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rPackages: try to unbreak reverse dependencies of cudatoolkit

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This commit is contained in:
Nikolay Amiantov 2017-02-28 17:20:27 +03:00
parent d7ecf89580
commit 6f3e071755
1 changed files with 5 additions and 17 deletions
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22
pkgs/development/r-modules/default.nix
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@ -345,7 +345,7 @@ let
seqminer = [ pkgs.zlib.dev pkgs.bzip2 ]; seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ]; 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.opencl-headers ];
spate = [ pkgs.fftw.dev ]; spate = [ pkgs.fftw.dev ];
sprint = [ pkgs.openmpi ]; sprint = [ pkgs.openmpi ];
ssanv = [ pkgs.proj ]; ssanv = [ pkgs.proj ];
@ -380,6 +380,7 @@ let
affyio = [ pkgs.zlib.dev ]; affyio = [ pkgs.zlib.dev ];
VariantAnnotation = [ pkgs.zlib.dev ]; VariantAnnotation = [ pkgs.zlib.dev ];
snpStats = [ pkgs.zlib.dev ]; snpStats = [ pkgs.zlib.dev ];
gputools = [ pkgs.pcre.dev pkgs.lzma.dev pkgs.zlib.dev pkgs.bzip2.dev pkgs.icu.dev ];
}; };
packagesWithBuildInputs = { packagesWithBuildInputs = {
@ -392,7 +393,7 @@ let
RPushbullet = [ pkgs.which ]; RPushbullet = [ pkgs.which ];
qtpaint = [ pkgs.cmake ]; qtpaint = [ pkgs.cmake ];
qtbase = [ pkgs.cmake pkgs.perl ]; qtbase = [ pkgs.cmake pkgs.perl ];
gmatrix = [ pkgs.cudatoolkit ]; gmatrix = [ pkgs.cudatoolkit pkgs.which ];
RCurl = [ pkgs.curl.dev ]; RCurl = [ pkgs.curl.dev ];
R2SWF = [ pkgs.pkgconfig ]; R2SWF = [ pkgs.pkgconfig ];
rggobi = [ pkgs.pkgconfig ]; rggobi = [ pkgs.pkgconfig ];
@ -692,6 +693,7 @@ let
packagesToSkipCheck = [ packagesToSkipCheck = [
"Rmpi" # tries to run MPI processes "Rmpi" # tries to run MPI processes
"gmatrix" # requires CUDA runtime "gmatrix" # requires CUDA runtime
"gputools" # requires CUDA runtime
"sprint" # tries to run MPI processes "sprint" # tries to run MPI processes
"pbdMPI" # tries to run MPI processes "pbdMPI" # tries to run MPI processes
]; ];
@ -741,6 +743,7 @@ let
"RefNet" # depends on broken package interactiveDisplayBase "RefNet" # depends on broken package interactiveDisplayBase
"pwOmics" # depends on broken package interactiveDisplayBase "pwOmics" # depends on broken package interactiveDisplayBase
"grasp2db" # depends on broken package interactiveDisplayBase "grasp2db" # depends on broken package interactiveDisplayBase
"gputools" # broken build
"EnsDb_Rnorvegicus_v79" # depends on broken package interactiveDisplayBase "EnsDb_Rnorvegicus_v79" # depends on broken package interactiveDisplayBase
"EnsDb_Rnorvegicus_v75" # depends on broken package interactiveDisplayBase "EnsDb_Rnorvegicus_v75" # depends on broken package interactiveDisplayBase
"EnsDb_Mmusculus_v79" # depends on broken package interactiveDisplayBase "EnsDb_Mmusculus_v79" # depends on broken package interactiveDisplayBase
@ -1089,13 +1092,11 @@ let
"GEWIST" # depends on broken package nlopt "GEWIST" # depends on broken package nlopt
"ggtree" # broken build "ggtree" # broken build
"gimme" # depends on broken package nlopt "gimme" # depends on broken package nlopt
"gmatrix" # depends on broken package cudatoolkit
"gMCP" # build is broken "gMCP" # build is broken
"gmum_r" # broken build "gmum_r" # broken build
"GPC" # broken build "GPC" # broken build
"gplm" # depends on broken package nlopt "gplm" # depends on broken package nlopt
"gpuR" # depends on GPU-specific header files "gpuR" # depends on GPU-specific header files
"gputools" # depends on broken package cudatoolkit
"granova" # depends on broken package nlopt "granova" # depends on broken package nlopt
"graphicalVAR" # depends on broken package nlopt "graphicalVAR" # depends on broken package nlopt
"GraphPAC" # broken build "GraphPAC" # broken build
@ -1435,7 +1436,6 @@ let
"smacof" # broken build "smacof" # broken build
"SNAGEE" # build is broken "SNAGEE" # build is broken
"snm" # depends on broken package nlopt "snm" # depends on broken package nlopt
"SOD" # depends on broken package cudatoolkit
"sodium" # broken build "sodium" # broken build
"soilphysics" # depends on broken package rpanel "soilphysics" # depends on broken package rpanel
"sortinghat" # broken build "sortinghat" # broken build
@ -1595,18 +1595,6 @@ let
PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas"; PKG_LIBS = "-L${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: { EMCluster = old.EMCluster.overrideDerivation (attrs: {
patches = [ ./patches/EMCluster.patch ]; patches = [ ./patches/EMCluster.patch ];
}); });