Merge pull request #22817 from jbedo/r

R: 3.2.4 -> 3.3.2

1 files changed, 0 insertions, 280 deletions

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index ec01d65bf37b..ad153a1c382b 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -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