diff options
author | Peter Simons <simons@cryp.to> | 2015-11-25 10:40:20 +0100 |
---|---|---|
committer | Peter Simons <simons@cryp.to> | 2015-11-25 11:39:28 +0100 |
commit | de02462a36cc58ca67226d4985bd3929e6024260 (patch) | |
tree | 459fcd14ababee45adde54f76f4074e2fcaf06a4 /pkgs/development/r-modules | |
parent | bd4297dc4dd061eff5ce3fcc71a8b80e84a4bccc (diff) |
r-modules: update list of broken packages
Diffstat (limited to 'pkgs/development/r-modules')
-rw-r--r-- | pkgs/development/r-modules/default.nix | 58 |
1 files changed, 23 insertions, 35 deletions
diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 0d30dc4c6b81..14be68988f84 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -235,7 +235,6 @@ let 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 ]; @@ -285,7 +284,6 @@ let rapportools = [ pkgs.which ]; rapport = [ pkgs.which ]; rbamtools = [ pkgs.zlib ]; - RCA = [ pkgs.gmp ]; rcdd = [ pkgs.gmp ]; RcppCNPy = [ pkgs.zlib ]; RcppGSL = [ pkgs.gsl ]; @@ -316,7 +314,6 @@ let Rpoppler = [ pkgs.poppler ]; RPostgreSQL = [ pkgs.postgresql ]; RProtoBuf = [ pkgs.protobuf ]; - rpud = [ pkgs.linuxPackages.nvidia_x11 ]; rPython = [ pkgs.python ]; RSclient = [ pkgs.openssl ]; Rserve = [ pkgs.openssl ]; @@ -368,7 +365,6 @@ let qtpaint = [ pkgs.cmake ]; qtbase = [ pkgs.cmake pkgs.perl ]; gmatrix = [ pkgs.cudatoolkit ]; - WideLM = [ pkgs.cudatoolkit ]; RCurl = [ pkgs.curl ]; R2SWF = [ pkgs.pkgconfig ]; rggobi = [ pkgs.pkgconfig ]; @@ -394,10 +390,8 @@ let tcltk2 = [ pkgs.tcl pkgs.tk ]; tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ]; 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 ]; @@ -805,6 +799,7 @@ let "bigmemoryExtras" # broken build "bioassayR" # broken build "Biobase" # broken build + "biobroom" # depends on broken package r-Biobase-2.30.0 "BiocCaseStudies" # broken build "BiocCheck" # broken build "BiocGenerics" # broken build @@ -929,6 +924,7 @@ let "CNORfeeder" # broken build "CNORfuzzy" # depends on broken package nlopt-2.4.2 "CNORode" # broken build + "CNPBayes" # depends on broken package r-BiocGenerics-0.16.1 "CNTools" # broken build "cnvGSA" # broken build "CNVPanelizer" # depends on broken cn.mops-1.15.1 @@ -988,12 +984,14 @@ let "dagbag" # build is broken "dagLogo" # depends on broken package Rsamtools-1.21.8 "DAMisc" # depends on broken package nlopt-2.4.2 + "DAPAR" # depends on broken package r-imputeLCMD-2.0 "DASiR" # broken build "datafsm" # depends on broken package r-caret-6.0-52 "DBChIP" # broken build "dbConnect" # broken build "DBKGrad" # depends on broken package rpanel-1.1-3 "dcGOR" # broken build + "DChIPRep" # depends on broken package r-DESeq2-1.10.0 "dcmle" "ddCt" # broken build "DDD" # depends on broken package r-phytools-0.5-00 @@ -1180,6 +1178,7 @@ let "gdtools" # broken build "gemtc" "GeneAnswers" # broken build + "GeneBreak" # depends on broken package r-CGHbase-1.30.0 "GENE_E" # depends on broken package rhdf5-2.13.1 "GeneExpressionSignature" # depends on broken package annaffy-1.41.1 "genefilter" # broken build @@ -1250,6 +1249,7 @@ let "goTools" # build is broken "GPC" # broken build "gplm" # depends on broken package nlopt-2.4.2 + "gpuR" # depends on GPU-specific header files "gputools" # depends on broken package cudatoolkit-5.5.22 "gQTLBase" # depends on broken package r-GenomicFiles-1.5.8 "gQTLstats" # depends on broken package snpStats-1.19.0 @@ -1277,6 +1277,7 @@ let "GSRI" # broken build "GSVA" # broken build "GUIDE" # depends on broken package rpanel-1.1-3 + "GUIDEseq" # depends on broken package r-BiocGenerics-0.16.1 "GUIProfiler" # broken build "Guitar" # depends on broken package r-GenomicAlignments-1.5.18 "Gviz" # depends on broken package Rsamtools-1.21.8 @@ -1331,15 +1332,16 @@ let "ibh" # build is broken "iBMQ" # broken build "iccbeta" # depends on broken package nlopt-2.4.2 + "iCheck" # depends on broken package r-affy-1.48.0 "IdeoViz" # depends on broken package Rsamtools-1.21.8 "idiogram" # broken build "IdMappingAnalysis" # broken build "IdMappingRetrieval" # broken build "idm" # broken build "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 "imager" # broken build + "Imetagene" # depends on broken package r-metagene-2.2.0 "immer" # depends on broken package r-sirt-1.8-9 "immunoClust" # build is broken "imputeLCMD" # broken build @@ -1456,6 +1458,7 @@ let "mcaGUI" # depends on broken package Rsamtools-1.21.8 "MCRestimate" # build is broken "mdgsa" # build is broken + "MEAL" # depends on broken package r-Biobase-2.30.0 "meboot" # depends on broken package nlopt-2.4.2 "medflex" # depends on broken package r-car-2.1-0 "mediation" # depends on broken package r-lme4-1.1-8 @@ -1477,6 +1480,7 @@ let "MetaDE" # broken build "metagear" # build is broken "metagene" # depends on broken package Rsamtools-1.21.8 + "metagenomeFeatures" # depends on broken package r-Biobase-2.30.0 "metagenomeSeq" # broken build "MetaLandSim" # broken build "metamisc" @@ -1516,6 +1520,7 @@ let "MinimumDistance" # depends on broken package affyio-1.37.0 "MiPP" # broken build "MiRaGE" # broken build + "miRcomp" # depends on broken package r-Biobase-2.30.0 "mirIntegrator" # build is broken "miRLAB" # broken build "miRNAtap" # broken build @@ -1590,7 +1595,9 @@ let "mzID" # broken build "mzR" # build is broken "NanoStringDiff" # broken build + "NanoStringNorm" # depends on broken package r-vsn-3.38.0 "NanoStringQCPro" # build is broken + "NAPPA" # depends on broken package r-vsn-3.38.0 "NarrowPeaks" # broken build "nCal" # depends on broken package nlopt-2.4.2 "ncdfFlow" # build is broken @@ -1699,7 +1706,6 @@ let "pepStat" # broken build "pequod" # depends on broken package nlopt-2.4.2 "PerfMeas" # broken build - "permGPU" # build is broken "PGA" # depends on broken package Rsamtools-1.21.8 "PGSEA" # depends on broken package annaffy-1.41.1 "PharmacoGx" @@ -1752,6 +1758,7 @@ let "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 "proteoQC" # depends on broken package affyio-1.37.0 @@ -1869,6 +1876,7 @@ let "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 @@ -1909,6 +1917,7 @@ let "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 @@ -2004,6 +2013,7 @@ let "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 @@ -2043,6 +2053,7 @@ let "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 @@ -2062,6 +2073,7 @@ let "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 @@ -2072,6 +2084,7 @@ let "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 @@ -2123,6 +2136,7 @@ let "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 @@ -2132,9 +2146,9 @@ let "sybilSBML" # build is broken "synapter" # depends on broken package affyio-1.37.0 "systemfit" # depends on broken package nlopt-2.4.2 - "systemPipeRdata" # broken build "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 @@ -2212,7 +2226,6 @@ let "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 "wikipediatrend" # broken build "wordbankr" # depends on broken package r-RMySQL-0.10.7 "XBSeq" # broken build @@ -2256,10 +2269,6 @@ let preConfigure = "patchShebangs configure"; }); - iFes = old.iFes.overrideDerivation (attrs: { - CUDA_HOME = "${pkgs.cudatoolkit}"; - }); - RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: { patchPhase = "patchShebangs configure"; }); @@ -2339,14 +2348,6 @@ let CUDA_HOME = "${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"; @@ -2354,19 +2355,6 @@ let 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 ]; }); |