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r-modules: Fix h5 and rhdf5

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and some packages that depend on them.
This commit is contained in:
Andreas Herrmann 2016-09-27 17:46:06 +02:00
parent 124f25bc7d
commit 54915ecf0d
1 changed files with 7 additions and 10 deletions
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17
pkgs/development/r-modules/default.nix
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@ -266,6 +266,8 @@ let
gmp = [ pkgs.gmp ]; gmp = [ pkgs.gmp ];
graphscan = [ pkgs.gsl_1 ]; graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ]; gsl = [ pkgs.gsl_1 ];
h5 = [ pkgs.hdf5-cpp pkgs.which ];
h5vc = [ pkgs.zlib.dev ];
HiCseg = [ pkgs.gsl_1 ]; HiCseg = [ pkgs.gsl_1 ];
iBMQ = [ pkgs.gsl_1 ]; iBMQ = [ pkgs.gsl_1 ];
igraph = [ pkgs.gmp ]; igraph = [ pkgs.gmp ];
@ -308,6 +310,7 @@ let
rgl = [ pkgs.mesa pkgs.xlibsWrapper ]; rgl = [ pkgs.mesa pkgs.xlibsWrapper ];
Rglpk = [ pkgs.glpk ]; Rglpk = [ pkgs.glpk ];
RGtk2 = [ pkgs.gtk2 ]; RGtk2 = [ pkgs.gtk2 ];
rhdf5 = [ pkgs.zlib ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ]; Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
Rhtslib = [ pkgs.zlib ]; Rhtslib = [ pkgs.zlib ];
RJaCGH = [ pkgs.zlib ]; RJaCGH = [ pkgs.zlib ];
@ -367,12 +370,12 @@ let
bamsignals = [ pkgs.zlib ]; bamsignals = [ pkgs.zlib ];
BitSeq = [ pkgs.zlib ]; BitSeq = [ pkgs.zlib ];
DiffBind = [ pkgs.zlib ]; DiffBind = [ pkgs.zlib ];
ShortRead = [ pkgs.zlib ]; ShortRead = [ pkgs.zlib.dev ];
oligo = [ pkgs.zlib ]; oligo = [ pkgs.zlib ];
gmapR = [ pkgs.zlib ]; gmapR = [ pkgs.zlib ];
Rsubread = [ pkgs.zlib ]; Rsubread = [ pkgs.zlib ];
XVector = [ pkgs.zlib ]; XVector = [ pkgs.zlib.dev ];
Rsamtools = [ pkgs.zlib ]; Rsamtools = [ pkgs.zlib.dev ];
rtracklayer = [ pkgs.zlib ]; rtracklayer = [ pkgs.zlib ];
affyio = [ pkgs.zlib ]; affyio = [ pkgs.zlib ];
VariantAnnotation = [ pkgs.zlib ]; VariantAnnotation = [ pkgs.zlib ];
@ -390,7 +393,7 @@ let
qtpaint = [ pkgs.cmake ]; qtpaint = [ pkgs.cmake ];
qtbase = [ pkgs.cmake pkgs.perl ]; qtbase = [ pkgs.cmake pkgs.perl ];
gmatrix = [ pkgs.cudatoolkit ]; gmatrix = [ pkgs.cudatoolkit ];
RCurl = [ pkgs.curl ]; RCurl = [ pkgs.curl.dev ];
R2SWF = [ pkgs.pkgconfig ]; R2SWF = [ pkgs.pkgconfig ];
rggobi = [ pkgs.pkgconfig ]; rggobi = [ pkgs.pkgconfig ];
RGtk2 = [ pkgs.pkgconfig ]; RGtk2 = [ pkgs.pkgconfig ];
@ -1142,7 +1145,6 @@ let
"proteoQC" # depends on broken package rTANDEM "proteoQC" # depends on broken package rTANDEM
"PGA" # depends on broken package rTANDEM "PGA" # depends on broken package rTANDEM
"MBESS" # depends on broken package OpenMx "MBESS" # depends on broken package OpenMx
"IONiseR" # depends on broken package rhdf5
"DOQTL" # depends on broken package rhdf5 "DOQTL" # depends on broken package rhdf5
"DmelSGI" # depends on broken package rhdf5 "DmelSGI" # depends on broken package rhdf5
"flowDiv" # depends on broken package ncdfFlow "flowDiv" # depends on broken package ncdfFlow
@ -1356,7 +1358,6 @@ let
"gcmr" # depends on broken package nlopt "gcmr" # depends on broken package nlopt
"GDAtools" # depends on broken package nlopt "GDAtools" # depends on broken package nlopt
"gdtools" # broken build "gdtools" # broken build
"GENE_E" # depends on broken package rhdf5
"GENESIS" # broken build "GENESIS" # broken build
"genridge" # depends on broken package nlopt "genridge" # depends on broken package nlopt
"geojsonio" # depends on broken package V8 "geojsonio" # depends on broken package V8
@ -1379,8 +1380,6 @@ let
"GUIDE" # depends on broken package rpanel "GUIDE" # depends on broken package rpanel
"GWAF" # depends on broken package nlopt "GWAF" # depends on broken package nlopt
"GWASTools" # broken build "GWASTools" # broken build
"h5" # build is broken
"h5vc" # depends on broken package rhdf5
"hbsae" # depends on broken package nlopt "hbsae" # depends on broken package nlopt
"heplots" # depends on broken package nlopt "heplots" # depends on broken package nlopt
"HiDimMaxStable" # broken build "HiDimMaxStable" # broken build
@ -1407,7 +1406,6 @@ let
"inSilicoMerging" # build is broken "inSilicoMerging" # build is broken
"INSPEcT" # depends on broken GenomicFeatures "INSPEcT" # depends on broken GenomicFeatures
"interplot" # depends on broken arm "interplot" # depends on broken arm
"IONiseR" # depends on broken rhdf5
"IsingFit" # depends on broken package nlopt "IsingFit" # depends on broken package nlopt
"ITEMAN" # depends on broken package car "ITEMAN" # depends on broken package car
"iteRates" # broken build "iteRates" # broken build
@ -1645,7 +1643,6 @@ let
"REST" # depends on broken package nlopt "REST" # depends on broken package nlopt
"rgbif" # depends on broken package V8 "rgbif" # depends on broken package V8
"Rgnuplot" # broken build "Rgnuplot" # broken build
"rhdf5" # build is broken
"rjade" # depends on broken package V8 "rjade" # depends on broken package V8
"rJPSGCS" # build is broken "rJPSGCS" # build is broken
"rLindo" # build is broken "rLindo" # build is broken