From 4c2d75f58c8e0133e8148ea1191e52f70d88dc4d Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Fri, 24 Feb 2017 15:52:10 +1100 Subject: [PATCH] R: unmark edgeR and limma as broken --- pkgs/development/r-modules/default.nix | 268 ------------------------- 1 file changed, 268 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 494cffb86f7d..24b1a8df1235 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -801,272 +801,6 @@ 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 - "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 - "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 - "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 @@ -1285,7 +1019,6 @@ 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 @@ -1300,7 +1033,6 @@ 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