broken build
"AnnotationHubData" # depends on broken package r-AnnotationForge-1.11.19
"AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0
"annotationTools" # broken build
"anota" # broken build
"aods3" # depends on broken package nlopt-2.4.2
"aop" # broken build
"apaTables" # depends on broken package r-car-2.1-0
"apComplex" # build is broken
"apex" # depends on broken package Biostrings-2.38.2
"apmsWAPP" # broken build
"apt" # depends on broken package nlopt-2.4.2
"ArfimaMLM" # depends on broken package nlopt-2.4.2
"arm" # depends on broken package nlopt-2.4.2
"ArrayBin" # broken build
"ArrayExpress" # depends on broken package affyio-1.37.0
"ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8
"arrayMvout" # depends on broken package affyio-1.37.0
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"ArrayTools" # depends on broken package affyio-1.37.0
"ArrayTV" # depends on broken package affyio-1.37.0
"ARRmNormalization" # Build Is Broken
"ART" # depends on broken package ar-car-2.1-0
"ARTool" # depends on broken package nlopt-2.4.2
"AssetPricing" # broken build
"AtelieR" # broken build
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"auRoc" # depends on broken package rjags-4-4
"AutoModel" # depends on broken package r-car-2.1-0
"babel" # broken build
"BACA" # depends on broken package Category-2.35.1
"backShift" # broken build
"BAGS" # build is broken
"ballgown" # depends on broken package Rsamtools-1.21.8
"bamdit"
"bamsignals" # build is broken
"BANOVA"
"bapred" # depends on broken package r-lme4-1.1-9
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"bayescount"
"bayesDem" # depends on broken package nlopt-2.4.2
"bayesLife" # depends on broken package nlopt-2.4.2
"BayesMed"
"bayesmix"
"BayesPeak" # broken build
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"Bayesthresh" # depends on broken package nlopt-2.4.2
"bayou" # broken build
"baySeq" # broken build
"BaySIC"
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"BcDiag" # broken build
"BCRANK" # broken build
"bcrypt"
"bdynsys" # depends on broken package car-2.1
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"beadarrayFilter" # broken build
"beadarrayMSV" # broken build
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"BEST"
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"biocGraph" # broken build
"biocViews" # broken build
"bioDist" # broken build
"BiodiversityR" # depends on broken package nlopt-2.4.2
"biomaRt" # broken build
"biomartr" # broken build
"BioMVCClass" # broken build
"biomvRCNS" # depends on broken package Rsamtools-1.21.8
"BioNet" # broken build
"BioSeqClass" # broken build
"Biostrings" # broken build
"biosvd" # broken build
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"birte" # build is broken
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"BitSeq" # depends on broken package Rsamtools-1.21.8
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"boral"
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"BrainStars" # broken build
"brms" # build is broken
"BrowserViz" # broken build
"BrowserVizDemo" # broken build
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"bsseq" # broken build
"BTSPAS"
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"CancerMutationAnalysis" # broken build
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"caret" # depends on broken package nlopt-2.4.2
"caretEnsemble" # depends on broken package nlopt-2.4.2
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"CellNOptR" # broken build
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"CGHcall" # broken build
"cghMCR" # broken build
"CGHnormaliter" # broken build
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"ChemmineR" # Build Is Broken
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"classify"
"ClassifyR" # broken build
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"DESeq2" # broken build
"DESeq" # broken build
"DESP" # broken build
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"DFP" # broken build
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"DirichletMultinomial" # Build Is Broken
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"EasyMARK"
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"embryogrowth" # broken build
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"eulerian" # broken build
"euroMix" # build is broken
"evobiR" # broken build
"evolqg" # broken build
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"fabia" # broken build
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"factDesign" # broken build
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"fastseg" # broken build
"fdrDiscreteNull" # broken build
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"FedData" # broken build
"FEM" # build is broken
"ffpe" # depends on broken package affyio-1.37.0
"FIACH" # broken build
"FindMyFriends" # broken build
"FISHalyseR" # broken build
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"flipflop" # broken build
"flowBeads" # broken build
"flowBin" # broken build
"flowcatchR" # broken build
"flowCHIC" # broken build
"flowCL" # broken build
"flowClean" # broken build
"flowClust" # broken build
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"flowFit" # broken build
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"flowMatch" # broken build
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"flowPeaks" # build is broken
"flowQB" # broken build
"flowQ" # build is broken
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"focalCall" # broken build
"FourCSeq" # depends on broken package Rsamtools-1.21.8
"fPortfolio" # depends on broken package Rsymphony-0.1-20
"fracprolif" # broken build
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"fulltext" # broken build
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"FunctionalNetworks" # Build Is Broken
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"gaga" # broken build
"gage" # broken build
"gaggle" # broken build
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"gemtc"
"GeneAnswers" # broken build
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"GENE_E" # depends on broken package rhdf5-2.13.1
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"genefilter" # broken build
"genefu" # broken build
"GeneMeta" # broken build
"GeneNetworkBuilder" # broken build
"geneplotter" # broken build
"geneRecommender" # broken build
"GeneRegionScan" # broken build
"geneRxCluster" # broken build
"GeneSelectMMD" # broken build
"GeneSelector" # broken build
"GENESIS" # broken build
"geNetClassifier" # broken build
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"GenomeGraphs" # broken build
"GenomeInfoDb" # broken build
"genomeIntervals" # broken build
"genomes" # broken build
"GenomicAlignments" # depends on broken package Rsamtools-1.21.8
"GenomicFeatures" # depends on broken package Rsamtools-1.21.8
"GenomicFiles" # depends on broken package Rsamtools-1.21.8
"GenomicInteractions" # depends on broken package Rsamtools-1.21.8
"GenomicRanges" # broken build
"GenomicTuples" # broken build
"Genominator" # broken build
"genoset" # broken build
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"GEOmetadb" # broken build
"geomorph" # broken build
"GEOquery" # broken build
"GEOsearch" # broken build
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"GERGM"
"gespeR" # depends on broken package Category-2.35.1
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"GExMap" # broken build
"gfcanalysis" # broken build
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"ggsubplot" # build is broken
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"gMCP" # build is broken
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"GOFunction" # build is broken
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"GoogleGenomics" # depends on broken package Rsamtools-1.21.8
"googlesheets" # broken build
"goProfiles" # build is broken
"GOSemSim" # Build Is Broken
"goseq" # build is broken
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"goTools" # build is broken
"GPC" # broken build
"gplm" # depends on broken package nlopt-2.4.2
"gpuR" # depends on GPU-specific header files
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"GraphAT" # broken build
"graph" # broken build
"gRapHD" # broken build
"graphicalVAR" # depends on broken package nlopt-2.4.2
"graphite" # broken build
"GraphPAC" # broken build
"GraphPCA" # depends on broken package nlopt-2.4.2
"gRbase" # broken build
"gRc" # broken build
"GreyListChIP" # depends on broken package Rsamtools-1.21.8
"gridDebug" # broken build
"gridGraphics" # build is broken
"gridGraphviz" # broken build
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"groHMM" # depends on broken package Rsamtools-1.21.8
"GSAgm" # broken build
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"GSEABase" # broken build
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"GSRI" # broken build
"GSVA" # broken build
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"GUIDEseq" # depends on broken package r-BiocGenerics-0.16.1
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"hasseDiagram" # broken build
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"HCsnip" # broken build
"hddplot" # broken build
"HELP" # broken build
"HEM" # broken build
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"hierGWAS"
"HierO" # Build Is Broken
"highriskzone"
"HilbertCurve" # broken build
"HilbertVisGUI" # Build Is Broken
"HiPLARM" # Build Is Broken
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"hisse" # broken build
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"HMMcopy" # broken build
"homomorpheR" # broken build
"hopach" # broken build
"hpcwld" # broken build
"hpoPlot" # broken build
"HTqPCR" # depends on broken package affyio-1.37.0
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"htSeqTools" # depends on broken package Rsamtools-1.21.8
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"hwwntest" # broken build
"HybridMTest" # broken build
"HydeNet" # broken build
"hyperdraw" # broken build
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"interactiveDisplayBase" # build is broken
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"ioncopy" # broken build
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"iptools"
"IRanges" # broken build
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"isobar" # broken build
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"IUPS"
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"KCsmart" # broken build
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"KEGGprofile" # Build Is Broken
"KEGGREST" # broken build
"KoNLP" # broken build
"ktspair" # broken build
"kza" # broken build
"kzft" # broken build
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"Libra" # broken build
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"lira"
"littler" # broken build
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"marked" # depends on broken package nlopt-2.4.2
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"MergeMaid" # broken build
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"methylMnM" # broken build
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"Mfuzz" # broken build
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"MiChip" # broken build
"microRNA" # broken build
"mi" # depends on broken package nlopt-2.4.2
"MigClim" # Build Is Broken
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"MiRaGE" # broken build
"miRcomp" # depends on broken package r-Biobase-2.30.0
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"miRLAB" # broken build
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"miRtest" # broken build
"missDeaths"
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"MIXFIM" # build is broken
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"MixMAP" # depends on broken package nlopt-2.4.2
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"MM2S" # broken build
"MM2Sdata" # broken build
"MM" # broken build
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"monocle" # build is broken
"monogeneaGM" # broken build
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"morse"
"mosaic" # depends on broken package nlopt-2.4.2
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"MotifDb" # depends on broken package Rsamtools-1.21.8
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"motifStack" # depends on broken package Rsamtools-1.21.8
"MotIV" # depends on broken package Rsamtools-1.21.8
"mpoly" # broken build
"mRMRe" # broken build
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"MSGFplus" # Build Is Broken
"MSIseq" # broken build
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"msmsTests" # depends on broken package affyio-1.37.0
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"munsellinterpol"
"muscle" # broken build
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"netbenchmark" # build is broken
"netClass" # broken build
"nethet" # broken build
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"NGScopy"
"nhanesA" # broken build
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"nondetects" # depends on broken package affyio-1.37.0
"nonrandom" # depends on broken package nlopt-2.4.2
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"NORRRM" # build is broken
"npGSEA" # broken build
"npIntFactRep" # depends on broken package nlopt-2.4.2
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"nucleR" # depends on broken package Rsamtools-1.21.8
"OCplus" # broken build
"OGSA" # broken build
"oligoClasses" # depends on broken package affyio-1.37.0
"oligo" # depends on broken package affyio-1.37.0
"OmicCircos" # broken build
"omics" # depends on broken package lme4-1.1-10
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"OncoSimulR" # broken build
"oneChannelGUI" # depends on broken package affyio-1.37.0
"OPDOE" # broken build
"OpenCL" # build is broken
"opencpu" # broken build
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"OpenMx" # build is broken
"openssl"
"OperaMate" # depends on broken package Category-2.35.1
"oposSOM" # broken build
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"orQA" # broken build
"orthopolynom" # broken build
"OTUbase" # depends on broken package Rsamtools-1.21.8
"OutlierD" # broken build
"OUwie" # depends on broken package nlopt-2.4.2
"oz" # broken build
"PAA" # broken build
"pacman" # broken build
"PADOG" # build is broken
"paircompviz" # broken build
"PairViz" # broken build
"paleotree" # broken build
"pamm" # depends on broken package nlopt-2.4.2
"PANDA" # build is broken
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"PAnnBuilder" # broken build
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"papeR" # depends on broken package nlopt-2.4.2
"PAPi" # broken build
"parboost" # depends on broken package nlopt-2.4.2
"parglms" # broken build
"parma" # depends on broken package nlopt-2.4.2
"partitions" # broken build
"Pasha" # depends on broken package GenomicAlignments-1.5.12
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"pathRender" # build is broken
"pathview" # build is broken
"PatternClass" # build is broken
"Pbase" # depends on broken package affyio-1.37.0
"pbdBASE" # depends on broken package pbdSLAP-0.2-0
"PBD" # broken build
"pbdDEMO" # depends on broken package pbdSLAP-0.2-0
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"pbdSLAP" # build is broken
"PBImisc" # depends on broken package nlopt-2.4.2
"pbkrtest" # depends on broken package nlopt-2.4.2
"PBSddesolve" # build is broken
"PBSmapping" # build is broken
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"pcaGoPromoter" # broken build
"pcaL1" # build is broken
"pcalg" # broken build
"pcaMethods" # broken build
"PCGSE" # broken build
"pcnetmeta"
"pcot2" # broken build
"PCpheno" # depends on broken package Category-2.35.1
"PCS" # broken build
"pdInfoBuilder" # depends on broken package affyio-1.37.0
"pdmclass" # build is broken
"PDQutils" # broken build
"PECA" # depends on broken package affyio-1.37.0
"pedigreemm" # depends on broken package nlopt-2.4.2
"pedometrics" # depends on broken package nlopt-2.4.2
"PepPrep" # broken build
"pepStat" # broken build
"pequod" # depends on broken package nlopt-2.4.2
"PerfMeas" # broken build
"PGA" # depends on broken package Rsamtools-1.21.8
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"PGSEA" # depends on broken package annaffy-1.41.1
"phangorn" # depends on broken package Biostrings-2.38.2
"PharmacoGx"
"phenoDist" # depends on broken package Category-2.35.1
"phenoTest" # depends on broken package Category-2.35.1
"PhenStat" # depends on broken package nlopt-2.4.2
"phia" # depends on broken package nlopt-2.4.2
"phreeqc" # broken build
"phylocurve" # depends on broken package nlopt-2.4.2
"phyloseq" # broken build
"PhySortR" # depends on broken package phytools-0.5-10
"phytools" # broken build
"piano" # broken build
"PICS" # depends on broken package Rsamtools-1.21.8
"piecewiseSEM" # depends on broken package r-lme4-1.1-10
"PING" # depends on broken package Rsamtools-1.21.8
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"plateCore" # depends on broken package ncdfFlow-2.15.2
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"plfMA" # broken build
"plgem" # broken build
"plier" # depends on broken package affyio-1.37.0
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"PLPE" # broken build
"plrs" # broken build
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"pmclust" # build is broken
"pmm" # depends on broken package nlopt-2.4.2
"podkat" # depends on broken package Rsamtools-1.21.8
"polyester" # broken build
"Polyfit" # broken build
"polynom" # broken build
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"prebs" # depends on broken package affyio-1.37.0
"PREDA" # broken build
"predictionet" # broken build
"predictmeans" # depends on broken package nlopt-2.4.2
"preprocomb" # depends on broken package r-caret-6.0-58
"prevalence"
"pRF" # broken build
"prLogistic" # depends on broken package nlopt-2.4.2
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"PROMISE" # broken build
"PROPER" # broken build
"propOverlap" # broken build
"Prostar" # depends on broken package r-imputeLCMD-2.0
"prot2D" # broken build
"ProteomicsAnnotationHubData" # depends on broken package r-AnnotationHub-2.1.40
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"ProtGenerics" # broken build
"protiq" # broken build
"provenance" # broken build
"PSAboot" # depends on broken package nlopt-2.4.2
"PSEA" # broken build
"PSICQUIC" # broken build
"ptw" # depends on broken nloptr-1.0.4
"puma" # depends on broken package affyio-1.37.0
"PurBayes"
"purge" # depends on broken package r-lme4-1.1-9
"pvac" # depends on broken package affyio-1.37.0
"PVAClone"
"pvca" # depends on broken package nlopt-2.4.2
"Pviz" # depends on broken package Rsamtools-1.21.8
"PWMEnrich" # broken build
"pwOmics" # depends on broken package interactiveDisplayBase-1.7.0
"PythonInR"
"qcmetrics" # build is broken
"QDNAseq" # depends on broken package Rsamtools-1.21.8
"QFRM"
"qgraph" # depends on broken package nlopt-2.4.2
"qpcrNorm" # depends on broken package affyio-1.37.0
"qpgraph" # depends on broken package Rsamtools-1.21.8
"qrqc" # depends on broken package Rsamtools-1.21.8
"qtbase" # build is broken
"qtlnet" # depends on broken package nlopt-2.4.2
"qtpaint" # depends on broken package qtbase-1.0.9
"qtutils" # depends on broken package qtbase-1.0.9
"QuACN" # broken build
"QUALIFIER" # depends on broken package ncdfFlow-2.15.2
"quantification" # depends on broken package nlopt-2.4.2
"quantro" # depends on broken package Rsamtools-1.21.8
"QuartPAC" # broken build
"QuasiSeq" # broken build
"QuasR" # depends on broken package Rsamtools-1.21.8
"qusage" # broken build
"R2jags"
"R2STATS" # depends on broken package nlopt-2.4.2
"R3CPET" # depends on broken package Rsamtools-1.21.8
"r3Cseq" # depends on broken package Rsamtools-1.21.8
"R453Plus1Toolbox" # depends on broken package Rsamtools-1.21.8
"RADami" # broken build
"rain" # broken build
"raincpc" # build is broken
"rainfreq" # build is broken
"RAM" # broken build
"RamiGO" # depends on broken package RCytoscape-1.19.0
"randPack" # broken build
"RANKS" # depends on broken package graph-1.48.0
"RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76
"RAPIDR" # depends on broken package Rsamtools-1.21.8
"RareVariantVis" # depends on broken VariantAnnotation-1.15.19
"Rariant" # depends on broken package Rsamtools-1.21.8
"rasclass" # depends on broken package nlopt-2.4.2
"rase" # broken build
"rationalfun" # broken build
"RbcBook1" # broken build
"RBerkeley"
"RBGL" # broken build
"RBioinf" # broken build
"RbioRXN" # depends on broken package ChemmineR-2.21.7
"Rblpapi" # broken build
"rbsurv" # broken build
"rbundler" # broken build
"Rcade" # depends on broken package Rsamtools-1.21.8
"rcellminer" # broken build
"rCGH" # depends on broken package r-affy-1.47.1
"Rchemcpp" # depends on broken package ChemmineR-2.21.7
"rchess" # depends on broken package r-V8-0.9
"Rchoice" # depends on broken package car-2.1
"RchyOptimyx" # broken build
"Rcmdr" # depends on broken package nlopt-2.4.2
"RcmdrMisc" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_BCA" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_coin" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_depthTools" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_DoE" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_doex" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_EACSPIR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_Export" # depends on broken package r-Rcmdr-2.2-3
"RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_IPSUR" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_KMggplot2" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_lfstat" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_MA" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_mosaic" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_MPAStats" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_NMBU" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_orloca" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_plotByGroup" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_pointG" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_qual" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_RMTCJags" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_ROC" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_sampling" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_SCDA" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_seeg" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_SLC" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_SM" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_sos" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_steepness" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_survival" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_TeachingDemos" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_temis" # depends on broken package nlopt-2.4.2
"RcmdrPlugin_UCA" # depends on broken package nlopt-2.4.2
"Rcpi" # depends on broken package ChemmineR-2.21.7
"Rcplex" # Build Is Broken
"RcppAPT" # Build Is Broken
"RcppOctave" # build is broken
"RcppRedis" # build is broken
"rcrypt" # broken build
"RCy3" # depends on broken package r-graph-1.48.0
"RCyjs" # broken build
"RCytoscape" # Build Is Broken
"RDAVIDWebService" # depends on broken package Category-2.35.1
"rdd" # depends on broken package nlopt-2.4.2
"rddtools" # depends on broken package r-AER-1.2-4
"rDEA" # build is broken
"RDieHarder" # build is broken
"ReactomePA" # depends on broken package GOSemSim-1.27.3
"ReadqPCR" # depends on broken package affyio-1.37.0
"REBayes" # depends on broken package Rmosek-1.2.5.1
"reb" # broken build
"recluster" # broken build
"REDseq" # depends on broken package Rsamtools-1.21.8
"referenceIntervals" # depends on broken package nlopt-2.4.2
"RefNet" # depends on broken package interactiveDisplayBase-1.7.0
"RefPlus" # depends on broken package affyio-1.37.0
"refund" # depends on broken package nlopt-2.4.2
"refund_shiny" # depends on broken package r-refund-0.1-13
"regioneR" # depends on broken package Rsamtools-1.21.8
"regionReport" # depends on broken package Rsamtools-1.21.8
"regRSM" # broken build
"REndo" # depends on broken package AER-1.2-4
"repijson" # depends on broken package V8-0.6
"Repitools" # depends on broken package affyio-1.37.0
"ReportingTools" # depends on broken package Category-2.35.1
"ReQON" # depends on broken package Rsamtools-1.21.8
"rerddap" # broken build
"REST" # depends on broken package nlopt-2.4.2
"rfPred" # depends on broken package Rsamtools-1.21.8
"rGADEM" # depends on broken package Rsamtools-1.21.8
"RGalaxy" # broken build
"rgbif" # depends on broken package V8-0.6
"Rgnuplot"
"rgp" # build is broken
"rgpui" # depends on broken package rgp-0.4-1
"Rgraphviz" # broken build
"rGREAT" # broken build
"RGSEA" # broken build
"rgsepd" # depends on broken package goseq-1.21.1
"rhdf5" # build is broken
"rHVDM" # depends on broken package affyio-1.37.0
"RiboProfiling" # depends on broken package r-BiocGenerics-0.16.1
"riboSeqR" # broken build
"Ringo" # depends on broken package affyio-1.37.0
"RIPSeeker" # depends on broken package Rsamtools-1.21.8
"Risa" # depends on broken package affyio-1.37.0
"rjade" # depends on broken package V8-0.6
"rjags"
"rJPSGCS" # build is broken
"rLindo" # build is broken
"RLRsim" # depends on broken package r-lme4-1.1-9
"Rmagpie" # broken build
"RMallow" # broken build
"RMassBank" # depends on broken package mzR-2.3.1
"rMAT" # build is broken
"rmgarch" # depends on broken package nlopt-2.4.2
"rminer" # depends on broken package nlopt-2.4.2
"RmiR" # Build Is Broken
"Rmosek" # build is broken
"rmumps" # build is broken
"RMySQL" # broken build
"RNAinteract" # depends on broken package Category-2.35.1
"RNAither" # depends on broken package nlopt-2.4.2
"RNAprobR" # depends on broken package Rsamtools-1.21.8
"rnaSeqMap" # depends on broken package Rsamtools-1.21.8
"RnaSeqSampleSize" # Build Is Broken
"RnavGraph" # build is broken
"RnBeads" # depends on broken package Rsamtools-1.21.8
"rnetcarto" # broken build
"Rnits" # depends on broken package affyio-1.37.0
"rNOMADS" # broken build
"roar" # depends on broken package Rsamtools-1.21.8
"RobLoxBioC" # depends on broken package affyio-1.37.0
"RobLox" # broken build
"robustlmm" # depends on broken package nlopt-2.4.2
"rockchalk" # depends on broken package nlopt-2.4.2
"RockFab" # broken build
"ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20
"Roleswitch" # broken build
"Rolexa" # depends on broken package Rsamtools-1.21.8
"rols" # build is broken
"ROntoTools" # broken build
"ROracle" # Build Is Broken
"RPA" # depends on broken package affyio-1.37.0
"rpanel" # build is broken
"Rphylopars" # broken build
"Rpoppler" # broken build
"RPPanalyzer" # broken build
"RpsiXML" # broken build
"rpubchem" # depends on broken package nlopt-2.4.2
"Rqc" # depends on broken package Rsamtools-1.21.8
"RQuantLib" # build is broken
"rqubic" # broken build
"rr" # depends on broken package nlopt-2.4.2
"rRDP" # broken build
"RRreg" # depends on broken package r-lme4-1.1-10
"Rsamtools" # Build Is Broken
"RSAP" # build is broken
"rsbml" # build is broken
"rscala" # build is broken
"RSDA" # depends on broken package nlopt-2.4.2
"RSeed" # broken build
"rSFFreader" # depends on broken package Rsamtools-1.21.8
"Rsomoclu"
"rstan" # build is broken
"RStoolbox" # depends on broken package r-caret-6.0-52
"Rsubread" # Build Is Broken
"RSVSim" # depends on broken package Rsamtools-1.21.8
"Rsymphony" # build is broken
"rTableICC" # broken build
"rTANDEM" # build is broken
"RTCA" # broken build
"RTCGA" # depends on broken package r-rvest-0.3.0
"RTN" # depends on broken package nlopt-2.4.2
"RTopper" # broken build
"rtracklayer" # depends on broken package Rsamtools-1.21.8
"Rtreemix" # broken build
"rTRM" # broken build
"rTRMui" # depends on broken package Rsamtools-1.21.8
"rugarch" # depends on broken package nlopt-2.4.2
"rUnemploymentData" # broken build
"RUVcorr" # build is broken
"RUVnormalize" # Build Is Broken
"RUVSeq" # depends on broken package Rsamtools-1.21.8
"RVAideMemoire" # depends on broken package nlopt-2.4.2
"rvest" # broken build
"RVFam" # depends on broken package nlopt-2.4.2
"RVideoPoker" # depends on broken package rpanel-1.1-3
"RWebServices" # broken build
"ryouready" # depends on broken package nlopt-2.4.2
"S4Vectors" # broken build
"sadists" # broken build
"safe" # broken build
"SAGx" # broken build
"sampleSelection" # depends on broken package nlopt-2.4.2
"sangerseqR" # broken build
"sapFinder" # depends on broken package rTANDEM-1.9.0
"saps" # broken build
"SCAN_UPC" # depends on broken package affyio-1.37.0
"scholar" # depends on broken package r-rvest-0.3.1
"ScISI" # depends on broken package apComplex-2.35.0
"scmamp" # broken build
"scsR" # broken build
"sdcMicro" # depends on broken package nlopt-2.4.2
"sdcMicroGUI" # depends on broken package nlopt-2.4.2
"SDD" # depends on broken package rpanel-1.1-3
"seeg" # depends on broken package nlopt-2.4.2
"segmentSeq" # depends on broken package Rsamtools-1.21.8
"sejmRP" # depends on broken package r-rvest-0.3.0
"Sejong" # broken build
"SELEX" # broken build
"sem" # depends on broken package nlopt-2.4.2
"semdiag" # depends on broken package nlopt-2.4.2
"SemDist" # Build Is Broken
"semGOF" # depends on broken package nlopt-2.4.2
"semPlot" # depends on broken package nlopt-2.4.2
"SensMixed" # depends on broken package r-lme4-1.1-9
"SensoMineR" # depends on broken package nlopt-2.4.2
"SEPA" # depends on broken package topGO-2.21.0
"seq2pathway" # depends on broken package WGCNA-1.47
"SeqArray" # depends on broken package Rsamtools-1.21.8
"seqbias" # depends on broken package Rsamtools-1.21.8
"seqCNA" # build is broken
"SeqFeatR" # broken build
"SeqGrapheR" # Build Is Broken
"SeqGSEA" # broken build
"seqHMM" # depends on broken package nloptr-1.0.4
"seqPattern" # broken build
"seqplots" # depends on broken package Rsamtools-1.21.8
"seqTools" # build is broken
"sequenza" # broken build
"SeqVarTools" # depends on broken package Rsamtools-1.21.8
"SGSeq" # depends on broken package Rsamtools-1.21.8
"SharpeR" # broken build
"sharx"
"shinyMethyl" # depends on broken package Rsamtools-1.21.8
"shinyTANDEM" # depends on broken package rTANDEM-1.9.0
"ShortRead" # depends on broken package Rsamtools-1.21.8
"Shrinkage" # depends on broken package r-multtest-2.25.2
"SIBER"
"SICtools" # depends on broken package r-Biostrings-2.38.2
"SID" # broken build
"sigaR" # broken build
"SigCheck" # broken build
"SigFuge" # broken build
"siggenes" # broken build
"sigsquared" # broken build
"SigTree" # broken build
"SIMAT" # depends on broken package mzR-2.3.1
"SimBindProfiles" # depends on broken package affyio-1.37.0
"SIM" # broken build
"similaRpeak" # depends on broken package Rsamtools-1.21.8
"simmr"
"simpleaffy" # depends on broken package affyio-1.37.0
"simPop" # depends on broken package r-VIM-4.4.1
"SimRAD" # depends on broken package Rsamtools-1.21.8
"simr" # depends on broken package r-lme4-1.1-10
"SimReg" # broken build
"simulatorZ" # broken build
"sirt" # depends on broken package nlopt-2.4.2
"SISPA" # depends on broken package r-GSVA-1.18.0
"SJava" # broken build
"sjPlot" # depends on broken package nlopt-2.4.2
"skewr" # depends on broken package affyio-1.37.0
"SLGI" # depends on broken package apComplex-2.35.0
"smacof" # broken build
"SNAGEE" # build is broken
"snapCGH" # depends on broken package tilingArray-1.47.0
"snm" # depends on broken package nlopt-2.4.2
"SNPchip" # depends on broken package affyio-1.37.0
"snpEnrichment" # depends on broken package snpStats-1.19.0
"SNPhood" # depends on broken package r-BiocGenerics-0.16.1
"snplist" # broken build
"snpStats" # build is broken
"snpStatsWriter" # depends on broken package snpStats-1.19.0
"SNPtools" # depends on broken package Rsamtools-1.21.8
"SOD" # depends on broken package cudatoolkit-5.5.22
"sodium" # broken build
"soGGi" # depends on broken package Rsamtools-1.21.8
"soilphysics" # depends on broken package rpanel-1.1-3
"SomatiCA" # broken build
"SomaticSignatures" # depends on broken package Rsamtools-1.21.8
"sortinghat" # broken build
"SoyNAM" # depends on broken package r-lme4-1.1-8
"SpacePAC" # broken build
"spacom" # depends on broken package nlopt-2.4.2
"spade" # broken build
"SparseLearner" # depends on broken package r-qgraph-1.3.1
"spdynmod" # broken build
"specificity" # depends on broken package nlopt-2.4.2
"specmine" # depends on broken package r-caret-6.0-58
"SpeCond" # broken build
"SPEM" # broken build
"SPIA" # broken build
"spkTools" # broken build
"splicegear" # broken build
"spliceR" # depends on broken package Rsamtools-1.21.8
"spliceSites" # broken build
"SplicingGraphs" # depends on broken package Rsamtools-1.21.8
"splm" # depends on broken package car-2.1-1
"spocc" # depends on broken package V8-0.6
"spoccutils" # depends on broken spocc-0.3.0
"spsann" # depends on broken package r-pedometrics-0.6-2
"SRAdb" # broken build
"srd" # broken build
"sscore" # depends on broken package affyio-1.37.0
"ssizeRNA" # broken build
"ssmrob" # depends on broken package nlopt-2.4.2
"ssviz" # depends on broken package Rsamtools-1.21.8
"stagePop" # depends on broken package PBSddesolve-1.11.29
"staRank" # depends on broken package Category-2.35.1
"Starr" # depends on broken package affyio-1.37.0
"STATegRa" # depends on broken package affyio-1.37.0
"StatMethRank"
"Statomica" # broken build
"stcm" # depends on broken package nlopt-2.4.2
"stepp" # depends on broken package nlopt-2.4.2
"stepwiseCM" # broken build
"stream" # broken build
"Streamer" # broken build
"streamMOA" # broken build
"stringgaussnet" # build is broken
"structSSI" # broken build
"strum" # broken build
"subSeq" # depends on broken package r-Biobase-2.30.0
"SummarizedExperiment" # broken build
"superbiclust" # broken build
"Surrogate" # depends on broken package nlopt-2.4.2
"Sushi" # broken build
"sva" # broken build
"svglite" # depends on broken package gdtools-0.0.6
"SVM2CRM" # depends on broken package Rsamtools-1.21.8
"sybilSBML" # build is broken
"synapter" # depends on broken package affyio-1.37.0
"synchronicity" # build is broken
"synthpop" # build is broken
"systemfit" # depends on broken package nlopt-2.4.2
"systemPipeR" # depends on broken package AnnotationForge-1.11.3
"TargetSearch" # depends on broken package mzR-2.3.1
"TarSeqQC" # depends on broken package r-BiocGenerics-0.16.1
"TCC" # broken build
"TCGA2STAT" # broken build
"TCGAbiolinks" # depends on broken package r-affy-1.47.1
"TcGSA" # depends on broken package nlopt-2.4.2
"TDARACNE" # broken build
"TDMR" # depends on broken package nlopt-2.4.2
"TED" # broken build
"TEQC" # depends on broken package Rsamtools-1.21.8
"TextoMineR" # depends on broken package FactoMineR-1.31.4
"TFBSTools" # depends on broken package DirichletMultinomial-1.11.1
"tigerstats" # depends on broken package nlopt-2.4.2
"tigre" # broken build
"tilingArray" # depends on broken package affyio-1.37.0
"timecourse" # broken build
"timeSeq" # broken build
"timetree" # depends on broken package Biostrings-2.38.2
"TIN" # depends on broken package WGCNA-1.47
"TitanCNA" # depends on broken package Rsamtools-1.21.8
"TKF" # broken build
"TLBC" # depends on broken package r-caret-6.0-58
"tmle" # broken build
"tnam" # depends on broken package r-lme4-1.1-9
"tolBasis" # depends on broken package r-polynom-1.3-8
"ToPASeq" # depends on broken package Rsamtools-1.21.8
"topGO" # build is broken
"topologyGSA" # depends on broken package Rsamtools-1.21.8
"TPP" # broken build
"tracktables" # depends on broken package Rsamtools-1.21.8
"trackViewer" # depends on broken package Rsamtools-1.21.8
"translateSPSS2R" # depends on broken car-2.0-25
"tRanslatome" # depends on broken package GOSemSim-1.27.3
"TransView" # depends on broken package Rsamtools-1.21.8
"traseR"
"treescape" # depends on broken package Biostrings-2.38.2
"triform" # broken build
"trigger" # broken build
"TriMatch" # depends on broken package nlopt-2.4.2
"triplex" # broken build
"TROM" # depends on broken package topGO-2.21.0
"TRONCO" # broken build
"TSdist" # broken build
"TSMySQL" # broken build
"tsoutliers" # broken build
"tspair" # broken build
"TSSi" # broken build
"ttScreening" # broken build
"TurboNorm" # depends on broken package affyio-1.37.0
"tweeDEseq" # broken build
"twilight" # broken build
"UBCRM" # broken build
"umx" # depends on broken package r-OpenMx-2.2.6
"UNDO" # broken build
"unifiedWMWqPCR" # depends on broken package affyio-1.37.0
"uniftest" # broken build
"UniProt_ws" # broken build
"untb" # broken build
"userfriendlyscience" # depends on broken package nlopt-2.4.2
"V8" # build is broken
"VanillaICE" # depends on broken package affyio-1.37.0
"varComp" # depends on broken package r-lme4-1.1-9
"varian" # build is broken
"variancePartition" # depends on broken package lme4-1.1-8
"VariantAnnotation" # depends on broken package Rsamtools-1.21.8
"VariantFiltering" # depends on broken package Rsamtools-1.21.8
"VariantTools" # depends on broken package Rsamtools-1.21.8
"VBmix" # broken build
"VegaMC" # broken build
"VIM" # depends on broken package nlopt-2.4.2
"VIMGUI" # depends on broken package nlopt-2.4.2
"viper" # broken build
"vmsbase" # depends on broken package PBSmapping-2.69.76
"vows" # depends on broken package nlopt-2.4.2
"vsn" # depends on broken package affyio-1.37.0
"vtpnet" # depends on broken package interactiveDisplayBase-1.7.0
"wateRmelon" # depends on broken package affyio-1.37.0
"wavClusteR" # depends on broken package Rsamtools-1.21.8
"waveTiling" # depends on broken package affyio-1.37.0
"webbioc" # depends on broken package affyio-1.37.0
"webp" # build is broken
"wfe" # depends on broken package nlopt-2.4.2
"WGCNA" # build is broken
"wgsea" # depends on broken package snpStats-1.19.0
"wikipediatrend" # broken build
"wordbankr" # depends on broken package r-RMySQL-0.10.7
"XBSeq" # broken build
"xcms" # depends on broken package mzR-2.3.1
"XDE" # broken build
"x_ent" # broken build
"xergm" # depends on broken package nlopt-2.4.2
"xps" # build is broken
"XVector" # broken build
"yaqcaffy" # depends on broken package affyio-1.37.0
"yCrypticRNAs" # depends on broken package biomaRt-2.26.1
"ZeligChoice" # depends on broken package r-AER-1.2-4
"Zelig" # depends on broken package r-AER-1.2-4
"ZeligMultilevel" # depends on broken package nlopt-2.4.2
"zetadiv" # depends on broken package nlopt-2.4.2
"zoib"
];
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}/include"
];
});
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
configureFlags = [
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
];
});
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
patches = [ ./patches/RAppArmor.patch ];
LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
});
RMySQL = old.RMySQL.overrideDerivation (attrs: {
patches = [ ./patches/RMySQL.patch ];
MYSQL_DIR="${pkgs.mysql.lib}";
});
devEMF = old.devEMF.overrideDerivation (attrs: {
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
});
slfm = old.slfm.overrideDerivation (attrs: {
PKG_LIBS = "-L${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}/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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