mirror of
https://github.com/NixOS/nixpkgs.git
synced 2024-11-21 13:10:33 +00:00
1719 lines
67 KiB
Nix
1719 lines
67 KiB
Nix
/* This file defines the composition for CRAN (R) packages. */
|
|
|
|
{ R, pkgs, overrides }:
|
|
|
|
let
|
|
inherit (pkgs) fetchurl stdenv lib;
|
|
|
|
buildRPackage = pkgs.callPackage ./generic-builder.nix { inherit R; };
|
|
|
|
# Generates package templates given per-repository settings
|
|
#
|
|
# some packages, e.g. cncaGUI, require X running while installation,
|
|
# so that we use xvfb-run if requireX is true.
|
|
mkDerive = {mkHomepage, mkUrls}: lib.makeOverridable ({
|
|
name, version, sha256,
|
|
depends ? [],
|
|
doCheck ? true,
|
|
requireX ? false,
|
|
broken ? false,
|
|
hydraPlatforms ? R.meta.hydraPlatforms
|
|
}: buildRPackage {
|
|
name = "${name}-${version}";
|
|
src = fetchurl {
|
|
inherit sha256;
|
|
urls = mkUrls { inherit name version; };
|
|
};
|
|
inherit doCheck requireX;
|
|
propagatedBuildInputs = depends;
|
|
nativeBuildInputs = depends;
|
|
meta.homepage = mkHomepage name;
|
|
meta.platforms = R.meta.platforms;
|
|
meta.hydraPlatforms = hydraPlatforms;
|
|
meta.broken = broken;
|
|
});
|
|
|
|
# Templates for generating Bioconductor and CRAN packages
|
|
# from the name, version, sha256, and optional per-package arguments above
|
|
#
|
|
deriveBioc = mkDerive {
|
|
mkHomepage = name: "http://cran.r-project.org/web/packages/${name}/";
|
|
mkUrls = {name, version}: [ "mirror://bioc/src/contrib/${name}_${version}.tar.gz" ];
|
|
};
|
|
deriveCran = mkDerive {
|
|
mkHomepage = name: "http://bioconductor.org/packages/release/bioc/html/${name}.html";
|
|
mkUrls = {name, version}: [
|
|
"mirror://cran/src/contrib/${name}_${version}.tar.gz"
|
|
"mirror://cran/src/contrib/00Archive/${name}/${name}_${version}.tar.gz"
|
|
];
|
|
};
|
|
|
|
# Overrides package definitions with nativeBuildInputs.
|
|
# For example,
|
|
#
|
|
# overrideNativeBuildInputs {
|
|
# foo = [ pkgs.bar ]
|
|
# } old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.overrideDerivation (attrs: {
|
|
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
|
|
# });
|
|
# }
|
|
overrideNativeBuildInputs = overrides: old:
|
|
lib.mapAttrs (name: value:
|
|
(builtins.getAttr name old).overrideDerivation (attrs: {
|
|
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
|
|
})
|
|
) overrides;
|
|
|
|
# Overrides package definitions with buildInputs.
|
|
# For example,
|
|
#
|
|
# overrideBuildInputs {
|
|
# foo = [ pkgs.bar ]
|
|
# } old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.overrideDerivation (attrs: {
|
|
# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
|
|
# });
|
|
# }
|
|
overrideBuildInputs = overrides: old:
|
|
lib.mapAttrs (name: value:
|
|
(builtins.getAttr name old).overrideDerivation (attrs: {
|
|
buildInputs = attrs.buildInputs ++ value;
|
|
})
|
|
) overrides;
|
|
|
|
# Overrides package definitions with new R dependencies.
|
|
# For example,
|
|
#
|
|
# overrideRDepends {
|
|
# foo = [ self.bar ]
|
|
# } old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.overrideDerivation (attrs: {
|
|
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
|
|
# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
|
|
# });
|
|
# }
|
|
overrideRDepends = overrides: old:
|
|
lib.mapAttrs (name: value:
|
|
(builtins.getAttr name old).overrideDerivation (attrs: {
|
|
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
|
|
propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
|
|
})
|
|
) overrides;
|
|
|
|
# Overrides package definition requiring X running to install.
|
|
# For example,
|
|
#
|
|
# overrideRequireX [
|
|
# "foo"
|
|
# ] old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.override {
|
|
# requireX = true;
|
|
# };
|
|
# }
|
|
overrideRequireX = packageNames: old:
|
|
let
|
|
nameValuePairs = map (name: {
|
|
inherit name;
|
|
value = (builtins.getAttr name old).override {
|
|
requireX = true;
|
|
};
|
|
}) packageNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
# Overrides package definition to skip check.
|
|
# For example,
|
|
#
|
|
# overrideSkipCheck [
|
|
# "foo"
|
|
# ] old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.override {
|
|
# doCheck = false;
|
|
# };
|
|
# }
|
|
overrideSkipCheck = packageNames: old:
|
|
let
|
|
nameValuePairs = map (name: {
|
|
inherit name;
|
|
value = (builtins.getAttr name old).override {
|
|
doCheck = false;
|
|
};
|
|
}) packageNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
# Overrides package definition to mark it broken.
|
|
# For example,
|
|
#
|
|
# overrideBroken [
|
|
# "foo"
|
|
# ] old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.override {
|
|
# broken = true;
|
|
# };
|
|
# }
|
|
overrideBroken = packageNames: old:
|
|
let
|
|
nameValuePairs = map (name: {
|
|
inherit name;
|
|
value = (builtins.getAttr name old).override {
|
|
broken = true;
|
|
};
|
|
}) packageNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
defaultOverrides = old: new:
|
|
let old0 = old; in
|
|
let
|
|
old1 = old0 // (overrideRequireX packagesRequireingX old0);
|
|
old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
|
|
old3 = old2 // (overrideRDepends packagesWithRDepends old2);
|
|
old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
|
|
old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
|
|
old6 = old5 // (overrideBroken brokenPackages old5);
|
|
old = old6;
|
|
in old // (otherOverrides old new);
|
|
|
|
# Recursive override pattern.
|
|
# `_self` is a collection of packages;
|
|
# `self` is `_self` with overridden packages;
|
|
# packages in `_self` may depends on overridden packages.
|
|
self = (defaultOverrides _self self) // overrides;
|
|
_self = import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
|
|
import ./cran-packages.nix { inherit self; derive = deriveCran; };
|
|
|
|
# tweaks for the individual packages and "in self" follow
|
|
|
|
packagesWithRDepends = {
|
|
FactoMineR = [ self.car ];
|
|
pander = [ self.codetools ];
|
|
};
|
|
|
|
packagesWithNativeBuildInputs = {
|
|
abn = [ pkgs.gsl ];
|
|
adimpro = [ pkgs.imagemagick ];
|
|
audio = [ pkgs.portaudio ];
|
|
BayesSAE = [ pkgs.gsl ];
|
|
BayesVarSel = [ pkgs.gsl ];
|
|
BayesXsrc = [ pkgs.readline pkgs.ncurses ];
|
|
bigGP = [ pkgs.openmpi ];
|
|
BiocCheck = [ pkgs.which ];
|
|
Biostrings = [ pkgs.zlib ];
|
|
bnpmr = [ pkgs.gsl ];
|
|
BNSP = [ pkgs.gsl ];
|
|
cairoDevice = [ pkgs.gtk2 ];
|
|
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
|
|
Cardinal = [ pkgs.which ];
|
|
CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
|
|
chebpol = [ pkgs.fftw ];
|
|
ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
|
|
cit = [ pkgs.gsl ];
|
|
curl = [ pkgs.curl ];
|
|
devEMF = [ pkgs.xorg.libXft ];
|
|
diversitree = [ pkgs.gsl pkgs.fftw ];
|
|
EMCluster = [ pkgs.liblapack ];
|
|
fftw = [ pkgs.fftw ];
|
|
fftwtools = [ pkgs.fftw ];
|
|
Formula = [ pkgs.gmp ];
|
|
geoCount = [ pkgs.gsl ];
|
|
git2r = [ pkgs.zlib pkgs.openssl ];
|
|
GLAD = [ pkgs.gsl ];
|
|
glpkAPI = [ pkgs.gmp pkgs.glpk ];
|
|
gmp = [ pkgs.gmp ];
|
|
graphscan = [ pkgs.gsl ];
|
|
gsl = [ pkgs.gsl ];
|
|
HiCseg = [ pkgs.gsl ];
|
|
iBMQ = [ pkgs.gsl ];
|
|
igraph = [ pkgs.gmp ];
|
|
JavaGD = [ pkgs.jdk ];
|
|
jpeg = [ pkgs.libjpeg ];
|
|
KFKSDS = [ pkgs.gsl ];
|
|
kza = [ pkgs.fftw ];
|
|
libamtrack = [ pkgs.gsl ];
|
|
mixcat = [ pkgs.gsl ];
|
|
mvabund = [ pkgs.gsl ];
|
|
mwaved = [ pkgs.fftw ];
|
|
ncdf4 = [ pkgs.netcdf ];
|
|
ncdf = [ pkgs.netcdf ];
|
|
nloptr = [ pkgs.nlopt ];
|
|
openssl = [ pkgs.openssl ];
|
|
outbreaker = [ pkgs.gsl ];
|
|
pander = [ pkgs.pandoc pkgs.which ];
|
|
pbdMPI = [ pkgs.openmpi ];
|
|
pbdNCDF4 = [ pkgs.netcdf ];
|
|
pbdPROF = [ pkgs.openmpi ];
|
|
PKI = [ pkgs.openssl ];
|
|
png = [ pkgs.libpng ];
|
|
PopGenome = [ pkgs.zlib ];
|
|
proj4 = [ pkgs.proj ];
|
|
qtbase = [ pkgs.qt4 ];
|
|
qtpaint = [ pkgs.qt4 ];
|
|
R2GUESS = [ pkgs.gsl ];
|
|
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
|
|
RAppArmor = [ pkgs.libapparmor ];
|
|
rapportools = [ pkgs.which ];
|
|
rapport = [ pkgs.which ];
|
|
rbamtools = [ pkgs.zlib ];
|
|
RCA = [ pkgs.gmp ];
|
|
rcdd = [ pkgs.gmp ];
|
|
RcppCNPy = [ pkgs.zlib ];
|
|
RcppGSL = [ pkgs.gsl ];
|
|
RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
|
|
RcppZiggurat = [ pkgs.gsl ];
|
|
rgdal = [ pkgs.proj pkgs.gdal ];
|
|
rgeos = [ pkgs.geos ];
|
|
rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ];
|
|
rgl = [ pkgs.mesa pkgs.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 ];
|
|
RJaCGH = [ pkgs.zlib ];
|
|
rjags = [ pkgs.jags ];
|
|
rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
|
|
Rlibeemd = [ pkgs.gsl ];
|
|
rmatio = [ pkgs.zlib ];
|
|
Rmpfr = [ pkgs.gmp pkgs.mpfr ];
|
|
Rmpi = [ pkgs.openmpi ];
|
|
RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
|
|
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
|
|
RODBCext = [ pkgs.libiodbc ];
|
|
RODBC = [ pkgs.libiodbc ];
|
|
rpg = [ pkgs.postgresql ];
|
|
rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
|
|
Rpoppler = [ pkgs.poppler ];
|
|
RPostgreSQL = [ pkgs.postgresql ];
|
|
RProtoBuf = [ pkgs.protobuf ];
|
|
rpud = [ pkgs.linuxPackages.nvidia_x11 ];
|
|
rPython = [ pkgs.python ];
|
|
RSclient = [ pkgs.openssl ];
|
|
Rserve = [ pkgs.openssl ];
|
|
Rssa = [ pkgs.fftw ];
|
|
rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ];
|
|
rtiff = [ pkgs.libtiff ];
|
|
runjags = [ pkgs.jags ];
|
|
RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
|
|
rzmq = [ pkgs.zeromq3 ];
|
|
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
|
|
sdcTable = [ pkgs.gmp pkgs.glpk ];
|
|
seewave = [ pkgs.fftw pkgs.libsndfile ];
|
|
SemiCompRisks = [ pkgs.gsl ];
|
|
seqinr = [ pkgs.zlib ];
|
|
seqminer = [ pkgs.zlib pkgs.bzip2 ];
|
|
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
|
|
simplexreg = [ pkgs.gsl ];
|
|
SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
|
|
spate = [ pkgs.fftw ];
|
|
sprint = [ pkgs.openmpi ];
|
|
ssanv = [ pkgs.proj ];
|
|
stsm = [ pkgs.gsl ];
|
|
stringi = [ pkgs.icu ];
|
|
survSNP = [ pkgs.gsl ];
|
|
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
|
|
TAQMNGR = [ pkgs.zlib ];
|
|
tiff = [ pkgs.libtiff ];
|
|
TKF = [ pkgs.gsl ];
|
|
tkrplot = [ pkgs.xorg.libX11 ];
|
|
topicmodels = [ pkgs.gsl ];
|
|
udunits2 = [ pkgs.udunits pkgs.expat ];
|
|
V8 = [ pkgs.v8 ];
|
|
VBLPCM = [ pkgs.gsl ];
|
|
VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
|
|
WhopGenome = [ pkgs.zlib ];
|
|
XBRL = [ pkgs.zlib pkgs.libxml2 ];
|
|
xml2 = [ pkgs.libxml2 ];
|
|
XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
|
|
};
|
|
|
|
packagesWithBuildInputs = {
|
|
# sort -t '=' -k 2
|
|
svKomodo = [ pkgs.which ];
|
|
nat = [ pkgs.which ];
|
|
nat_nblast = [ pkgs.which ];
|
|
nat_templatebrains = [ pkgs.which ];
|
|
RMark = [ pkgs.which ];
|
|
RPushbullet = [ pkgs.which ];
|
|
qtpaint = [ pkgs.cmake ];
|
|
qtbase = [ pkgs.cmake pkgs.perl ];
|
|
gmatrix = [ pkgs.cudatoolkit ];
|
|
WideLM = [ pkgs.cudatoolkit ];
|
|
RCurl = [ pkgs.curl ];
|
|
R2SWF = [ pkgs.pkgconfig ];
|
|
rggobi = [ pkgs.pkgconfig ];
|
|
RGtk2 = [ pkgs.pkgconfig ];
|
|
RProtoBuf = [ pkgs.pkgconfig ];
|
|
Rpoppler = [ pkgs.pkgconfig ];
|
|
VBmix = [ pkgs.pkgconfig ];
|
|
XML = [ pkgs.pkgconfig ];
|
|
cairoDevice = [ pkgs.pkgconfig ];
|
|
chebpol = [ pkgs.pkgconfig ];
|
|
fftw = [ pkgs.pkgconfig ];
|
|
geoCount = [ pkgs.pkgconfig ];
|
|
kza = [ pkgs.pkgconfig ];
|
|
mwaved = [ pkgs.pkgconfig ];
|
|
showtext = [ pkgs.pkgconfig ];
|
|
spate = [ pkgs.pkgconfig ];
|
|
stringi = [ pkgs.pkgconfig ];
|
|
sysfonts = [ pkgs.pkgconfig ];
|
|
Cairo = [ pkgs.pkgconfig ];
|
|
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
|
|
qtutils = [ pkgs.qt4 ];
|
|
ecoretriever = [ pkgs.which ];
|
|
tcltk2 = [ pkgs.tcl pkgs.tk ];
|
|
tikzDevice = [ pkgs.which pkgs.texLive ];
|
|
rPython = [ pkgs.which ];
|
|
CARramps = [ pkgs.which pkgs.cudatoolkit ];
|
|
gridGraphics = [ pkgs.which ];
|
|
gputools = [ pkgs.which pkgs.cudatoolkit ];
|
|
rpud = [ pkgs.which pkgs.cudatoolkit ];
|
|
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
|
|
PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
|
|
dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
|
|
};
|
|
|
|
packagesRequireingX = [
|
|
"accrual"
|
|
"ade4TkGUI"
|
|
"adehabitat"
|
|
"analogue"
|
|
"analogueExtra"
|
|
"AnalyzeFMRI"
|
|
"AnnotLists"
|
|
"AnthropMMD"
|
|
"aplpack"
|
|
"aqfig"
|
|
"arf3DS4"
|
|
"asbio"
|
|
"AtelieR"
|
|
"BAT"
|
|
"bayesDem"
|
|
"BCA"
|
|
"BEQI2"
|
|
"betapart"
|
|
"betaper"
|
|
"BiodiversityR"
|
|
"BioGeoBEARS"
|
|
"bio_infer"
|
|
"bipartite"
|
|
"biplotbootGUI"
|
|
"blender"
|
|
"cairoDevice"
|
|
"CCTpack"
|
|
"cncaGUI"
|
|
"cocorresp"
|
|
"CommunityCorrelogram"
|
|
"confidence"
|
|
"constrainedKriging"
|
|
"ConvergenceConcepts"
|
|
"cpa"
|
|
"DALY"
|
|
"dave"
|
|
"debug"
|
|
"Deducer"
|
|
"DeducerExtras"
|
|
"DeducerPlugInExample"
|
|
"DeducerPlugInScaling"
|
|
"DeducerSpatial"
|
|
"DeducerSurvival"
|
|
"DeducerText"
|
|
"Demerelate"
|
|
"DescTools"
|
|
"detrendeR"
|
|
"dgmb"
|
|
"DivMelt"
|
|
"dpa"
|
|
"DSpat"
|
|
"dynamicGraph"
|
|
"dynBiplotGUI"
|
|
"EasyqpcR"
|
|
"EcoVirtual"
|
|
"ENiRG"
|
|
"EnQuireR"
|
|
"eVenn"
|
|
"exactLoglinTest"
|
|
"FAiR"
|
|
"fat2Lpoly"
|
|
"fbati"
|
|
"FD"
|
|
"feature"
|
|
"FeedbackTS"
|
|
"FFD"
|
|
"fgui"
|
|
"fisheyeR"
|
|
"fit4NM"
|
|
"forams"
|
|
"forensim"
|
|
"FreeSortR"
|
|
"fscaret"
|
|
"fSRM"
|
|
"gcmr"
|
|
"Geneland"
|
|
"GeoGenetix"
|
|
"geomorph"
|
|
"geoR"
|
|
"geoRglm"
|
|
"georob"
|
|
"GeoXp"
|
|
"GGEBiplotGUI"
|
|
"gnm"
|
|
"GPCSIV"
|
|
"GrammR"
|
|
"GrapheR"
|
|
"GroupSeq"
|
|
"gsubfn"
|
|
"GUniFrac"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"gWidgetsRGtk2"
|
|
"gWidgetstcltk"
|
|
"HH"
|
|
"HiveR"
|
|
"HomoPolymer"
|
|
"iBUGS"
|
|
"ic50"
|
|
"iDynoR"
|
|
"in2extRemes"
|
|
"iplots"
|
|
"isopam"
|
|
"IsotopeR"
|
|
"JGR"
|
|
"KappaGUI"
|
|
"likeLTD"
|
|
"loe"
|
|
"logmult"
|
|
"LS2Wstat"
|
|
"MAR1"
|
|
"MareyMap"
|
|
"memgene"
|
|
"MergeGUI"
|
|
"metacom"
|
|
"Meth27QC"
|
|
"MetSizeR"
|
|
"MicroStrategyR"
|
|
"migui"
|
|
"miniGUI"
|
|
"MissingDataGUI"
|
|
"mixsep"
|
|
"mlDNA"
|
|
"MplusAutomation"
|
|
"mpmcorrelogram"
|
|
"mritc"
|
|
"MTurkR"
|
|
"multgee"
|
|
"multibiplotGUI"
|
|
"nodiv"
|
|
"OligoSpecificitySystem"
|
|
"onemap"
|
|
"OpenRepGrid"
|
|
"palaeoSig"
|
|
"paleoMAS"
|
|
"pbatR"
|
|
"PBSadmb"
|
|
"PBSmodelling"
|
|
"PCPS"
|
|
"pez"
|
|
"phylotools"
|
|
"picante"
|
|
"PKgraph"
|
|
"playwith"
|
|
"plotSEMM"
|
|
"plsRbeta"
|
|
"plsRglm"
|
|
"pmg"
|
|
"PopGenReport"
|
|
"poppr"
|
|
"powerpkg"
|
|
"PredictABEL"
|
|
"prefmod"
|
|
"PrevMap"
|
|
"ProbForecastGOP"
|
|
"QCAGUI"
|
|
"qtbase"
|
|
"qtpaint"
|
|
"qtutils"
|
|
"R2STATS"
|
|
"r4ss"
|
|
"RandomFields"
|
|
"rareNMtests"
|
|
"rAverage"
|
|
"Rcmdr"
|
|
"RcmdrPlugin_BCA"
|
|
"RcmdrPlugin_coin"
|
|
"RcmdrPlugin_depthTools"
|
|
"RcmdrPlugin_DoE"
|
|
"RcmdrPlugin_doex"
|
|
"RcmdrPlugin_EACSPIR"
|
|
"RcmdrPlugin_EBM"
|
|
"RcmdrPlugin_EcoVirtual"
|
|
"RcmdrPlugin_epack"
|
|
"RcmdrPlugin_EZR"
|
|
"RcmdrPlugin_FactoMineR"
|
|
"RcmdrPlugin_HH"
|
|
"RcmdrPlugin_IPSUR"
|
|
"RcmdrPlugin_KMggplot2"
|
|
"RcmdrPlugin_lfstat"
|
|
"RcmdrPlugin_MA"
|
|
"RcmdrPlugin_mosaic"
|
|
"RcmdrPlugin_MPAStats"
|
|
"RcmdrPlugin_orloca"
|
|
"RcmdrPlugin_plotByGroup"
|
|
"RcmdrPlugin_pointG"
|
|
"RcmdrPlugin_qual"
|
|
"RcmdrPlugin_ROC"
|
|
"RcmdrPlugin_sampling"
|
|
"RcmdrPlugin_SCDA"
|
|
"RcmdrPlugin_SLC"
|
|
"RcmdrPlugin_SM"
|
|
"RcmdrPlugin_sos"
|
|
"RcmdrPlugin_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
|
|
"a4" # depends on broken package annaffy-1.41.1
|
|
"a4Reporting" # depends on broken package annaffy-1.41.1
|
|
"abd" # depends on broken package nlopt-2.4.2
|
|
"Actigraphy" # Build Is Broken
|
|
"adabag" # depends on broken package nlopt-2.4.2
|
|
"ADaCGH2" # depends on broken package tilingArray-1.47.0
|
|
"adSplit" # build is broken
|
|
"AER" # depends on broken package nlopt-2.4.2
|
|
"afex" # depends on broken package nlopt-2.4.2
|
|
"affyContam" # depends on broken package affyio-1.37.0
|
|
"affycoretools" # depends on broken package affyio-1.37.0
|
|
"affy" # depends on broken package affyio-1.37.0
|
|
"AffyExpress" # depends on broken package affyio-1.37.0
|
|
"affyILM" # depends on broken package affyio-1.37.0
|
|
"affyio" # build is broken
|
|
"affylmGUI" # depends on broken package affyio-1.37.0
|
|
"affyPara" # depends on broken package affyio-1.37.0
|
|
"affypdnn" # depends on broken package affyio-1.37.0
|
|
"affyPLM" # depends on broken package affyio-1.37.0
|
|
"affyQCReport" # depends on broken package affyio-1.37.0
|
|
"AffyRNADegradation" # depends on broken package affyio-1.37.0
|
|
"AffyTiling" # depends on broken package affyio-1.37.0
|
|
"AgiMicroRna" # depends on broken package affyio-1.37.0
|
|
"agRee" # depends on broken package nlopt-2.4.2
|
|
"aLFQ" # depends on broken package nlopt-2.4.2
|
|
"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
|
|
"annaffy" # build is broken
|
|
"annmap" # depends on broken package Rsamtools-1.21.8
|
|
"AnnotationForge" # Build Is Broken
|
|
"AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0
|
|
"aods3" # depends on broken package nlopt-2.4.2
|
|
"apComplex" # build is broken
|
|
"apt" # depends on broken package nlopt-2.4.2
|
|
"ArfimaMLM" # depends on broken package nlopt-2.4.2
|
|
"arm" # depends on broken package nlopt-2.4.2
|
|
"ArrayExpress" # depends on broken package affyio-1.37.0
|
|
"ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8
|
|
"arrayMvout" # depends on broken package affyio-1.37.0
|
|
"arrayQualityMetrics" # depends on broken package affyio-1.37.0
|
|
"ArrayTools" # depends on broken package affyio-1.37.0
|
|
"ArrayTV" # depends on broken package affyio-1.37.0
|
|
"ARRmNormalization" # Build Is Broken
|
|
"ARTool" # depends on broken package nlopt-2.4.2
|
|
"attract" # depends on broken package AnnotationForge-1.11.3
|
|
"BACA" # depends on broken package Category-2.35.1
|
|
"BAGS" # build is broken
|
|
"ballgown" # depends on broken package Rsamtools-1.21.8
|
|
"bamsignals" # build is broken
|
|
"bartMachine" # depends on broken package nlopt-2.4.2
|
|
"Basic4Cseq" # depends on broken package Rsamtools-1.21.8
|
|
"bayesDem" # depends on broken package nlopt-2.4.2
|
|
"bayesLife" # depends on broken package nlopt-2.4.2
|
|
"bayesPop" # depends on broken package nlopt-2.4.2
|
|
"Bayesthresh" # depends on broken package nlopt-2.4.2
|
|
"BBRecapture" # depends on broken package nlopt-2.4.2
|
|
"BCA" # depends on broken package nlopt-2.4.2
|
|
"BEAT" # depends on broken package Rsamtools-1.21.8
|
|
"bgmm" # depends on broken package nlopt-2.4.2
|
|
"bgx" # depends on broken package affyio-1.37.0
|
|
"BIFIEsurvey" # depends on broken package nlopt-2.4.2
|
|
"bigGP" # build is broken
|
|
"BiGGR" # depends on broken package rsbml-2.27.0
|
|
"BiodiversityR" # depends on broken package nlopt-2.4.2
|
|
"biomvRCNS" # depends on broken package Rsamtools-1.21.8
|
|
"biotools" # depends on broken package rpanel-1.1-3
|
|
"biovizBase" # depends on broken package Rsamtools-1.21.8
|
|
"birte" # build is broken
|
|
"BiSEp" # depends on broken package GOSemSim-1.27.3
|
|
"BiSeq" # depends on broken package Rsamtools-1.21.8
|
|
"BitSeq" # depends on broken package Rsamtools-1.21.8
|
|
"BLCOP" # depends on broken package Rsymphony-0.1-20
|
|
"blmeco" # depends on broken package nlopt-2.4.2
|
|
"blme" # depends on broken package nlopt-2.4.2
|
|
"bmd" # depends on broken package nlopt-2.4.2
|
|
"bmem" # depends on broken package nlopt-2.4.2
|
|
"bootnet" # depends on broken package nlopt-2.4.2
|
|
"boss" # depends on broken package nlopt-2.4.2
|
|
"BradleyTerry2" # depends on broken package nlopt-2.4.2
|
|
"BRugs" # build is broken
|
|
"BSgenome" # depends on broken package Rsamtools-1.21.8
|
|
"bumphunter" # depends on broken package Rsamtools-1.21.8
|
|
"CADFtest" # depends on broken package nlopt-2.4.2
|
|
"CAFE" # depends on broken package affyio-1.37.0
|
|
"CAGEr" # depends on broken package Rsamtools-1.21.8
|
|
"cAIC4" # depends on broken package nlopt-2.4.2
|
|
"CAMERA" # depends on broken package mzR-2.3.1
|
|
"canceR" # depends on broken package Category-2.35.1
|
|
"candisc" # depends on broken package nlopt-2.4.2
|
|
"carcass" # depends on broken package nlopt-2.4.2
|
|
"car" # depends on broken package nlopt-2.4.2
|
|
"caret" # depends on broken package nlopt-2.4.2
|
|
"caretEnsemble" # depends on broken package nlopt-2.4.2
|
|
"CARrampsOcl" # depends on broken package OpenCL-0.1-3
|
|
"casper" # depends on broken package Rsamtools-1.21.8
|
|
"Category" # Build Is Broken
|
|
"categoryCompare" # depends on broken package Category-2.35.1
|
|
"CCpop" # depends on broken package nlopt-2.4.2
|
|
"cellHTS2" # depends on broken package Category-2.35.1
|
|
"CexoR" # depends on broken package Rsamtools-1.21.8
|
|
"ChainLadder" # depends on broken package nlopt-2.4.2
|
|
"ChAMP" # depends on broken package affyio-1.37.0
|
|
"charm" # depends on broken package affyio-1.37.0
|
|
"ChemmineR" # Build Is Broken
|
|
"chimera" # depends on broken package Rsamtools-1.21.8
|
|
"chipenrich" # build is broken
|
|
"chipPCR" # depends on broken nloptr-1.0.4
|
|
"ChIPpeakAnno" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPQC" # depends on broken package AnnotationForge-1.11.3
|
|
"ChIPseeker" # depends on broken package Rsamtools-1.21.8
|
|
"chipseq" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPseqR" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPsim" # depends on broken package Rsamtools-1.21.8
|
|
"ChIPXpress" # depends on broken package affyio-1.37.0
|
|
"ChromHeatMap" # depends on broken package Rsamtools-1.21.8
|
|
"cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8
|
|
"climwin" # depends on broken package nlopt-2.4.2
|
|
"clipper" # depends on broken package Rsamtools-1.21.8
|
|
"CLME" # depends on broken package nlopt-2.4.2
|
|
"clpAPI" # build is broken
|
|
"clusterPower" # depends on broken package nlopt-2.4.2
|
|
"clusterProfiler" # depends on broken package GOSemSim-1.27.3
|
|
"clusterSEs" # depends on broken AER-1.2-4
|
|
"ClustGeo" # depends on broken FactoMineR-1.31.3
|
|
"CNEr" # depends on broken package Rsamtools-1.21.8
|
|
"cn_farms" # depends on broken package affyio-1.37.0
|
|
"cn_mops" # depends on broken package Rsamtools-1.21.8
|
|
"CNORfuzzy" # depends on broken package nlopt-2.4.2
|
|
"CNVPanelizer" # depends on broken cn.mops-1.15.1
|
|
"CNVrd2" # depends on broken package Rsamtools-1.21.8
|
|
"cobindR" # depends on broken package Rsamtools-1.21.8
|
|
"CoCiteStats" # Build Is Broken
|
|
"CODEX" # depends on broken package Rsamtools-1.21.8
|
|
"COHCAP" # build is broken
|
|
"colorscience"
|
|
"coMET" # depends on broken package Rsamtools-1.21.8
|
|
"compEpiTools" # depends on broken package topGO-2.21.0
|
|
"CompGO" # depends on broken package Category-2.35.1
|
|
"conformal" # depends on broken package nlopt-2.4.2
|
|
"ConsensusClusterPlus" # Build Is Broken
|
|
"conumee" # depends on broken package Rsamtools-1.21.8
|
|
"CopyNumber450k" # depends on broken package Rsamtools-1.21.8
|
|
"CopywriteR" # depends on broken package Rsamtools-1.21.8
|
|
"corHMM" # depends on broken package nlopt-2.4.2
|
|
"Cormotif" # depends on broken package affyio-1.37.0
|
|
"coRNAi" # depends on broken package Category-2.35.1
|
|
"cosmiq" # depends on broken package mzR-2.3.1
|
|
"CosmoPhotoz" # depends on broken package nlopt-2.4.2
|
|
"CoverageView" # depends on broken package Rsamtools-1.21.8
|
|
"cplexAPI" # build is broken
|
|
"cpvSNP" # depends on broken package Rsamtools-1.21.8
|
|
"CRISPRseek" # depends on broken package Rsamtools-1.21.8
|
|
"crlmm" # depends on broken package affyio-1.37.0
|
|
"Crossover" # Build Is Broken
|
|
"CrypticIBDcheck" # depends on broken package nlopt-2.4.2
|
|
"csaw" # depends on broken package Rsamtools-1.21.8
|
|
"cudaBayesreg" # build is broken
|
|
"cummeRbund" # depends on broken package Rsamtools-1.21.8
|
|
"customProDB" # depends on broken package Rsamtools-1.21.8
|
|
"daff" # depends on broken package V8-0.6
|
|
"dagbag" # build is broken
|
|
"dagLogo" # depends on broken package Rsamtools-1.21.8
|
|
"DAMisc" # depends on broken package nlopt-2.4.2
|
|
"DBKGrad" # depends on broken package rpanel-1.1-3
|
|
"Deducer" # depends on broken package nlopt-2.4.2
|
|
"DeducerExtras" # depends on broken package nlopt-2.4.2
|
|
"DeducerPlugInExample" # depends on broken package nlopt-2.4.2
|
|
"DeducerPlugInScaling" # depends on broken package nlopt-2.4.2
|
|
"DeducerSpatial" # depends on broken package nlopt-2.4.2
|
|
"DeducerSurvival" # depends on broken package nlopt-2.4.2
|
|
"DeducerText" # depends on broken package nlopt-2.4.2
|
|
"deepSNV" # depends on broken package Rsamtools-1.21.8
|
|
"DEGraph" # depends on broken package RCytoscape-1.19.0
|
|
"demi" # depends on broken package affyio-1.37.0
|
|
"derfinder" # depends on broken package Rsamtools-1.21.8
|
|
"derfinderPlot" # depends on broken package Rsamtools-1.21.8
|
|
"destiny" # depends on broken package VIM-4.3.0
|
|
"DEXSeq" # depends on broken package Rsamtools-1.21.8
|
|
"DiagTest3Grp" # depends on broken package nlopt-2.4.2
|
|
"DiffBind" # depends on broken package AnnotationForge-1.11.3
|
|
"diffHic" # depends on broken package rhdf5-2.13.1
|
|
"difR" # depends on broken package nlopt-2.4.2
|
|
"DirichletMultinomial" # Build Is Broken
|
|
"discSurv" # depends on broken package nlopt-2.4.2
|
|
"DistatisR" # depends on broken package nlopt-2.4.2
|
|
"diveRsity" # depends on broken package nlopt-2.4.2
|
|
"DMRcate" # depends on broken package Rsamtools-1.21.8
|
|
"DMRforPairs" # depends on broken package Rsamtools-1.21.8
|
|
"domainsignatures" # build is broken
|
|
"doMPI" # build is broken
|
|
"DOQTL" # depends on broken package Rsamtools-1.21.8
|
|
"DOSE" # depends on broken package GOSemSim-1.27.3
|
|
"dpa" # depends on broken package nlopt-2.4.2
|
|
"dpcR" # depends on broken nloptr-1.0.4
|
|
"drc" # depends on broken package nlopt-2.4.2
|
|
"drfit" # depends on broken package nlopt-2.4.2
|
|
"drsmooth" # depends on broken package nlopt-2.4.2
|
|
"DrugVsDisease" # depends on broken package affyio-1.37.0
|
|
"dualKS" # depends on broken package affyio-1.37.0
|
|
"dynlm" # depends on broken package nlopt-2.4.2
|
|
"easyanova" # depends on broken package nlopt-2.4.2
|
|
"easyRNASeq" # depends on broken package Rsamtools-1.21.8
|
|
"EDASeq" # depends on broken package Rsamtools-1.21.8
|
|
"edge" # depends on broken package nlopt-2.4.2
|
|
"eeptools" # depends on broken package nlopt-2.4.2
|
|
"EffectLiteR" # depends on broken package nlopt-2.4.2
|
|
"effects" # depends on broken package nlopt-2.4.2
|
|
"eiR" # depends on broken package ChemmineR-2.21.7
|
|
"eisa" # depends on broken package Category-2.35.1
|
|
"ELMER" # depends on broken package Rsamtools-1.21.8
|
|
"EMA" # depends on broken package nlopt-2.4.2
|
|
"ENmix" # depends on broken package affyio-1.37.0
|
|
"EnQuireR" # depends on broken package nlopt-2.4.2
|
|
"EnrichmentBrowser" # depends on broken package r-EDASeq-2.3.2
|
|
"ensembldb" # depends on broken package interactiveDisplayBase-1.7.0
|
|
"ensemblVEP" # depends on broken package Rsamtools-1.21.8
|
|
"epigenomix" # depends on broken package Rsamtools-1.21.8
|
|
"episplineDensity" # depends on broken package nlopt-2.4.2
|
|
"epivizr" # depends on broken package Rsamtools-1.21.8
|
|
"epr" # depends on broken package nlopt-2.4.2
|
|
"erer" # depends on broken package nlopt-2.4.2
|
|
"erma" # depends on broken GenomicFiles-1.5.4
|
|
"erpR" # depends on broken package rpanel-1.1-3
|
|
"ExiMiR" # depends on broken package affyio-1.37.0
|
|
"exomeCopy" # depends on broken package Rsamtools-1.21.8
|
|
"ExomeDepth" # depends on broken package Rsamtools-1.21.8
|
|
"exomePeak" # depends on broken package Rsamtools-1.21.8
|
|
"ExpressionView" # depends on broken package Category-2.35.1
|
|
"extRemes" # depends on broken package nlopt-2.4.2
|
|
"ez" # depends on broken package nlopt-2.4.2
|
|
"facopy" # depends on broken package nlopt-2.4.2
|
|
"FactoMineR" # depends on broken package nlopt-2.4.2
|
|
"Factoshiny" # depends on broken package nlopt-2.4.2
|
|
"faoutlier" # depends on broken package nlopt-2.4.2
|
|
"farms" # depends on broken package affyio-1.37.0
|
|
"fastLiquidAssociation" # depends on broken package LiquidAssociation-1.23.0
|
|
"fastR" # depends on broken package nlopt-2.4.2
|
|
"FDRreg" # depends on broken package nlopt-2.4.2
|
|
"FEM" # build is broken
|
|
"ffpe" # depends on broken package affyio-1.37.0
|
|
"flagme" # depends on broken package mzR-2.3.1
|
|
"flowDensity" # depends on broken package nlopt-2.4.2
|
|
"flowPeaks" # build is broken
|
|
"flowQ" # build is broken
|
|
"FlowSOM" # depends on broken package ConsensusClusterPlus-1.23.0
|
|
"flowStats" # depends on broken package ncdfFlow-2.15.2
|
|
"flowVS" # depends on broken package ncdfFlow-2.15.2
|
|
"flowWorkspace" # depends on broken package ncdfFlow-2.15.2
|
|
"fmcsR" # depends on broken package ChemmineR-2.21.7
|
|
"FourCSeq" # depends on broken package Rsamtools-1.21.8
|
|
"fPortfolio" # depends on broken package Rsymphony-0.1-20
|
|
"freqweights" # depends on broken package nlopt-2.4.2
|
|
"frma" # depends on broken package affyio-1.37.0
|
|
"frmaTools" # depends on broken package affyio-1.37.0
|
|
"fscaret" # depends on broken package nlopt-2.4.2
|
|
"FunciSNP" # depends on broken package snpStats-1.19.0
|
|
"FunctionalNetworks" # Build Is Broken
|
|
"fxregime" # depends on broken package nlopt-2.4.2
|
|
"gamclass" # depends on broken package nlopt-2.4.2
|
|
"gamlss_demo" # depends on broken package rpanel-1.1-3
|
|
"gamm4" # depends on broken package nlopt-2.4.2
|
|
"gCMAP" # depends on broken package Category-2.35.1
|
|
"gCMAPWeb" # depends on broken package Category-2.35.1
|
|
"gcmr" # depends on broken package nlopt-2.4.2
|
|
"gcrma" # depends on broken package affyio-1.37.0
|
|
"GDAtools" # depends on broken package nlopt-2.4.2
|
|
"GENE_E" # depends on broken package rhdf5-2.13.1
|
|
"GeneExpressionSignature" # depends on broken package annaffy-1.41.1
|
|
"GeneticTools" # depends on broken package snpStats-1.19.0
|
|
"genomation" # depends on broken package Rsamtools-1.21.8
|
|
"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
|
|
"genotypeeval" # depends on broken package r-rtracklayer-1.29.12
|
|
"GenoView" # depends on broken package Rsamtools-1.21.8
|
|
"genridge" # depends on broken package nlopt-2.4.2
|
|
"geojsonio" # depends on broken package V8-0.6
|
|
"GEOsubmission" # depends on broken package affyio-1.37.0
|
|
"gespeR" # depends on broken package Category-2.35.1
|
|
"GEWIST" # depends on broken package nlopt-2.4.2
|
|
"GGBase" # depends on broken package snpStats-1.19.0
|
|
"ggbio" # depends on broken package Rsamtools-1.21.8
|
|
"GGtools" # depends on broken package snpStats-1.19.0
|
|
"gimme" # depends on broken package nlopt-2.4.2
|
|
"girafe" # depends on broken package Rsamtools-1.21.8
|
|
"gmapR" # depends on broken package Rsamtools-1.21.8
|
|
"gmatrix" # depends on broken package cudatoolkit-5.5.22
|
|
"gMCP" # build is broken
|
|
"GOFunction" # build is broken
|
|
"GOGANPA" # depends on broken package WGCNA-1.47
|
|
"GoogleGenomics" # depends on broken package Rsamtools-1.21.8
|
|
"goProfiles" # build is broken
|
|
"GOSemSim" # Build Is Broken
|
|
"goseq" # build is broken
|
|
"GOSim" # depends on broken package topGO-2.21.0
|
|
"GOstats" # depends on broken package AnnotationForge-1.11.3
|
|
"GOTHiC" # depends on broken package Rsamtools-1.21.8
|
|
"goTools" # build is broken
|
|
"gplm" # depends on broken package nlopt-2.4.2
|
|
"gputools" # depends on broken package cudatoolkit-5.5.22
|
|
"gQTLstats" # depends on broken package snpStats-1.19.0
|
|
"granova" # depends on broken package nlopt-2.4.2
|
|
"graphicalVAR" # depends on broken package nlopt-2.4.2
|
|
"GraphPCA" # depends on broken package nlopt-2.4.2
|
|
"GreyListChIP" # depends on broken package Rsamtools-1.21.8
|
|
"groHMM" # depends on broken package Rsamtools-1.21.8
|
|
"GSCA" # depends on broken package rhdf5-2.13.1
|
|
"GUIDE" # depends on broken package rpanel-1.1-3
|
|
"Gviz" # depends on broken package Rsamtools-1.21.8
|
|
"GWAF" # depends on broken package nlopt-2.4.2
|
|
"gwascat" # depends on broken package interactiveDisplayBase-1.7.0
|
|
"h2o" # build is broken
|
|
"h5" # build is broken
|
|
"h5vc" # depends on broken package rhdf5-2.13.1
|
|
"Harshlight" # depends on broken package affyio-1.37.0
|
|
"hbsae" # depends on broken package nlopt-2.4.2
|
|
"heplots" # depends on broken package nlopt-2.4.2
|
|
"hiAnnotator" # depends on broken package Rsamtools-1.21.8
|
|
"hierGWAS"
|
|
"HierO" # Build Is Broken
|
|
"highriskzone"
|
|
"HilbertVisGUI" # Build Is Broken
|
|
"HiPLARM" # Build Is Broken
|
|
"hiReadsProcessor" # depends on broken package Rsamtools-1.21.8
|
|
"HistDAWass" # depends on broken package nlopt-2.4.2
|
|
"HiTC" # depends on broken package Rsamtools-1.21.8
|
|
"HLMdiag" # depends on broken package nlopt-2.4.2
|
|
"HTqPCR" # depends on broken package affyio-1.37.0
|
|
"HTSanalyzeR" # depends on broken package Category-2.35.1
|
|
"HTSeqGenie" # depends on broken package Rsamtools-1.21.8
|
|
"htSeqTools" # depends on broken package Rsamtools-1.21.8
|
|
"hysteresis" # depends on broken package nlopt-2.4.2
|
|
"IATscores" # depends on broken package nlopt-2.4.2
|
|
"ibd" # depends on broken package nlopt-2.4.2
|
|
"ibh" # build is broken
|
|
"iccbeta" # depends on broken package nlopt-2.4.2
|
|
"IdeoViz" # depends on broken package Rsamtools-1.21.8
|
|
"ifaTools" # depends on broken package r-OpenMx-2.2.6
|
|
"iFes" # depends on broken package cudatoolkit-5.5.22
|
|
"imageHTS" # depends on broken package Category-2.35.1
|
|
"immunoClust" # build is broken
|
|
"imputeR" # depends on broken package nlopt-2.4.2
|
|
"in2extRemes" # depends on broken package nlopt-2.4.2
|
|
"inferference" # depends on broken package nlopt-2.4.2
|
|
"influence_ME" # depends on broken package nlopt-2.4.2
|
|
"InPAS" # depends on broken package Rsamtools-1.21.8
|
|
"inSilicoMerging" # build is broken
|
|
"INSPEcT" # depends on broken GenomicFeatures-1.21.13
|
|
"intansv" # depends on broken package Rsamtools-1.21.8
|
|
"interactiveDisplayBase" # build is broken
|
|
"interactiveDisplay" # depends on broken package Category-2.35.1
|
|
"interplot" # depends on broken arm-1.8-5
|
|
"IONiseR" # depends on broken rhdf5-2.13.4
|
|
"iptools"
|
|
"IsingFit" # depends on broken package nlopt-2.4.2
|
|
"IsoGene" # depends on broken package affyio-1.37.0
|
|
"IsoGeneGUI" # depends on broken package affyio-1.37.0
|
|
"ITALICS" # depends on broken package oligo-1.33.0
|
|
"IVAS" # depends on broken package nlopt-2.4.2
|
|
"ivpack" # depends on broken package nlopt-2.4.2
|
|
"JAGUAR" # depends on broken package nlopt-2.4.2
|
|
"jetset"
|
|
"joda" # depends on broken package nlopt-2.4.2
|
|
"jomo" # build is broken
|
|
"js" # depends on broken package V8-0.6
|
|
"KANT" # depends on broken package affyio-1.37.0
|
|
"keggorthology" # build is broken
|
|
"KEGGprofile" # Build Is Broken
|
|
"lawn" # depends on broken package V8-0.6
|
|
"learnstats" # depends on broken package nlopt-2.4.2
|
|
"lefse" # build is broken
|
|
"lessR" # depends on broken package nlopt-2.4.2
|
|
"lfe" # build is broken
|
|
"lgcp" # depends on broken package rpanel-1.1-3
|
|
"limmaGUI" # depends on broken package affyio-1.37.0
|
|
"LinRegInteractive" # depends on broken package rpanel-1.1-3
|
|
"LiquidAssociation" # build is broken
|
|
"lmdme" # build is broken
|
|
"lme4" # depends on broken package nlopt-2.4.2
|
|
"LMERConvenienceFunctions" # depends on broken package nlopt-2.4.2
|
|
"lmerTest" # depends on broken package nlopt-2.4.2
|
|
"LMGene" # depends on broken package affyio-1.37.0
|
|
"lmSupport" # depends on broken package nlopt-2.4.2
|
|
"LogisticDx" # depends on broken package nlopt-2.4.2
|
|
"logitT" # depends on broken package affyio-1.37.0
|
|
"longpower" # depends on broken package nlopt-2.4.2
|
|
"LowMACA" # depends on broken package Rsamtools-1.21.8
|
|
"lumi" # depends on broken package affyio-1.37.0
|
|
"LVSmiRNA" # depends on broken package affyio-1.37.0
|
|
"M3D" # depends on broken package Rsamtools-1.21.8
|
|
"MAIT" # depends on broken package nlopt-2.4.2
|
|
"makecdfenv" # depends on broken package affyio-1.37.0
|
|
"mAPKL" # build is broken
|
|
"maPredictDSC" # depends on broken package nlopt-2.4.2
|
|
"marked" # depends on broken package nlopt-2.4.2
|
|
"maskBAD" # depends on broken package affyio-1.37.0
|
|
"MatrixRider" # depends on broken package DirichletMultinomial-1.11.1
|
|
"MaxPro" # depends on broken package nlopt-2.4.2
|
|
"mbest" # depends on broken package nlopt-2.4.2
|
|
"MBmca" # depends on broken nloptr-1.0.4
|
|
"mBPCR" # depends on broken package affyio-1.37.0
|
|
"mcaGUI" # depends on broken package Rsamtools-1.21.8
|
|
"MCRestimate" # build is broken
|
|
"mdgsa" # build is broken
|
|
"meboot" # depends on broken package nlopt-2.4.2
|
|
"mediation" # depends on broken package r-lme4-1.1-8
|
|
"MEDIPS" # depends on broken package Rsamtools-1.21.8
|
|
"MEDME" # depends on broken package nlopt-2.4.2
|
|
"MEMSS" # depends on broken package nlopt-2.4.2
|
|
"meshr" # depends on broken package Category-2.35.1
|
|
"Metab" # depends on broken package mzR-2.3.1
|
|
"metagear" # build is broken
|
|
"metagene" # depends on broken package Rsamtools-1.21.8
|
|
"metaMix" # build is broken
|
|
"metaMS" # depends on broken package mzR-2.3.1
|
|
"metaplus" # depends on broken package nlopt-2.4.2
|
|
"metaSEM" # depends on broken package OpenMx-2.2.4
|
|
"metaseqR" # depends on broken package affyio-1.37.0
|
|
"Metatron" # depends on broken package nlopt-2.4.2
|
|
"methyAnalysis" # depends on broken package affyio-1.37.0
|
|
"MethylAid" # depends on broken package Rsamtools-1.21.8
|
|
"methylPipe" # depends on broken package Rsamtools-1.21.8
|
|
"MethylSeekR" # depends on broken package Rsamtools-1.21.8
|
|
"methylumi" # depends on broken package Rsamtools-1.21.8
|
|
"miceadds" # depends on broken package nlopt-2.4.2
|
|
"micEconAids" # depends on broken package nlopt-2.4.2
|
|
"micEconCES" # depends on broken package nlopt-2.4.2
|
|
"micEconSNQP" # depends on broken package nlopt-2.4.2
|
|
"mi" # depends on broken package nlopt-2.4.2
|
|
"MigClim" # Build Is Broken
|
|
"migui" # depends on broken package nlopt-2.4.2
|
|
"MineICA" # depends on broken package AnnotationForge-1.11.3
|
|
"minfi" # depends on broken package Rsamtools-1.21.8
|
|
"minimist" # depends on broken package V8-0.6
|
|
"MinimumDistance" # depends on broken package affyio-1.37.0
|
|
"mirIntegrator" # build is broken
|
|
"missDeaths"
|
|
"missMDA" # depends on broken package nlopt-2.4.2
|
|
"missMethyl" # depends on broken package Rsamtools-1.21.8
|
|
"mitoODE" # build is broken
|
|
"mixAK" # depends on broken package nlopt-2.4.2
|
|
"mixlm" # depends on broken package nlopt-2.4.2
|
|
"MixMAP" # depends on broken package nlopt-2.4.2
|
|
"mlmRev" # depends on broken package nlopt-2.4.2
|
|
"MLP" # depends on broken package affyio-1.37.0
|
|
"MLSeq" # depends on broken package nlopt-2.4.2
|
|
"mlVAR" # depends on broken package nlopt-2.4.2
|
|
"MMDiff" # depends on broken package AnnotationForge-1.11.3
|
|
"MmPalateMiRNA" # depends on broken package affyio-1.37.0
|
|
"mongolite" # build is broken
|
|
"monocle" # build is broken
|
|
"mosaic" # depends on broken package nlopt-2.4.2
|
|
"MotifDb" # depends on broken package Rsamtools-1.21.8
|
|
"motifRG" # depends on broken package Rsamtools-1.21.8
|
|
"motifStack" # depends on broken package Rsamtools-1.21.8
|
|
"MotIV" # depends on broken package Rsamtools-1.21.8
|
|
"MSeasy" # depends on broken package mzR-2.3.1
|
|
"MSeasyTkGUI" # depends on broken package mzR-2.3.1
|
|
"MSGFgui" # depends on broken package MSGFplus-1.3.0
|
|
"MSGFplus" # Build Is Broken
|
|
"msmsEDA" # depends on broken package affyio-1.37.0
|
|
"msmsTests" # depends on broken package affyio-1.37.0
|
|
"MSnbase" # depends on broken package affyio-1.37.0
|
|
"MSnID" # depends on broken package affyio-1.37.0
|
|
"MSstats" # depends on broken package nlopt-2.4.2
|
|
"multiDimBio" # depends on broken package nlopt-2.4.2
|
|
"MultiRR" # depends on broken package nlopt-2.4.2
|
|
"muma" # depends on broken package nlopt-2.4.2
|
|
"munsellinterpol"
|
|
"mutossGUI" # build is broken
|
|
"mvGST" # depends on broken package AnnotationForge-1.11.3
|
|
"mvinfluence" # depends on broken package nlopt-2.4.2
|
|
"mygene" # depends on broken package Rsamtools-1.21.8
|
|
"mzR" # build is broken
|
|
"NanoStringQCPro" # build is broken
|
|
"nCal" # depends on broken package nlopt-2.4.2
|
|
"ncdfFlow" # build is broken
|
|
"NCIgraph" # depends on broken package RCytoscape-1.19.0
|
|
"netbenchmark" # build is broken
|
|
"nettools" # depends on broken package WGCNA-1.47
|
|
"NGScopy"
|
|
"NHPoisson" # depends on broken package nlopt-2.4.2
|
|
"nloptr" # depends on broken package nlopt-2.4.2
|
|
"nondetects" # depends on broken package affyio-1.37.0
|
|
"nonrandom" # depends on broken package nlopt-2.4.2
|
|
"NormqPCR" # depends on broken package affyio-1.37.0
|
|
"NORRRM" # build is broken
|
|
"npIntFactRep" # depends on broken package nlopt-2.4.2
|
|
"nucleR" # depends on broken package Rsamtools-1.21.8
|
|
"oligoClasses" # depends on broken package affyio-1.37.0
|
|
"oligo" # depends on broken package affyio-1.37.0
|
|
"OmicsMarkeR" # depends on broken package nlopt-2.4.2
|
|
"oneChannelGUI" # depends on broken package affyio-1.37.0
|
|
"OpenCL" # build is broken
|
|
"openCyto" # depends on broken package ncdfFlow-2.15.2
|
|
"OpenMx" # build is broken
|
|
"OperaMate" # depends on broken package Category-2.35.1
|
|
"optBiomarker" # depends on broken package rpanel-1.1-3
|
|
"ora" # depends on broken package ROracle-1.1-12
|
|
"ordBTL" # depends on broken package nlopt-2.4.2
|
|
"OrganismDbi" # depends on broken package Rsamtools-1.21.8
|
|
"OTUbase" # depends on broken package Rsamtools-1.21.8
|
|
"OUwie" # depends on broken package nlopt-2.4.2
|
|
"PADOG" # build is broken
|
|
"pamm" # depends on broken package nlopt-2.4.2
|
|
"PANDA" # build is broken
|
|
"panelAR" # depends on broken package nlopt-2.4.2
|
|
"panp" # depends on broken package affyio-1.37.0
|
|
"papeR" # depends on broken package nlopt-2.4.2
|
|
"parboost" # depends on broken package nlopt-2.4.2
|
|
"parma" # depends on broken package nlopt-2.4.2
|
|
"Pasha" # depends on broken package GenomicAlignments-1.5.12
|
|
"pathClass" # depends on broken package affyio-1.37.0
|
|
"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
|
|
"pbdDEMO" # depends on broken package pbdSLAP-0.2-0
|
|
"pbdDMAT" # depends on broken package pbdSLAP-0.2-0
|
|
"pbdSLAP" # build is broken
|
|
"PBImisc" # depends on broken package nlopt-2.4.2
|
|
"pbkrtest" # depends on broken package nlopt-2.4.2
|
|
"PBSddesolve" # build is broken
|
|
"PBSmapping" # build is broken
|
|
"pcaBootPlot" # depends on broken FactoMineR-1.31.3
|
|
"pcaL1" # build is broken
|
|
"PCpheno" # depends on broken package Category-2.35.1
|
|
"pdInfoBuilder" # depends on broken package affyio-1.37.0
|
|
"pdmclass" # build is broken
|
|
"PECA" # depends on broken package affyio-1.37.0
|
|
"pedigreemm" # depends on broken package nlopt-2.4.2
|
|
"pedometrics" # depends on broken package nlopt-2.4.2
|
|
"pequod" # depends on broken package nlopt-2.4.2
|
|
"permGPU" # build is broken
|
|
"PGA" # depends on broken package Rsamtools-1.21.8
|
|
"PGSEA" # depends on broken package annaffy-1.41.1
|
|
"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
|
|
"phylocurve" # depends on broken package nlopt-2.4.2
|
|
"phyloTop" # depends on broken package nlopt-2.4.2
|
|
"PICS" # depends on broken package Rsamtools-1.21.8
|
|
"PING" # depends on broken package Rsamtools-1.21.8
|
|
"plateCore" # depends on broken package ncdfFlow-2.15.2
|
|
"plier" # depends on broken package affyio-1.37.0
|
|
"plsRbeta" # depends on broken package nlopt-2.4.2
|
|
"plsRcox" # depends on broken package nlopt-2.4.2
|
|
"plsRglm" # depends on broken package nlopt-2.4.2
|
|
"plw" # depends on broken package affyio-1.37.0
|
|
"pmclust" # build is broken
|
|
"pmm" # depends on broken package nlopt-2.4.2
|
|
"podkat" # depends on broken package Rsamtools-1.21.8
|
|
"polytomous" # depends on broken package nlopt-2.4.2
|
|
"pomp" # depends on broken package nlopt-2.4.2
|
|
"ppiPre" # depends on broken package GOSemSim-1.27.3
|
|
"ppiStats" # depends on broken package Category-2.35.1
|
|
"prebs" # depends on broken package affyio-1.37.0
|
|
"predictmeans" # depends on broken package nlopt-2.4.2
|
|
"prLogistic" # depends on broken package nlopt-2.4.2
|
|
"proBAMr" # depends on broken package Rsamtools-1.21.8
|
|
"ProCoNA" # depends on broken package AnnotationForge-1.11.3
|
|
"pRoloc" # depends on broken package nlopt-2.4.2
|
|
"pRolocGUI" # depends on broken package nlopt-2.4.2
|
|
"proteoQC" # depends on broken package affyio-1.37.0
|
|
"PSAboot" # depends on broken package nlopt-2.4.2
|
|
"ptw" # depends on broken nloptr-1.0.4
|
|
"puma" # depends on broken package affyio-1.37.0
|
|
"pvac" # depends on broken package affyio-1.37.0
|
|
"pvca" # depends on broken package nlopt-2.4.2
|
|
"Pviz" # depends on broken package Rsamtools-1.21.8
|
|
"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
|
|
"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
|
|
"QuasR" # depends on broken package Rsamtools-1.21.8
|
|
"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
|
|
"radiant" # depends on broken package nlopt-2.4.2
|
|
"raincpc" # build is broken
|
|
"rainfreq" # build is broken
|
|
"RamiGO" # depends on broken package RCytoscape-1.19.0
|
|
"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
|
|
"RBerkeley"
|
|
"RbioRXN" # depends on broken package ChemmineR-2.21.7
|
|
"Rcade" # depends on broken package Rsamtools-1.21.8
|
|
"rCGH" # depends on broken package r-affy-1.47.1
|
|
"Rchemcpp" # depends on broken package ChemmineR-2.21.7
|
|
"Rcmdr" # depends on broken package nlopt-2.4.2
|
|
"RcmdrMisc" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_BCA" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_coin" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_depthTools" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_DoE" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_doex" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_EACSPIR" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_IPSUR" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_KMggplot2" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_lfstat" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_MA" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_mosaic" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_MPAStats" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_NMBU" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_orloca" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_plotByGroup" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_pointG" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_qual" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_RMTCJags" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_ROC" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_sampling" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_SCDA" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_seeg" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_SLC" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_SM" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_sos" # depends on broken package nlopt-2.4.2
|
|
"RcmdrPlugin_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
|
|
"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
|
|
"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
|
|
"regioneR" # depends on broken package Rsamtools-1.21.8
|
|
"regionReport" # depends on broken package Rsamtools-1.21.8
|
|
"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
|
|
"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
|
|
"rgbif" # depends on broken package V8-0.6
|
|
"Rgnuplot"
|
|
"rgp" # build is broken
|
|
"rgpui" # depends on broken package rgp-0.4-1
|
|
"rgsepd" # depends on broken package goseq-1.21.1
|
|
"rhdf5" # build is broken
|
|
"rHVDM" # depends on broken package affyio-1.37.0
|
|
"Ringo" # depends on broken package affyio-1.37.0
|
|
"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
|
|
"rJPSGCS" # build is broken
|
|
"rLindo" # build is broken
|
|
"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
|
|
"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
|
|
"Rnits" # depends on broken package affyio-1.37.0
|
|
"roar" # depends on broken package Rsamtools-1.21.8
|
|
"RobLoxBioC" # depends on broken package affyio-1.37.0
|
|
"robustlmm" # depends on broken package nlopt-2.4.2
|
|
"rockchalk" # depends on broken package nlopt-2.4.2
|
|
"ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20
|
|
"Rolexa" # depends on broken package Rsamtools-1.21.8
|
|
"rols" # build is broken
|
|
"ROracle" # Build Is Broken
|
|
"RPA" # depends on broken package affyio-1.37.0
|
|
"rpanel" # build is broken
|
|
"rpubchem" # depends on broken package nlopt-2.4.2
|
|
"Rqc" # depends on broken package Rsamtools-1.21.8
|
|
"RQuantLib" # build is broken
|
|
"rr" # depends on broken package nlopt-2.4.2
|
|
"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
|
|
"rSFFreader" # depends on broken package Rsamtools-1.21.8
|
|
"Rsubread" # Build Is Broken
|
|
"RSVSim" # depends on broken package Rsamtools-1.21.8
|
|
"Rsymphony" # build is broken
|
|
"rTANDEM" # build is broken
|
|
"RTN" # depends on broken package nlopt-2.4.2
|
|
"rtracklayer" # depends on broken package Rsamtools-1.21.8
|
|
"rTRMui" # depends on broken package Rsamtools-1.21.8
|
|
"rugarch" # depends on broken package nlopt-2.4.2
|
|
"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
|
|
"RVFam" # depends on broken package nlopt-2.4.2
|
|
"RVideoPoker" # depends on broken package rpanel-1.1-3
|
|
"ryouready" # depends on broken package nlopt-2.4.2
|
|
"sampleSelection" # depends on broken package nlopt-2.4.2
|
|
"sapFinder" # depends on broken package rTANDEM-1.9.0
|
|
"SCAN_UPC" # depends on broken package affyio-1.37.0
|
|
"ScISI" # depends on broken package apComplex-2.35.0
|
|
"sdcMicro" # depends on broken package nlopt-2.4.2
|
|
"sdcMicroGUI" # depends on broken package nlopt-2.4.2
|
|
"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
|
|
"sem" # depends on broken package nlopt-2.4.2
|
|
"semdiag" # depends on broken package nlopt-2.4.2
|
|
"SemDist" # Build Is Broken
|
|
"semGOF" # depends on broken package nlopt-2.4.2
|
|
"semPlot" # depends on broken package nlopt-2.4.2
|
|
"SensoMineR" # depends on broken package nlopt-2.4.2
|
|
"SEPA" # depends on broken package topGO-2.21.0
|
|
"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
|
|
"SeqGrapheR" # Build Is Broken
|
|
"seqplots" # depends on broken package Rsamtools-1.21.8
|
|
"seqTools" # build is broken
|
|
"SeqVarTools" # depends on broken package Rsamtools-1.21.8
|
|
"SGSeq" # depends on broken package Rsamtools-1.21.8
|
|
"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
|
|
"SIMAT" # depends on broken package mzR-2.3.1
|
|
"SimBindProfiles" # depends on broken package affyio-1.37.0
|
|
"similaRpeak" # depends on broken package Rsamtools-1.21.8
|
|
"simpleaffy" # depends on broken package affyio-1.37.0
|
|
"SimRAD" # depends on broken package Rsamtools-1.21.8
|
|
"sirt" # depends on broken package nlopt-2.4.2
|
|
"sjPlot" # depends on broken package nlopt-2.4.2
|
|
"skewr" # depends on broken package affyio-1.37.0
|
|
"SLGI" # depends on broken package apComplex-2.35.0
|
|
"SNAGEE" # build is broken
|
|
"snapCGH" # depends on broken package tilingArray-1.47.0
|
|
"snm" # depends on broken package nlopt-2.4.2
|
|
"SNPchip" # depends on broken package affyio-1.37.0
|
|
"snpEnrichment" # depends on broken package snpStats-1.19.0
|
|
"snpStats" # build is broken
|
|
"snpStatsWriter" # depends on broken package snpStats-1.19.0
|
|
"SNPtools" # depends on broken package Rsamtools-1.21.8
|
|
"SOD" # depends on broken package cudatoolkit-5.5.22
|
|
"soGGi" # depends on broken package Rsamtools-1.21.8
|
|
"soilphysics" # depends on broken package rpanel-1.1-3
|
|
"SomaticSignatures" # depends on broken package Rsamtools-1.21.8
|
|
"SoyNAM" # depends on broken package r-lme4-1.1-8
|
|
"spacom" # depends on broken package nlopt-2.4.2
|
|
"specificity" # depends on broken package nlopt-2.4.2
|
|
"spliceR" # depends on broken package Rsamtools-1.21.8
|
|
"SplicingGraphs" # depends on broken package Rsamtools-1.21.8
|
|
"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
|
|
"sscore" # depends on broken package affyio-1.37.0
|
|
"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
|
|
"stcm" # depends on broken package nlopt-2.4.2
|
|
"stepp" # depends on broken package nlopt-2.4.2
|
|
"stringgaussnet" # build is broken
|
|
"Surrogate" # depends on broken package nlopt-2.4.2
|
|
"SVM2CRM" # depends on broken package Rsamtools-1.21.8
|
|
"sybilSBML" # build is broken
|
|
"synapter" # depends on broken package affyio-1.37.0
|
|
"systemfit" # depends on broken package nlopt-2.4.2
|
|
"systemPipeR" # depends on broken package AnnotationForge-1.11.3
|
|
"TargetSearch" # depends on broken package mzR-2.3.1
|
|
"TcGSA" # depends on broken package nlopt-2.4.2
|
|
"TDMR" # depends on broken package nlopt-2.4.2
|
|
"TEQC" # depends on broken package Rsamtools-1.21.8
|
|
"TFBSTools" # depends on broken package DirichletMultinomial-1.11.1
|
|
"tigerstats" # depends on broken package nlopt-2.4.2
|
|
"tilingArray" # depends on broken package affyio-1.37.0
|
|
"TIN" # depends on broken package WGCNA-1.47
|
|
"TitanCNA" # depends on broken package Rsamtools-1.21.8
|
|
"ToPASeq" # depends on broken package Rsamtools-1.21.8
|
|
"topGO" # build is broken
|
|
"topologyGSA" # depends on broken package Rsamtools-1.21.8
|
|
"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"
|
|
"TriMatch" # depends on broken package nlopt-2.4.2
|
|
"TROM" # depends on broken package topGO-2.21.0
|
|
"TurboNorm" # depends on broken package affyio-1.37.0
|
|
"unifiedWMWqPCR" # depends on broken package affyio-1.37.0
|
|
"userfriendlyscience" # depends on broken package nlopt-2.4.2
|
|
"V8" # build is broken
|
|
"VanillaICE" # depends on broken package affyio-1.37.0
|
|
"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
|
|
"VIM" # depends on broken package nlopt-2.4.2
|
|
"VIMGUI" # depends on broken package nlopt-2.4.2
|
|
"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
|
|
"wfe" # depends on broken package nlopt-2.4.2
|
|
"WGCNA" # build is broken
|
|
"wgsea" # depends on broken package snpStats-1.19.0
|
|
"WideLM" # depends on broken package cudatoolkit-5.5.22
|
|
"xcms" # depends on broken package mzR-2.3.1
|
|
"xergm" # depends on broken package nlopt-2.4.2
|
|
"xps" # build is broken
|
|
"yaqcaffy" # depends on broken package affyio-1.37.0
|
|
"ZeligMultilevel" # depends on broken package nlopt-2.4.2
|
|
"zetadiv" # depends on broken package nlopt-2.4.2
|
|
];
|
|
|
|
otherOverrides = old: new: {
|
|
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}/include/libxml2";
|
|
});
|
|
|
|
curl = old.curl.overrideDerivation (attrs: {
|
|
preConfigure = "patchShebangs configure";
|
|
});
|
|
|
|
iFes = old.iFes.overrideDerivation (attrs: {
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
rpf = old.rpf.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesXsrc.patch ];
|
|
});
|
|
|
|
rJava = old.rJava.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
JavaGD = old.JavaGD.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
Mposterior = old.Mposterior.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
qtbase = old.qtbase.overrideDerivation (attrs: {
|
|
patches = [ ./patches/qtbase.patch ];
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${pkgs.mpfr}/include"
|
|
];
|
|
});
|
|
|
|
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
|
|
];
|
|
});
|
|
|
|
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
|
|
patches = [ ./patches/RAppArmor.patch ];
|
|
LIBAPPARMOR_HOME = "${pkgs.libapparmor}";
|
|
});
|
|
|
|
RMySQL = old.RMySQL.overrideDerivation (attrs: {
|
|
patches = [ ./patches/RMySQL.patch ];
|
|
MYSQL_DIR="${pkgs.mysql.lib}";
|
|
});
|
|
|
|
devEMF = old.devEMF.overrideDerivation (attrs: {
|
|
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft}/lib -lXft";
|
|
});
|
|
|
|
slfm = old.slfm.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
|
|
});
|
|
|
|
gputools = old.gputools.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gputools.patch ];
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
# It seems that we cannot override meta attributes with overrideDerivation.
|
|
CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
|
|
patches = [ ./patches/CARramps.patch ];
|
|
configureFlags = [
|
|
"--with-cuda-home=${pkgs.cudatoolkit}"
|
|
];
|
|
});
|
|
|
|
gmatrix = old.gmatrix.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gmatrix.patch ];
|
|
CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
|
|
R_INC_PATH = "${pkgs.R}/lib/R/include";
|
|
CUDA_INC_PATH = "${pkgs.cudatoolkit}/include";
|
|
});
|
|
|
|
# It seems that we cannot override meta attributes with overrideDerivation.
|
|
rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
|
|
patches = [ ./patches/rpud.patch ];
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
WideLM = old.WideLM.overrideDerivation (attrs: {
|
|
patches = [ ./patches/WideLM.patch ];
|
|
configureFlags = [
|
|
"--with-cuda-home=${pkgs.cudatoolkit}"
|
|
];
|
|
});
|
|
|
|
EMCluster = old.EMCluster.overrideDerivation (attrs: {
|
|
patches = [ ./patches/EMCluster.patch ];
|
|
});
|
|
|
|
spMC = old.spMC.overrideDerivation (attrs: {
|
|
patches = [ ./patches/spMC.patch ];
|
|
});
|
|
|
|
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesLogit.patch ];
|
|
buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
|
|
});
|
|
|
|
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesBridge.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
OPENSSL_INCLUDES = "${pkgs.openssl}/include";
|
|
});
|
|
|
|
Rserve = old.Rserve.overrideDerivation (attrs: {
|
|
patches = [ ./patches/Rserve.patch ];
|
|
configureFlags = [
|
|
"--with-server" "--with-client"
|
|
];
|
|
});
|
|
|
|
nloptr = old.nloptr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-nlopt-cflags=-I${pkgs.nlopt}/include"
|
|
"--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
|
|
];
|
|
});
|
|
|
|
V8 = old.V8.overrideDerivation (attrs: {
|
|
preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
|
|
});
|
|
|
|
};
|
|
in
|
|
self
|