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Merge pull request #22817 from jbedo/r

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R: 3.2.4 -> 3.3.2
This commit is contained in:
Domen Kožar
2017-02-27 14:02:13 +01:00
committed by GitHub
parent 7ed28a0b78 4c2d75f58c
commit 4ccb553b70
8 changed files with 6662 additions and 4698 deletions
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pkgs/development/r-modules/default.nix
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@@ -246,7 +246,6 @@ let
BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ];
bnpmr = [ pkgs.gsl_1 ];
BNSP = [ pkgs.gsl_1 ];
cairoDevice = [ pkgs.gtk2.dev ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
Cardinal = [ pkgs.which ];
@@ -643,7 +642,6 @@ let
"rsgcc"
"RSurvey"
"RunuranGUI"
"sdcMicroGUI"
"sharpshootR"
"simba"
"Simile"
@@ -767,7 +765,6 @@ let
"Metab" # broken build
"Crossover" # broken build
"CardinalWorkflows" # broken build
"spoccutils" # depends on broken package spocc
"mapr" # depends on broken package spocc
"vmsbase" # broken build
"vcfR" # broken build
@@ -805,275 +802,6 @@ let
"AnthropMMD" # depends on broken package euroMix
"ilc" # depends on broken package demography
"demography" # broken build
"webbioc" # depends on broken package limma
"davidTiling" # depends on broken package limma
"tilingArray" # depends on broken package limma
"NAPPA" # depends on broken package limma
"NanoStringNorm" # depends on broken package limma
"synapterdata" # depends on broken package limma
"synapter" # depends on broken package limma
"RforProteomics" # depends on broken package limma
"pRolocdata" # depends on broken package limma
"ProCoNA" # depends on broken package limma
"Pbase" # depends on broken package limma
"MSnID" # depends on broken package limma
"msmsEDA" # depends on broken package limma
"MSnbase" # depends on broken package limma
"staRank" # depends on broken package limma
"phenoDist" # depends on broken package limma
"imageHTS" # depends on broken package limma
"Mulder2012" # depends on broken package limma
"HTSanalyzeR" # depends on broken package limma
"gespeR" # depends on broken package limma
"cellHTS2" # depends on broken package limma
"affyPara" # depends on broken package limma
"vsn" # depends on broken package limma
"ttScreening" # depends on broken package limma
"metaX" # depends on broken package limma
"SSPA" # depends on broken package limma
"SQDA" # depends on broken package limma
"ADaCGH2" # depends on broken package limma
"snapCGH" # depends on broken package limma
"Shrinkage" # depends on broken package limma
"SafeQuant" # depends on broken package limma
"RTopper" # depends on broken package limma
"RTCGAToolbox" # depends on broken package limma
"RPPanalyzer" # depends on broken package limma
"Rnits" # depends on broken package limma
"RNAinteractMAPK" # depends on broken package limma
"RNAinteract" # depends on broken package limma
"SimBindProfiles" # depends on broken package limma
"ccTutorial" # depends on broken package limma
"Ringo" # depends on broken package limma
"rCGH" # depends on broken package limma
"qusage" # depends on broken package limma
"qpcrNorm" # depends on broken package limma
"prot2D" # depends on broken package limma
"polyester" # depends on broken package limma
"plmDE" # depends on broken package limma
"phenoTest" # depends on broken package limma
"RANKS" # depends on broken package limma
"PerfMeas" # depends on broken package limma
"pepStat" # depends on broken package limma
"PECA" # depends on broken package limma
"PADOG" # depends on broken package limma
"OGSA" # depends on broken package limma
"nethet" # depends on broken package limma
"lpNet" # depends on broken package limma
"nem" # depends on broken package limma
"monocle" # depends on broken package limma
"MmPalateMiRNA" # depends on broken package limma
"miRtest" # depends on broken package limma
"miRLAB" # depends on broken package limma
"mGSZ" # depends on broken package limma
"MAMA" # depends on broken package limma
"metaMA" # depends on broken package limma
"msd16s" # depends on broken package limma
"metagenomeSeq" # depends on broken package limma
"metabolomics" # depends on broken package limma
"maSigPro" # depends on broken package limma
"timecourse" # depends on broken package limma
"stepNorm" # depends on broken package limma
"RBM" # depends on broken package limma
"saps" # depends on broken package limma
"PharmacoGx" # depends on broken package limma
"piano" # depends on broken package limma
"OLINgui" # depends on broken package limma
"OLIN" # depends on broken package limma
"nnNorm" # depends on broken package limma
"ListerEtAlBSseq" # depends on broken package limma
"compEpiTools" # depends on broken package limma
"methylPipe" # depends on broken package limma
"dyebiasexamples" # depends on broken package limma
"dyebias" # depends on broken package limma
"CluMix" # depends on broken package limma
"HCsnip" # depends on broken package limma
"sigaR" # depends on broken package limma
"plrs" # depends on broken package limma
"CGHregions" # depends on broken package limma
"QDNAseq_mm10" # depends on broken package limma
"QDNAseq_hg19" # depends on broken package limma
"QDNAseq" # depends on broken package limma
"GeneBreak" # depends on broken package limma
"focalCall" # depends on broken package limma
"CGHnormaliter" # depends on broken package limma
"CGHcall" # depends on broken package limma
"CGHbase" # depends on broken package limma
"beta7" # depends on broken package limma
"marray" # depends on broken package limma
"LVSmiRNA" # depends on broken package limma
"lmdme" # depends on broken package limma
"limmaGUI" # depends on broken package limma
"InPAS" # depends on broken package limma
"iChip" # depends on broken package limma
"unifiedWMWqPCR" # depends on broken package limma
"nondetects" # depends on broken package limma
"HTqPCR" # depends on broken package limma
"HD2013SGI" # depends on broken package limma
"vtpnet" # depends on broken package limma
"gwascat" # depends on broken package limma
"gQTLstats" # depends on broken package limma
"GOsummaries" # depends on broken package limma
"yri1kgv" # depends on broken package limma
"hmyriB36" # depends on broken package limma
"cheung2010" # depends on broken package limma
"GGtools" # depends on broken package limma
"GGdata" # depends on broken package limma
"encoDnaseI" # depends on broken package limma
"dsQTL" # depends on broken package limma
"ceuhm3" # depends on broken package limma
"ceu1kgv" # depends on broken package limma
"ceu1kg" # depends on broken package limma
"GGBase" # depends on broken package limma
"GeneSelector" # depends on broken package limma
"GeneSelectMMD" # depends on broken package limma
"gCMAPWeb" # depends on broken package limma
"gCMAP" # depends on broken package limma
"flowBin" # depends on broken package limma
"Fletcher2013a" # depends on broken package limma
"FEM" # depends on broken package limma
"explorase" # depends on broken package limma
"ExiMiR" # depends on broken package limma
"tweeDEseq" # depends on broken package limma
"tRanslatome" # depends on broken package limma
"ToPASeq" # depends on broken package limma
"timeSeq" # depends on broken package limma
"TCGAbiolinks" # depends on broken package limma
"TCC" # depends on broken package limma
"systemPipeR" # depends on broken package limma
"STATegRa" # depends on broken package limma
"ssizeRNA" # depends on broken package limma
"RUVSeq" # depends on broken package limma
"RnaSeqSampleSizeData" # depends on broken package limma
"RnaSeqSampleSize" # depends on broken package limma
"rnaSeqMap" # depends on broken package limma
"ReportingTools" # depends on broken package limma
"QuasiSeq" # depends on broken package limma
"PROPER" # depends on broken package limma
"myTAI" # depends on broken package limma
"msmsTests" # depends on broken package limma
"methylMnM" # depends on broken package limma
"metaseqR" # depends on broken package limma
"MEDIPS" # depends on broken package limma
"manta" # depends on broken package limma
"HTSFilter" # depends on broken package limma
"HTSCluster" # depends on broken package limma
"GSAgm" # depends on broken package limma
"fdrDiscreteNull" # depends on broken package limma
"erccdashboard" # depends on broken package limma
"EnrichmentBrowser" # depends on broken package limma
"edgeRun" # depends on broken package limma
"EDDA" # depends on broken package limma
"RnaSeqTutorial" # depends on broken package limma
"easyRNASeq" # depends on broken package limma
"DEGreport" # depends on broken package limma
"Imetagene" # depends on broken package limma
"metagene" # depends on broken package limma
"DBChIP" # depends on broken package limma
"babel" # depends on broken package limma
"apmsWAPP" # depends on broken package limma
"ampliQueso" # depends on broken package limma
"edgeR" # depends on broken package limma
"MMDiff" # depends on broken package limma
"ChIPQC" # depends on broken package limma
"DiffBind" # depends on broken package limma
"DCGL" # depends on broken package limma
"Prostar" # depends on broken package limma
"DAPAR" # depends on broken package limma
"DAAGbio" # depends on broken package limma
"csaw" # depends on broken package limma
"cp4p" # depends on broken package limma
"coRNAi" # depends on broken package limma
"Cormotif" # depends on broken package limma
"CORM" # depends on broken package limma
"TurboNorm" # depends on broken package limma
"maigesPack" # depends on broken package limma
"convert" # depends on broken package limma
"compcodeR" # depends on broken package limma
"codelink" # depends on broken package limma
"clippda" # depends on broken package limma
"REDseq" # depends on broken package limma
"GUIDEseq" # depends on broken package limma
"ggtut" # depends on broken package limma
"FunciSNP" # depends on broken package limma
"ChIPpeakAnno" # depends on broken package limma
"ChIPComp" # depends on broken package limma
"ChimpHumanBrainData" # depends on broken package limma
"charmData" # depends on broken package limma
"charm" # depends on broken package limma
"cghMCR" # depends on broken package limma
"CCl4" # depends on broken package limma
"casper" # depends on broken package limma
"CancerMutationAnalysis" # depends on broken package limma
"CALIB" # depends on broken package limma
"quantro" # depends on broken package limma
"RnBeads" # depends on broken package limma
"mvoutData" # depends on broken package limma
"MineICA" # depends on broken package limma
"methyAnalysis" # depends on broken package limma
"MAQCsubsetILM" # depends on broken package limma
"MAQCsubset" # depends on broken package limma
"lumiRatIDMapping" # depends on broken package limma
"lumiMouseIDMapping" # depends on broken package limma
"lumiHumanIDMapping" # depends on broken package limma
"lumiBarnes" # depends on broken package limma
"iCheck" # depends on broken package limma
"ffpeExampleData" # depends on broken package limma
"arrayMvout" # depends on broken package limma
"lumi" # depends on broken package limma
"ffpe" # depends on broken package limma
"methylumi" # depends on broken package limma
"shinyMethyl" # depends on broken package limma
"MethylAidData" # depends on broken package limma
"MethylAid" # depends on broken package limma
"IlluminaHumanMethylation450kmanifest" # depends on broken package limma
"skewr" # depends on broken package limma
"wateRmelon" # depends on broken package limma
"missMethyl" # depends on broken package limma
"minfiData" # depends on broken package limma
"IlluminaHumanMethylation450kanno_ilmn12_hg19" # depends on broken package limma
"IlluminaHumanMethylation27kmanifest" # depends on broken package limma
"FlowSorted_DLPFC_450k" # depends on broken package limma
"FlowSorted_Blood_450k" # depends on broken package limma
"ENmix" # depends on broken package limma
"ELMER" # depends on broken package limma
"MEAL" # depends on broken package limma
"DMRcate" # depends on broken package limma
"CopyNumber450kData" # depends on broken package limma
"CopyNumber450k" # depends on broken package limma
"conumee" # depends on broken package limma
"ChAMP" # depends on broken package limma
"minfi" # depends on broken package limma
"regionReport" # depends on broken package limma
"derfinderPlot" # depends on broken package limma
"derfinder" # depends on broken package limma
"bumphunter" # depends on broken package limma
"birta" # depends on broken package limma
"betr" # depends on broken package limma
"beadarrayMSV" # depends on broken package limma
"RobLoxBioC" # depends on broken package limma
"maGUI" # depends on broken package limma
"epigenomix" # depends on broken package limma
"blima" # depends on broken package limma
"BeadArrayUseCases" # depends on broken package limma
"beadarrayFilter" # depends on broken package limma
"beadarrayExampleData" # depends on broken package limma
"beadarray" # depends on broken package limma
"ballgown" # depends on broken package limma
"attract" # depends on broken package limma
"ArrayTools" # depends on broken package limma
"arrayQuality" # depends on broken package limma
"DrugVsDisease" # depends on broken package limma
"ArrayExpress" # depends on broken package limma
"oneChannelGUI" # depends on broken package limma
"affylmGUI" # depends on broken package limma
"AffyExpress" # depends on broken package limma
"AgiMicroRna" # depends on broken package limma
"affycoretools" # depends on broken package limma
"ABSSeq" # depends on broken package limma
"a4" # depends on broken package limma
"a4Base" # depends on broken package limma
"limma" # broken build
"TransView" # broken build
"Starr" # broken build
"SICtools" # broken build
@@ -1162,7 +890,6 @@ let
"tadaatoolbox" # depends on broken package car
"lavaan_shiny" # depends on broken package car
"RcmdrPlugin_GWRM" # depends on broken package car
"TextoMineR" # depends on broken package car
"pcaBootPlot" # depends on broken package car
"ClustGeo" # depends on broken package car
"preproviz" # depends on broken package car
@@ -1279,7 +1006,6 @@ let
"daff" # depends on broken package V8
"dagbag" # build is broken
"DAMisc" # depends on broken package nlopt
"datafsm" # depends on broken package caret
"dbConnect" # broken build
"DBKGrad" # depends on broken package rpanel
#"dcmle" # broken build
@@ -1294,7 +1020,6 @@ let
"DEGraph" # depends on broken package RCytoscape
"destiny" # depends on broken package VIM
"DiagTest3Grp" # depends on broken package nlopt
"diffHic" # depends on broken package edgeR
"difR" # depends on broken package nlopt
"DirichletMultinomial" # Build Is Broken
"DistatisR" # depends on broken package nlopt
@@ -1309,7 +1034,6 @@ let
"easyanova" # depends on broken package nlopt
"ecd" # depends on broken package polynom
"edge" # depends on broken package nlopt
"edgeR" # broken url
"eeptools" # depends on broken package nlopt
"EffectLiteR" # depends on broken package nlopt
"effects" # depends on broken package nlopt
@@ -1368,7 +1092,6 @@ let
"gmatrix" # depends on broken package cudatoolkit
"gMCP" # build is broken
"gmum_r" # broken build
"Goslate" # depends on broken package PythonInR
"GPC" # broken build
"gplm" # depends on broken package nlopt
"gpuR" # depends on GPU-specific header files
@@ -1688,7 +1411,6 @@ let
"sampleSelection" # depends on broken package nlopt
"sapFinder" # depends on broken package rTANDEM
"sdcMicro" # depends on broken package nlopt
"sdcMicroGUI" # depends on broken package nlopt
"SDD" # depends on broken package rpanel
"seeg" # depends on broken package nlopt
"Sejong" # broken build
@@ -1724,7 +1446,6 @@ let
"specmine" # depends on broken package caret
"splm" # depends on broken package car
"spocc" # depends on broken package V8
"spoccutils" # depends on broken spocc
"ssmrob" # depends on broken package nlopt
"StatMethRank" # broken build
"stepp" # depends on broken package nlopt
@@ -1735,7 +1456,6 @@ let
"systemfit" # depends on broken package nlopt
"TcGSA" # depends on broken package nlopt
"TDMR" # depends on broken package nlopt
"TextoMineR" # depends on broken package FactoMineR
"TFBSTools" # depends on broken package DirichletMultinomial
"tigerstats" # depends on broken package nlopt
"TLBC" # depends on broken package caret