mirror of
https://github.com/ilyakooo0/nixpkgs.git
synced 2024-12-27 05:43:50 +03:00
r-modules: update list of broken packages
This commit is contained in:
Peter Simons
parent
bd4297dc4d
commit
de02462a36
@ -235,7 +235,6 @@ let
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cairoDevice = [ pkgs.gtk2 ];
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Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
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Cardinal = [ pkgs.which ];
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CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
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chebpol = [ pkgs.fftw ];
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ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
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cit = [ pkgs.gsl ];
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@ -285,7 +284,6 @@ let
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rapportools = [ pkgs.which ];
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rapport = [ pkgs.which ];
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rbamtools = [ pkgs.zlib ];
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RCA = [ pkgs.gmp ];
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rcdd = [ pkgs.gmp ];
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RcppCNPy = [ pkgs.zlib ];
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RcppGSL = [ pkgs.gsl ];
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@ -316,7 +314,6 @@ let
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Rpoppler = [ pkgs.poppler ];
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RPostgreSQL = [ pkgs.postgresql ];
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RProtoBuf = [ pkgs.protobuf ];
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rpud = [ pkgs.linuxPackages.nvidia_x11 ];
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rPython = [ pkgs.python ];
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RSclient = [ pkgs.openssl ];
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Rserve = [ pkgs.openssl ];
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@ -368,7 +365,6 @@ let
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qtpaint = [ pkgs.cmake ];
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qtbase = [ pkgs.cmake pkgs.perl ];
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gmatrix = [ pkgs.cudatoolkit ];
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WideLM = [ pkgs.cudatoolkit ];
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RCurl = [ pkgs.curl ];
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R2SWF = [ pkgs.pkgconfig ];
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rggobi = [ pkgs.pkgconfig ];
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@ -394,10 +390,8 @@ let
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tcltk2 = [ pkgs.tcl pkgs.tk ];
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tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
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rPython = [ pkgs.which ];
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CARramps = [ pkgs.which pkgs.cudatoolkit ];
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gridGraphics = [ pkgs.which ];
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gputools = [ pkgs.which pkgs.cudatoolkit ];
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rpud = [ pkgs.which pkgs.cudatoolkit ];
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adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
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PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
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dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
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@ -805,6 +799,7 @@ let
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"bigmemoryExtras" # broken build
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"bioassayR" # broken build
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"Biobase" # broken build
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"biobroom" # depends on broken package r-Biobase-2.30.0
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"BiocCaseStudies" # broken build
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"BiocCheck" # broken build
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"BiocGenerics" # broken build
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@ -929,6 +924,7 @@ let
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"CNORfeeder" # broken build
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"CNORfuzzy" # depends on broken package nlopt-2.4.2
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"CNORode" # broken build
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"CNPBayes" # depends on broken package r-BiocGenerics-0.16.1
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"CNTools" # broken build
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"cnvGSA" # broken build
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"CNVPanelizer" # depends on broken cn.mops-1.15.1
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@ -988,12 +984,14 @@ let
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"dagbag" # build is broken
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"dagLogo" # depends on broken package Rsamtools-1.21.8
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"DAMisc" # depends on broken package nlopt-2.4.2
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"DAPAR" # depends on broken package r-imputeLCMD-2.0
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"DASiR" # broken build
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"datafsm" # depends on broken package r-caret-6.0-52
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"DBChIP" # broken build
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"dbConnect" # broken build
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"DBKGrad" # depends on broken package rpanel-1.1-3
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"dcGOR" # broken build
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"DChIPRep" # depends on broken package r-DESeq2-1.10.0
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"dcmle"
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"ddCt" # broken build
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"DDD" # depends on broken package r-phytools-0.5-00
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@ -1180,6 +1178,7 @@ let
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"gdtools" # broken build
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"gemtc"
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"GeneAnswers" # broken build
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"GeneBreak" # depends on broken package r-CGHbase-1.30.0
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"GENE_E" # depends on broken package rhdf5-2.13.1
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"GeneExpressionSignature" # depends on broken package annaffy-1.41.1
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"genefilter" # broken build
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@ -1250,6 +1249,7 @@ let
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"goTools" # build is broken
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"GPC" # broken build
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"gplm" # depends on broken package nlopt-2.4.2
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"gpuR" # depends on GPU-specific header files
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"gputools" # depends on broken package cudatoolkit-5.5.22
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"gQTLBase" # depends on broken package r-GenomicFiles-1.5.8
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"gQTLstats" # depends on broken package snpStats-1.19.0
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@ -1277,6 +1277,7 @@ let
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"GSRI" # broken build
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"GSVA" # broken build
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"GUIDE" # depends on broken package rpanel-1.1-3
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"GUIDEseq" # depends on broken package r-BiocGenerics-0.16.1
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"GUIProfiler" # broken build
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"Guitar" # depends on broken package r-GenomicAlignments-1.5.18
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"Gviz" # depends on broken package Rsamtools-1.21.8
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@ -1331,15 +1332,16 @@ let
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"ibh" # build is broken
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"iBMQ" # broken build
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"iccbeta" # depends on broken package nlopt-2.4.2
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"iCheck" # depends on broken package r-affy-1.48.0
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"IdeoViz" # depends on broken package Rsamtools-1.21.8
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"idiogram" # broken build
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"IdMappingAnalysis" # broken build
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"IdMappingRetrieval" # broken build
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"idm" # broken build
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"ifaTools" # depends on broken package r-OpenMx-2.2.6
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"iFes" # depends on broken package cudatoolkit-5.5.22
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"imageHTS" # depends on broken package Category-2.35.1
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"imager" # broken build
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"Imetagene" # depends on broken package r-metagene-2.2.0
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"immer" # depends on broken package r-sirt-1.8-9
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"immunoClust" # build is broken
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"imputeLCMD" # broken build
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@ -1456,6 +1458,7 @@ let
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"mcaGUI" # depends on broken package Rsamtools-1.21.8
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"MCRestimate" # build is broken
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"mdgsa" # build is broken
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"MEAL" # depends on broken package r-Biobase-2.30.0
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"meboot" # depends on broken package nlopt-2.4.2
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"medflex" # depends on broken package r-car-2.1-0
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"mediation" # depends on broken package r-lme4-1.1-8
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@ -1477,6 +1480,7 @@ let
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"MetaDE" # broken build
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"metagear" # build is broken
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"metagene" # depends on broken package Rsamtools-1.21.8
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"metagenomeFeatures" # depends on broken package r-Biobase-2.30.0
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"metagenomeSeq" # broken build
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"MetaLandSim" # broken build
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"metamisc"
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@ -1516,6 +1520,7 @@ let
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"MinimumDistance" # depends on broken package affyio-1.37.0
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"MiPP" # broken build
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"MiRaGE" # broken build
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"miRcomp" # depends on broken package r-Biobase-2.30.0
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"mirIntegrator" # build is broken
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"miRLAB" # broken build
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"miRNAtap" # broken build
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@ -1590,7 +1595,9 @@ let
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"mzID" # broken build
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"mzR" # build is broken
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"NanoStringDiff" # broken build
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"NanoStringNorm" # depends on broken package r-vsn-3.38.0
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"NanoStringQCPro" # build is broken
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"NAPPA" # depends on broken package r-vsn-3.38.0
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"NarrowPeaks" # broken build
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"nCal" # depends on broken package nlopt-2.4.2
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"ncdfFlow" # build is broken
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@ -1699,7 +1706,6 @@ let
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"pepStat" # broken build
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"pequod" # depends on broken package nlopt-2.4.2
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"PerfMeas" # broken build
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"permGPU" # build is broken
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"PGA" # depends on broken package Rsamtools-1.21.8
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"PGSEA" # depends on broken package annaffy-1.41.1
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"PharmacoGx"
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@ -1752,6 +1758,7 @@ let
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"PROMISE" # broken build
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"PROPER" # broken build
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"propOverlap" # broken build
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"Prostar" # depends on broken package r-imputeLCMD-2.0
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"prot2D" # broken build
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"ProteomicsAnnotationHubData" # depends on broken package r-AnnotationHub-2.1.40
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"proteoQC" # depends on broken package affyio-1.37.0
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@ -1869,6 +1876,7 @@ let
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"RcppOctave" # build is broken
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"RcppRedis" # build is broken
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"rcrypt" # broken build
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"RCy3" # depends on broken package r-graph-1.48.0
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"RCyjs" # broken build
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"RCytoscape" # Build Is Broken
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"RDAVIDWebService" # depends on broken package Category-2.35.1
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@ -1909,6 +1917,7 @@ let
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"rgsepd" # depends on broken package goseq-1.21.1
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"rhdf5" # build is broken
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"rHVDM" # depends on broken package affyio-1.37.0
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"RiboProfiling" # depends on broken package r-BiocGenerics-0.16.1
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"riboSeqR" # broken build
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"Ringo" # depends on broken package affyio-1.37.0
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"RIPSeeker" # depends on broken package Rsamtools-1.21.8
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@ -2004,6 +2013,7 @@ let
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"sapFinder" # depends on broken package rTANDEM-1.9.0
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"saps" # broken build
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"SCAN_UPC" # depends on broken package affyio-1.37.0
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"scholar" # depends on broken package r-rvest-0.3.1
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"ScISI" # depends on broken package apComplex-2.35.0
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"scmamp" # broken build
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"scsR" # broken build
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@ -2043,6 +2053,7 @@ let
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"ShortRead" # depends on broken package Rsamtools-1.21.8
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"Shrinkage" # depends on broken package r-multtest-2.25.2
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"SIBER"
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"SICtools" # depends on broken package r-Biostrings-2.38.2
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"SID" # broken build
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"sigaR" # broken build
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"SigCheck" # broken build
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@ -2062,6 +2073,7 @@ let
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"SimReg" # broken build
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"simulatorZ" # broken build
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"sirt" # depends on broken package nlopt-2.4.2
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"SISPA" # depends on broken package r-GSVA-1.18.0
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"SJava" # broken build
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"sjPlot" # depends on broken package nlopt-2.4.2
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"skewr" # depends on broken package affyio-1.37.0
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@ -2072,6 +2084,7 @@ let
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"snm" # depends on broken package nlopt-2.4.2
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"SNPchip" # depends on broken package affyio-1.37.0
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"snpEnrichment" # depends on broken package snpStats-1.19.0
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"SNPhood" # depends on broken package r-BiocGenerics-0.16.1
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"snplist" # broken build
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"snpStats" # build is broken
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"snpStatsWriter" # depends on broken package snpStats-1.19.0
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@ -2123,6 +2136,7 @@ let
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"stringgaussnet" # build is broken
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"structSSI" # broken build
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"strum" # broken build
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"subSeq" # depends on broken package r-Biobase-2.30.0
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"SummarizedExperiment" # broken build
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"superbiclust" # broken build
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"Surrogate" # depends on broken package nlopt-2.4.2
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@ -2132,9 +2146,9 @@ let
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"sybilSBML" # build is broken
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"synapter" # depends on broken package affyio-1.37.0
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"systemfit" # depends on broken package nlopt-2.4.2
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"systemPipeRdata" # broken build
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"systemPipeR" # depends on broken package AnnotationForge-1.11.3
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"TargetSearch" # depends on broken package mzR-2.3.1
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"TarSeqQC" # depends on broken package r-BiocGenerics-0.16.1
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"TCC" # broken build
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"TCGA2STAT" # broken build
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"TCGAbiolinks" # depends on broken package r-affy-1.47.1
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@ -2212,7 +2226,6 @@ let
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"wfe" # depends on broken package nlopt-2.4.2
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"WGCNA" # build is broken
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"wgsea" # depends on broken package snpStats-1.19.0
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"WideLM" # depends on broken package cudatoolkit-5.5.22
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"wikipediatrend" # broken build
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"wordbankr" # depends on broken package r-RMySQL-0.10.7
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"XBSeq" # broken build
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@ -2256,10 +2269,6 @@ let
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preConfigure = "patchShebangs configure";
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});
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iFes = old.iFes.overrideDerivation (attrs: {
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CUDA_HOME = "${pkgs.cudatoolkit}";
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});
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RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
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patchPhase = "patchShebangs configure";
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});
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@ -2339,14 +2348,6 @@ let
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CUDA_HOME = "${pkgs.cudatoolkit}";
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});
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# It seems that we cannot override meta attributes with overrideDerivation.
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CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
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patches = [ ./patches/CARramps.patch ];
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configureFlags = [
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"--with-cuda-home=${pkgs.cudatoolkit}"
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];
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});
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gmatrix = old.gmatrix.overrideDerivation (attrs: {
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patches = [ ./patches/gmatrix.patch ];
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CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
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@ -2354,19 +2355,6 @@ let
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CUDA_INC_PATH = "${pkgs.cudatoolkit}/include";
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});
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# It seems that we cannot override meta attributes with overrideDerivation.
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rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
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patches = [ ./patches/rpud.patch ];
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CUDA_HOME = "${pkgs.cudatoolkit}";
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});
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WideLM = old.WideLM.overrideDerivation (attrs: {
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patches = [ ./patches/WideLM.patch ];
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configureFlags = [
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"--with-cuda-home=${pkgs.cudatoolkit}"
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];
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});
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EMCluster = old.EMCluster.overrideDerivation (attrs: {
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patches = [ ./patches/EMCluster.patch ];
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});
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