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 ];
});