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Merge pull request #21722 from mimadrid/fix/r-modules

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Fix a lot of rPackages
This commit is contained in:
Peter Simons 2017-01-07 12:19:42 +01:00 committed by GitHub
commit c5f8c7fe36
1 changed files with 58 additions and 53 deletions
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111
pkgs/development/r-modules/default.nix
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@ -240,30 +240,30 @@ let
audio = [ pkgs.portaudio ]; audio = [ pkgs.portaudio ];
BayesSAE = [ pkgs.gsl_1 ]; BayesSAE = [ pkgs.gsl_1 ];
BayesVarSel = [ pkgs.gsl_1 ]; BayesVarSel = [ pkgs.gsl_1 ];
BayesXsrc = [ pkgs.readline pkgs.ncurses ]; BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
bigGP = [ pkgs.openmpi ]; bigGP = [ pkgs.openmpi ];
BiocCheck = [ pkgs.which ]; BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ]; Biostrings = [ pkgs.zlib ];
bnpmr = [ pkgs.gsl_1 ]; bnpmr = [ pkgs.gsl_1 ];
BNSP = [ pkgs.gsl_1 ]; BNSP = [ pkgs.gsl_1 ];
cairoDevice = [ pkgs.gtk2 ]; cairoDevice = [ pkgs.gtk2.dev ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ]; Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
Cardinal = [ pkgs.which ]; Cardinal = [ pkgs.which ];
chebpol = [ pkgs.fftw ]; chebpol = [ pkgs.fftw ];
ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
cit = [ pkgs.gsl_1 ]; cit = [ pkgs.gsl_1 ];
curl = [ pkgs.curl.dev ]; curl = [ pkgs.curl.dev ];
devEMF = [ pkgs.xorg.libXft ]; devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
diversitree = [ pkgs.gsl_1 pkgs.fftw ]; diversitree = [ pkgs.gsl_1 pkgs.fftw ];
EMCluster = [ pkgs.liblapack ]; EMCluster = [ pkgs.liblapack ];
fftw = [ pkgs.fftw ]; fftw = [ pkgs.fftw.dev ];
fftwtools = [ pkgs.fftw ]; fftwtools = [ pkgs.fftw.dev ];
Formula = [ pkgs.gmp ]; Formula = [ pkgs.gmp ];
geoCount = [ pkgs.gsl_1 ]; geoCount = [ pkgs.gsl_1 ];
git2r = [ pkgs.zlib pkgs.openssl ]; git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
GLAD = [ pkgs.gsl_1 ]; GLAD = [ pkgs.gsl_1 ];
glpkAPI = [ pkgs.gmp pkgs.glpk ]; glpkAPI = [ pkgs.gmp pkgs.glpk ];
gmp = [ pkgs.gmp ]; gmp = [ pkgs.gmp.dev ];
graphscan = [ pkgs.gsl_1 ]; graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ]; gsl = [ pkgs.gsl_1 ];
h5 = [ pkgs.hdf5-cpp pkgs.which ]; h5 = [ pkgs.hdf5-cpp pkgs.which ];
@ -272,13 +272,13 @@ let
iBMQ = [ pkgs.gsl_1 ]; iBMQ = [ pkgs.gsl_1 ];
igraph = [ pkgs.gmp ]; igraph = [ pkgs.gmp ];
JavaGD = [ pkgs.jdk ]; JavaGD = [ pkgs.jdk ];
jpeg = [ pkgs.libjpeg ]; jpeg = [ pkgs.libjpeg.dev ];
KFKSDS = [ pkgs.gsl_1 ]; KFKSDS = [ pkgs.gsl_1 ];
kza = [ pkgs.fftw ]; kza = [ pkgs.fftw.dev ];
libamtrack = [ pkgs.gsl_1 ]; libamtrack = [ pkgs.gsl_1 ];
mixcat = [ pkgs.gsl_1 ]; mixcat = [ pkgs.gsl_1 ];
mvabund = [ pkgs.gsl_1 ]; mvabund = [ pkgs.gsl_1 ];
mwaved = [ pkgs.fftw ]; mwaved = [ pkgs.fftw.dev ];
ncdf4 = [ pkgs.netcdf ]; ncdf4 = [ pkgs.netcdf ];
nloptr = [ pkgs.nlopt ]; nloptr = [ pkgs.nlopt ];
openssl = [ pkgs.openssl.dev ]; openssl = [ pkgs.openssl.dev ];
@ -287,99 +287,99 @@ let
pbdMPI = [ pkgs.openmpi ]; pbdMPI = [ pkgs.openmpi ];
pbdNCDF4 = [ pkgs.netcdf ]; pbdNCDF4 = [ pkgs.netcdf ];
pbdPROF = [ pkgs.openmpi ]; pbdPROF = [ pkgs.openmpi ];
PKI = [ pkgs.openssl ]; PKI = [ pkgs.openssl.dev ];
png = [ pkgs.libpng.dev ]; png = [ pkgs.libpng.dev ];
PopGenome = [ pkgs.zlib ]; PopGenome = [ pkgs.zlib.dev ];
proj4 = [ pkgs.proj ]; proj4 = [ pkgs.proj ];
qtbase = [ pkgs.qt4 ]; qtbase = [ pkgs.qt4 ];
qtpaint = [ pkgs.qt4 ]; qtpaint = [ pkgs.qt4 ];
R2GUESS = [ pkgs.gsl_1 ]; R2GUESS = [ pkgs.gsl_1 ];
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
RAppArmor = [ pkgs.libapparmor ]; RAppArmor = [ pkgs.libapparmor ];
rapportools = [ pkgs.which ]; rapportools = [ pkgs.which ];
rapport = [ pkgs.which ]; rapport = [ pkgs.which ];
rbamtools = [ pkgs.zlib ]; rbamtools = [ pkgs.zlib.dev ];
rcdd = [ pkgs.gmp ]; rcdd = [ pkgs.gmp.dev ];
RcppCNPy = [ pkgs.zlib ]; RcppCNPy = [ pkgs.zlib.dev ];
RcppGSL = [ pkgs.gsl_1 ]; RcppGSL = [ pkgs.gsl_1 ];
RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ]; RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.octave ];
RcppZiggurat = [ pkgs.gsl_1 ]; RcppZiggurat = [ pkgs.gsl_1 ];
rgdal = [ pkgs.proj pkgs.gdal ]; rgdal = [ pkgs.proj pkgs.gdal ];
rgeos = [ pkgs.geos ]; rgeos = [ pkgs.geos ];
rggobi = [ pkgs.ggobi pkgs.gtk2 pkgs.libxml2 ]; rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ];
rgl = [ pkgs.mesa pkgs.xlibsWrapper ]; rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
Rglpk = [ pkgs.glpk ]; Rglpk = [ pkgs.glpk ];
RGtk2 = [ pkgs.gtk2 ]; RGtk2 = [ pkgs.gtk2.dev ];
rhdf5 = [ pkgs.zlib ]; rhdf5 = [ pkgs.zlib ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ]; Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
Rhtslib = [ pkgs.zlib ]; Rhtslib = [ pkgs.zlib.dev ];
RJaCGH = [ pkgs.zlib ]; RJaCGH = [ pkgs.zlib.dev ];
rjags = [ pkgs.jags ]; rjags = [ pkgs.jags ];
rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ]; rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ]; Rlibeemd = [ pkgs.gsl_1 ];
rmatio = [ pkgs.zlib ]; rmatio = [ pkgs.zlib.dev ];
Rmpfr = [ pkgs.gmp pkgs.mpfr ]; Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
Rmpi = [ pkgs.openmpi ]; Rmpi = [ pkgs.openmpi ];
RMySQL = [ pkgs.zlib pkgs.mysql.lib ]; RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ]; RNetCDF = [ pkgs.netcdf pkgs.udunits ];
RODBCext = [ pkgs.libiodbc ]; RODBCext = [ pkgs.libiodbc ];
RODBC = [ pkgs.libiodbc ]; RODBC = [ pkgs.libiodbc ];
rpg = [ pkgs.postgresql ]; rpg = [ pkgs.postgresql ];
rphast = [ pkgs.pcre pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ]; rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
Rpoppler = [ pkgs.poppler ]; Rpoppler = [ pkgs.poppler ];
RPostgreSQL = [ pkgs.postgresql ]; RPostgreSQL = [ pkgs.postgresql ];
RProtoBuf = [ pkgs.protobuf ]; RProtoBuf = [ pkgs.protobuf ];
rPython = [ pkgs.python ]; rPython = [ pkgs.python ];
RSclient = [ pkgs.openssl ]; RSclient = [ pkgs.openssl.dev ];
Rserve = [ pkgs.openssl ]; Rserve = [ pkgs.openssl ];
Rssa = [ pkgs.fftw ]; Rssa = [ pkgs.fftw.dev ];
rtfbs = [ pkgs.zlib pkgs.pcre pkgs.bzip2 pkgs.gzip pkgs.readline ]; rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
rtiff = [ pkgs.libtiff ]; rtiff = [ pkgs.libtiff.dev ];
runjags = [ pkgs.jags ]; runjags = [ pkgs.jags ];
RVowpalWabbit = [ pkgs.zlib pkgs.boost ]; RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
rzmq = [ pkgs.zeromq3 ]; rzmq = [ pkgs.zeromq3 ];
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ]; SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
sdcTable = [ pkgs.gmp pkgs.glpk ]; sdcTable = [ pkgs.gmp pkgs.glpk ];
seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ]; seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
seqinr = [ pkgs.zlib ]; seqinr = [ pkgs.zlib.dev ];
seqminer = [ pkgs.zlib pkgs.bzip2 ]; seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ]; showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
simplexreg = [ pkgs.gsl_1 ]; simplexreg = [ pkgs.gsl_1 ];
SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
spate = [ pkgs.fftw ]; spate = [ pkgs.fftw.dev ];
sprint = [ pkgs.openmpi ]; sprint = [ pkgs.openmpi ];
ssanv = [ pkgs.proj ]; ssanv = [ pkgs.proj ];
stsm = [ pkgs.gsl_1 ]; stsm = [ pkgs.gsl_1 ];
stringi = [ pkgs.icu.dev ]; stringi = [ pkgs.icu.dev ];
survSNP = [ pkgs.gsl_1 ]; survSNP = [ pkgs.gsl_1 ];
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ]; sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
TAQMNGR = [ pkgs.zlib ]; TAQMNGR = [ pkgs.zlib.dev ];
tiff = [ pkgs.libtiff ]; tiff = [ pkgs.libtiff.dev ];
TKF = [ pkgs.gsl_1 ]; TKF = [ pkgs.gsl_1 ];
tkrplot = [ pkgs.xorg.libX11 ]; tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
topicmodels = [ pkgs.gsl_1 ]; topicmodels = [ pkgs.gsl_1 ];
udunits2 = [ pkgs.udunits pkgs.expat ]; udunits2 = [ pkgs.udunits pkgs.expat ];
V8 = [ pkgs.v8 ]; V8 = [ pkgs.v8 ];
VBLPCM = [ pkgs.gsl_1 ]; VBLPCM = [ pkgs.gsl_1 ];
VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ]; VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
WhopGenome = [ pkgs.zlib ]; WhopGenome = [ pkgs.zlib.dev ];
XBRL = [ pkgs.zlib pkgs.libxml2 ]; XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
xml2 = [ pkgs.libxml2 ]; xml2 = [ pkgs.libxml2.dev ];
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
affyPLM = [ pkgs.zlib ]; affyPLM = [ pkgs.zlib.dev ];
bamsignals = [ pkgs.zlib ]; bamsignals = [ pkgs.zlib.dev ];
BitSeq = [ pkgs.zlib ]; BitSeq = [ pkgs.zlib.dev ];
DiffBind = [ pkgs.zlib ]; DiffBind = [ pkgs.zlib ];
ShortRead = [ pkgs.zlib.dev ]; ShortRead = [ pkgs.zlib.dev ];
oligo = [ pkgs.zlib ]; oligo = [ pkgs.zlib.dev ];
gmapR = [ pkgs.zlib ]; gmapR = [ pkgs.zlib.dev ];
Rsubread = [ pkgs.zlib ]; Rsubread = [ pkgs.zlib.dev ];
XVector = [ pkgs.zlib.dev ]; XVector = [ pkgs.zlib.dev ];
Rsamtools = [ pkgs.zlib.dev ]; Rsamtools = [ pkgs.zlib.dev ];
rtracklayer = [ pkgs.zlib ]; rtracklayer = [ pkgs.zlib.dev ];
affyio = [ pkgs.zlib ]; affyio = [ pkgs.zlib.dev ];
VariantAnnotation = [ pkgs.zlib ]; VariantAnnotation = [ pkgs.zlib.dev ];
snpStats = [ pkgs.zlib ]; snpStats = [ pkgs.zlib.dev ];
}; };
packagesWithBuildInputs = { packagesWithBuildInputs = {
@ -1791,6 +1791,10 @@ let
''; '';
}); });
Cairo = old.Cairo.overrideDerivation (attrs: {
NIX_LDFLAGS = "-lfontconfig";
});
curl = old.curl.overrideDerivation (attrs: { curl = old.curl.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure"; preConfigure = "patchShebangs configure";
}); });
@ -1859,6 +1863,7 @@ let
devEMF = old.devEMF.overrideDerivation (attrs: { devEMF = old.devEMF.overrideDerivation (attrs: {
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft"; NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
NIX_LDFLAGS = "-lX11";
}); });
slfm = old.slfm.overrideDerivation (attrs: { slfm = old.slfm.overrideDerivation (attrs: {