diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 2175ff7e6977..c24d5af7ddfb 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -678,6 +678,7 @@ let "a4" # depends on broken package annaffy-1.41.1 "a4Reporting" # depends on broken package annaffy-1.41.1 "abd" # depends on broken package nlopt-2.4.2 + "Actigraphy" # Build Is Broken "adabag" # depends on broken package nlopt-2.4.2 "ADaCGH2" # depends on broken package tilingArray-1.47.0 "adSplit" # build is broken @@ -699,11 +700,15 @@ let "AgiMicroRna" # depends on broken package affyio-1.37.0 "agRee" # depends on broken package nlopt-2.4.2 "aLFQ" # depends on broken package nlopt-2.4.2 + "AllelicImbalance" # depends on broken package Rsamtools-1.21.8 "alr3" # depends on broken package nlopt-2.4.2 "alr4" # depends on broken package nlopt-2.4.2 + "alsace" # depends on broken nloptr-1.0.4 "altcdfenvs" # depends on broken package affyio-1.37.0 + "ampliQueso" # depends on broken package Rsamtools-1.21.8 "anacor" # depends on broken package nlopt-2.4.2 "annaffy" # build is broken + "annmap" # depends on broken package Rsamtools-1.21.8 "AnnotationForge" # Build Is Broken "AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0 "aods3" # depends on broken package nlopt-2.4.2 @@ -712,6 +717,7 @@ let "ArfimaMLM" # depends on broken package nlopt-2.4.2 "arm" # depends on broken package nlopt-2.4.2 "ArrayExpress" # depends on broken package affyio-1.37.0 + "ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8 "arrayMvout" # depends on broken package affyio-1.37.0 "arrayQualityMetrics" # depends on broken package affyio-1.37.0 "ArrayTools" # depends on broken package affyio-1.37.0 @@ -721,20 +727,31 @@ let "attract" # depends on broken package AnnotationForge-1.11.3 "BACA" # depends on broken package Category-2.35.1 "BAGS" # build is broken + "ballgown" # depends on broken package Rsamtools-1.21.8 + "bamsignals" # build is broken "bartMachine" # depends on broken package nlopt-2.4.2 + "Basic4Cseq" # depends on broken package Rsamtools-1.21.8 "bayesDem" # depends on broken package nlopt-2.4.2 "bayesLife" # depends on broken package nlopt-2.4.2 "bayesPop" # depends on broken package nlopt-2.4.2 "Bayesthresh" # depends on broken package nlopt-2.4.2 "BBRecapture" # depends on broken package nlopt-2.4.2 "BCA" # depends on broken package nlopt-2.4.2 + "BEAT" # depends on broken package Rsamtools-1.21.8 "bgmm" # depends on broken package nlopt-2.4.2 "bgx" # depends on broken package affyio-1.37.0 "BIFIEsurvey" # depends on broken package nlopt-2.4.2 + "bigGP" # build is broken "BiGGR" # depends on broken package rsbml-2.27.0 "BiodiversityR" # depends on broken package nlopt-2.4.2 + "biomvRCNS" # depends on broken package Rsamtools-1.21.8 + "biotools" # depends on broken package rpanel-1.1-3 + "biovizBase" # depends on broken package Rsamtools-1.21.8 "birte" # build is broken "BiSEp" # depends on broken package GOSemSim-1.27.3 + "BiSeq" # depends on broken package Rsamtools-1.21.8 + "BitSeq" # depends on broken package Rsamtools-1.21.8 + "BLCOP" # depends on broken package Rsymphony-0.1-20 "blmeco" # depends on broken package nlopt-2.4.2 "blme" # depends on broken package nlopt-2.4.2 "bmd" # depends on broken package nlopt-2.4.2 @@ -743,295 +760,90 @@ let "boss" # depends on broken package nlopt-2.4.2 "BradleyTerry2" # depends on broken package nlopt-2.4.2 "BRugs" # build is broken + "BSgenome" # depends on broken package Rsamtools-1.21.8 + "bumphunter" # depends on broken package Rsamtools-1.21.8 "CADFtest" # depends on broken package nlopt-2.4.2 "CAFE" # depends on broken package affyio-1.37.0 + "CAGEr" # depends on broken package Rsamtools-1.21.8 "cAIC4" # depends on broken package nlopt-2.4.2 + "CAMERA" # depends on broken package mzR-2.3.1 "canceR" # depends on broken package Category-2.35.1 "candisc" # depends on broken package nlopt-2.4.2 "carcass" # depends on broken package nlopt-2.4.2 "car" # depends on broken package nlopt-2.4.2 "caret" # depends on broken package nlopt-2.4.2 "caretEnsemble" # depends on broken package nlopt-2.4.2 + "CARrampsOcl" # depends on broken package OpenCL-0.1-3 + "casper" # depends on broken package Rsamtools-1.21.8 "Category" # Build Is Broken "categoryCompare" # depends on broken package Category-2.35.1 "CCpop" # depends on broken package nlopt-2.4.2 "cellHTS2" # depends on broken package Category-2.35.1 + "CexoR" # depends on broken package Rsamtools-1.21.8 "ChainLadder" # depends on broken package nlopt-2.4.2 "ChAMP" # depends on broken package affyio-1.37.0 "charm" # depends on broken package affyio-1.37.0 "ChemmineR" # Build Is Broken + "chimera" # depends on broken package Rsamtools-1.21.8 "chipenrich" # build is broken + "chipPCR" # depends on broken nloptr-1.0.4 + "ChIPpeakAnno" # depends on broken package Rsamtools-1.21.8 "ChIPQC" # depends on broken package AnnotationForge-1.11.3 + "ChIPseeker" # depends on broken package Rsamtools-1.21.8 + "chipseq" # depends on broken package Rsamtools-1.21.8 + "ChIPseqR" # depends on broken package Rsamtools-1.21.8 + "ChIPsim" # depends on broken package Rsamtools-1.21.8 "ChIPXpress" # depends on broken package affyio-1.37.0 + "ChromHeatMap" # depends on broken package Rsamtools-1.21.8 + "cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8 "climwin" # depends on broken package nlopt-2.4.2 + "clipper" # depends on broken package Rsamtools-1.21.8 "CLME" # depends on broken package nlopt-2.4.2 "clpAPI" # build is broken "clusterPower" # depends on broken package nlopt-2.4.2 - "Actigraphy" # Build Is Broken - "Crossover" # Build Is Broken - "FunctionalNetworks" # Build Is Broken - "HiPLARM" # Build Is Broken - "HierO" # Build Is Broken - "KEGGprofile" # Build Is Broken - "MigClim" # Build Is Broken - "ROracle" # Build Is Broken - "Rcplex" # Build Is Broken - "RcppAPT" # Build Is Broken - "RnaSeqSampleSize" # Build Is Broken - "Rsamtools" # Build Is Broken - "SeqGrapheR" # Build Is Broken - "bamsignals" # build is broken - "bigGP" # build is broken - "cudaBayesreg" # build is broken - "dagbag" # build is broken - "gMCP" # build is broken - "h5" # build is broken - "lefse" # build is broken - "metaMix" # build is broken - "mirIntegrator" # build is broken - "pathview" # build is broken - "pcaL1" # build is broken - "permGPU" # build is broken - "pmclust" # build is broken - "qtbase" # build is broken - "rDEA" # build is broken - "rJPSGCS" # build is broken - "rLindo" # build is broken - "seqCNA" # build is broken - "sybilSBML" # build is broken - "AllelicImbalance" # depends on broken package Rsamtools-1.21.8 - "ArrayExpressHTS" # depends on broken package Rsamtools-1.21.8 - "BEAT" # depends on broken package Rsamtools-1.21.8 - "BLCOP" # depends on broken package Rsymphony-0.1-20 - "BSgenome" # depends on broken package Rsamtools-1.21.8 - "Basic4Cseq" # depends on broken package Rsamtools-1.21.8 - "BiSeq" # depends on broken package Rsamtools-1.21.8 - "BitSeq" # depends on broken package Rsamtools-1.21.8 - "CAGEr" # depends on broken package Rsamtools-1.21.8 - "CAMERA" # depends on broken package mzR-2.3.1 - "CARrampsOcl" # depends on broken package OpenCL-0.1-3 - "CNEr" # depends on broken package Rsamtools-1.21.8 - "CNVrd2" # depends on broken package Rsamtools-1.21.8 - "CODEX" # depends on broken package Rsamtools-1.21.8 - "CRISPRseek" # depends on broken package Rsamtools-1.21.8 - "CexoR" # depends on broken package Rsamtools-1.21.8 - "ChIPpeakAnno" # depends on broken package Rsamtools-1.21.8 - "ChIPseeker" # depends on broken package Rsamtools-1.21.8 - "ChIPseqR" # depends on broken package Rsamtools-1.21.8 - "ChIPsim" # depends on broken package Rsamtools-1.21.8 - "ChromHeatMap" # depends on broken package Rsamtools-1.21.8 - "CopyNumber450k" # depends on broken package Rsamtools-1.21.8 - "CopywriteR" # depends on broken package Rsamtools-1.21.8 - "CoverageView" # depends on broken package Rsamtools-1.21.8 - "DBKGrad" # depends on broken package rpanel-1.1-3 - "DEXSeq" # depends on broken package Rsamtools-1.21.8 - "DMRcate" # depends on broken package Rsamtools-1.21.8 - "DMRforPairs" # depends on broken package Rsamtools-1.21.8 - "DOQTL" # depends on broken package Rsamtools-1.21.8 - "EDASeq" # depends on broken package Rsamtools-1.21.8 - "ELMER" # depends on broken package Rsamtools-1.21.8 - "ExomeDepth" # depends on broken package Rsamtools-1.21.8 - "FourCSeq" # depends on broken package Rsamtools-1.21.8 - "GOGANPA" # depends on broken package WGCNA-1.47 - "GOTHiC" # depends on broken package Rsamtools-1.21.8 - "GUIDE" # depends on broken package rpanel-1.1-3 - "GenoView" # depends on broken package Rsamtools-1.21.8 - "GenomicAlignments" # depends on broken package Rsamtools-1.21.8 - "GenomicFeatures" # depends on broken package Rsamtools-1.21.8 - "GenomicFiles" # depends on broken package Rsamtools-1.21.8 - "GenomicInteractions" # depends on broken package Rsamtools-1.21.8 - "GoogleGenomics" # depends on broken package Rsamtools-1.21.8 - "GreyListChIP" # depends on broken package Rsamtools-1.21.8 - "Gviz" # depends on broken package Rsamtools-1.21.8 - "HTSeqGenie" # depends on broken package Rsamtools-1.21.8 - "HiTC" # depends on broken package Rsamtools-1.21.8 - "IdeoViz" # depends on broken package Rsamtools-1.21.8 - "InPAS" # depends on broken package Rsamtools-1.21.8 - "LinRegInteractive" # depends on broken package rpanel-1.1-3 - "LowMACA" # depends on broken package Rsamtools-1.21.8 - "M3D" # depends on broken package Rsamtools-1.21.8 - "MEDIPS" # depends on broken package Rsamtools-1.21.8 - "MSeasy" # depends on broken package mzR-2.3.1 - "MSeasyTkGUI" # depends on broken package mzR-2.3.1 - "Metab" # depends on broken package mzR-2.3.1 - "MethylAid" # depends on broken package Rsamtools-1.21.8 - "MethylSeekR" # depends on broken package Rsamtools-1.21.8 - "MotIV" # depends on broken package Rsamtools-1.21.8 - "MotifDb" # depends on broken package Rsamtools-1.21.8 - "OTUbase" # depends on broken package Rsamtools-1.21.8 - "OrganismDbi" # depends on broken package Rsamtools-1.21.8 - "PGA" # depends on broken package Rsamtools-1.21.8 - "PICS" # depends on broken package Rsamtools-1.21.8 - "PING" # depends on broken package Rsamtools-1.21.8 - "Pviz" # depends on broken package Rsamtools-1.21.8 - "QDNAseq" # depends on broken package Rsamtools-1.21.8 - "QuasR" # depends on broken package Rsamtools-1.21.8 - "R3CPET" # depends on broken package Rsamtools-1.21.8 - "R453Plus1Toolbox" # depends on broken package Rsamtools-1.21.8 - "RAPIDR" # depends on broken package Rsamtools-1.21.8 - "REBayes" # depends on broken package Rmosek-1.2.5.1 - "REDseq" # depends on broken package Rsamtools-1.21.8 - "RIPSeeker" # depends on broken package Rsamtools-1.21.8 - "RMassBank" # depends on broken package mzR-2.3.1 - "RNAprobR" # depends on broken package Rsamtools-1.21.8 - "ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20 - "RSVSim" # depends on broken package Rsamtools-1.21.8 - "RUVSeq" # depends on broken package Rsamtools-1.21.8 - "RVideoPoker" # depends on broken package rpanel-1.1-3 - "RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76 - "Rariant" # depends on broken package Rsamtools-1.21.8 - "Rcade" # depends on broken package Rsamtools-1.21.8 - "ReQON" # depends on broken package Rsamtools-1.21.8 - "RnBeads" # depends on broken package Rsamtools-1.21.8 - "Rolexa" # depends on broken package Rsamtools-1.21.8 - "Rqc" # depends on broken package Rsamtools-1.21.8 - "SDD" # depends on broken package rpanel-1.1-3 - "SGSeq" # depends on broken package Rsamtools-1.21.8 - "SIMAT" # depends on broken package mzR-2.3.1 - "SNPtools" # depends on broken package Rsamtools-1.21.8 - "SVM2CRM" # depends on broken package Rsamtools-1.21.8 - "SeqArray" # depends on broken package Rsamtools-1.21.8 - "SeqVarTools" # depends on broken package Rsamtools-1.21.8 - "ShortRead" # depends on broken package Rsamtools-1.21.8 - "SimRAD" # depends on broken package Rsamtools-1.21.8 - "SomaticSignatures" # depends on broken package Rsamtools-1.21.8 - "SplicingGraphs" # depends on broken package Rsamtools-1.21.8 - "TEQC" # depends on broken package Rsamtools-1.21.8 - "TIN" # depends on broken package WGCNA-1.47 - "TargetSearch" # depends on broken package mzR-2.3.1 - "TitanCNA" # depends on broken package Rsamtools-1.21.8 - "ToPASeq" # depends on broken package Rsamtools-1.21.8 - "TransView" # depends on broken package Rsamtools-1.21.8 - "VariantAnnotation" # depends on broken package Rsamtools-1.21.8 - "VariantFiltering" # depends on broken package Rsamtools-1.21.8 - "VariantTools" # depends on broken package Rsamtools-1.21.8 - "ampliQueso" # depends on broken package Rsamtools-1.21.8 - "annmap" # depends on broken package Rsamtools-1.21.8 - "ballgown" # depends on broken package Rsamtools-1.21.8 - "biomvRCNS" # depends on broken package Rsamtools-1.21.8 - "biotools" # depends on broken package rpanel-1.1-3 - "biovizBase" # depends on broken package Rsamtools-1.21.8 - "bumphunter" # depends on broken package Rsamtools-1.21.8 - "casper" # depends on broken package Rsamtools-1.21.8 - "chimera" # depends on broken package Rsamtools-1.21.8 - "chipseq" # depends on broken package Rsamtools-1.21.8 - "cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8 - "clipper" # depends on broken package Rsamtools-1.21.8 - "cn_mops" # depends on broken package Rsamtools-1.21.8 - "coMET" # depends on broken package Rsamtools-1.21.8 - "cobindR" # depends on broken package Rsamtools-1.21.8 - "conumee" # depends on broken package Rsamtools-1.21.8 - "cosmiq" # depends on broken package mzR-2.3.1 - "cpvSNP" # depends on broken package Rsamtools-1.21.8 - "csaw" # depends on broken package Rsamtools-1.21.8 - "cummeRbund" # depends on broken package Rsamtools-1.21.8 - "customProDB" # depends on broken package Rsamtools-1.21.8 - "daff" # depends on broken package V8-0.6 - "dagLogo" # depends on broken package Rsamtools-1.21.8 - "deepSNV" # depends on broken package Rsamtools-1.21.8 - "derfinder" # depends on broken package Rsamtools-1.21.8 - "derfinderPlot" # depends on broken package Rsamtools-1.21.8 - "easyRNASeq" # depends on broken package Rsamtools-1.21.8 - "ensemblVEP" # depends on broken package Rsamtools-1.21.8 - "epigenomix" # depends on broken package Rsamtools-1.21.8 - "epivizr" # depends on broken package Rsamtools-1.21.8 - "erpR" # depends on broken package rpanel-1.1-3 - "exomeCopy" # depends on broken package Rsamtools-1.21.8 - "exomePeak" # depends on broken package Rsamtools-1.21.8 - "fPortfolio" # depends on broken package Rsymphony-0.1-20 - "fastLiquidAssociation" # depends on broken package LiquidAssociation-1.23.0 - "flagme" # depends on broken package mzR-2.3.1 - "gamlss_demo" # depends on broken package rpanel-1.1-3 - "genomation" # depends on broken package Rsamtools-1.21.8 - "geojsonio" # depends on broken package V8-0.6 - "ggbio" # depends on broken package Rsamtools-1.21.8 - "girafe" # depends on broken package Rsamtools-1.21.8 - "gmapR" # depends on broken package Rsamtools-1.21.8 - "groHMM" # depends on broken package Rsamtools-1.21.8 - "hiAnnotator" # depends on broken package Rsamtools-1.21.8 - "hiReadsProcessor" # depends on broken package Rsamtools-1.21.8 - "htSeqTools" # depends on broken package Rsamtools-1.21.8 - "intansv" # depends on broken package Rsamtools-1.21.8 - "js" # depends on broken package V8-0.6 - "lawn" # depends on broken package V8-0.6 - "lgcp" # depends on broken package rpanel-1.1-3 - "mcaGUI" # depends on broken package Rsamtools-1.21.8 - "metaMS" # depends on broken package mzR-2.3.1 - "metaSEM" # depends on broken package OpenMx-2.2.4 - "metagene" # depends on broken package Rsamtools-1.21.8 - "methylPipe" # depends on broken package Rsamtools-1.21.8 - "methylumi" # depends on broken package Rsamtools-1.21.8 - "minfi" # depends on broken package Rsamtools-1.21.8 - "minimist" # depends on broken package V8-0.6 - "missMethyl" # depends on broken package Rsamtools-1.21.8 - "motifRG" # depends on broken package Rsamtools-1.21.8 - "motifStack" # depends on broken package Rsamtools-1.21.8 - "mygene" # depends on broken package Rsamtools-1.21.8 - "nettools" # depends on broken package WGCNA-1.47 - "nucleR" # depends on broken package Rsamtools-1.21.8 - "optBiomarker" # depends on broken package rpanel-1.1-3 - "ora" # depends on broken package ROracle-1.1-12 - "pbdBASE" # depends on broken package pbdSLAP-0.2-0 - "pbdDEMO" # depends on broken package pbdSLAP-0.2-0 - "pbdDMAT" # depends on broken package pbdSLAP-0.2-0 - "podkat" # depends on broken package Rsamtools-1.21.8 - "proBAMr" # depends on broken package Rsamtools-1.21.8 - "qpgraph" # depends on broken package Rsamtools-1.21.8 - "qrqc" # depends on broken package Rsamtools-1.21.8 - "qtpaint" # depends on broken package qtbase-1.0.9 - "qtutils" # depends on broken package qtbase-1.0.9 - "quantro" # depends on broken package Rsamtools-1.21.8 - "r3Cseq" # depends on broken package Rsamtools-1.21.8 - "rGADEM" # depends on broken package Rsamtools-1.21.8 - "rSFFreader" # depends on broken package Rsamtools-1.21.8 - "rTRMui" # depends on broken package Rsamtools-1.21.8 - "regionReport" # depends on broken package Rsamtools-1.21.8 - "regioneR" # depends on broken package Rsamtools-1.21.8 - "repijson" # depends on broken package V8-0.6 - "rfPred" # depends on broken package Rsamtools-1.21.8 - "rgbif" # depends on broken package V8-0.6 - "rgpui" # depends on broken package rgp-0.4-1 - "rjade" # depends on broken package V8-0.6 - "rnaSeqMap" # depends on broken package Rsamtools-1.21.8 - "roar" # depends on broken package Rsamtools-1.21.8 - "rtracklayer" # depends on broken package Rsamtools-1.21.8 - "sapFinder" # depends on broken package rTANDEM-1.9.0 - "segmentSeq" # depends on broken package Rsamtools-1.21.8 - "seq2pathway" # depends on broken package WGCNA-1.47 - "seqbias" # depends on broken package Rsamtools-1.21.8 - "seqplots" # depends on broken package Rsamtools-1.21.8 - "shinyMethyl" # depends on broken package Rsamtools-1.21.8 - "shinyTANDEM" # depends on broken package rTANDEM-1.9.0 - "similaRpeak" # depends on broken package Rsamtools-1.21.8 - "soGGi" # depends on broken package Rsamtools-1.21.8 - "soilphysics" # depends on broken package rpanel-1.1-3 - "spliceR" # depends on broken package Rsamtools-1.21.8 - "spocc" # depends on broken package V8-0.6 - "ssviz" # depends on broken package Rsamtools-1.21.8 - "stagePop" # depends on broken package PBSddesolve-1.11.29 - "topologyGSA" # depends on broken package Rsamtools-1.21.8 - "trackViewer" # depends on broken package Rsamtools-1.21.8 - "tracktables" # depends on broken package Rsamtools-1.21.8 - "vmsbase" # depends on broken package PBSmapping-2.69.76 - "wavClusteR" # depends on broken package Rsamtools-1.21.8 - "xcms" # depends on broken package mzR-2.3.1 "clusterProfiler" # depends on broken package GOSemSim-1.27.3 + "clusterSEs" # depends on broken AER-1.2-4 + "ClustGeo" # depends on broken FactoMineR-1.31.3 + "CNEr" # depends on broken package Rsamtools-1.21.8 "cn_farms" # depends on broken package affyio-1.37.0 + "cn_mops" # depends on broken package Rsamtools-1.21.8 "CNORfuzzy" # depends on broken package nlopt-2.4.2 + "CNVPanelizer" # depends on broken cn.mops-1.15.1 + "CNVrd2" # depends on broken package Rsamtools-1.21.8 + "cobindR" # depends on broken package Rsamtools-1.21.8 "CoCiteStats" # Build Is Broken + "CODEX" # depends on broken package Rsamtools-1.21.8 "COHCAP" # build is broken + "colorscience" + "coMET" # depends on broken package Rsamtools-1.21.8 "compEpiTools" # depends on broken package topGO-2.21.0 "CompGO" # depends on broken package Category-2.35.1 "conformal" # depends on broken package nlopt-2.4.2 "ConsensusClusterPlus" # Build Is Broken + "conumee" # depends on broken package Rsamtools-1.21.8 + "CopyNumber450k" # depends on broken package Rsamtools-1.21.8 + "CopywriteR" # depends on broken package Rsamtools-1.21.8 "corHMM" # depends on broken package nlopt-2.4.2 "Cormotif" # depends on broken package affyio-1.37.0 "coRNAi" # depends on broken package Category-2.35.1 + "cosmiq" # depends on broken package mzR-2.3.1 "CosmoPhotoz" # depends on broken package nlopt-2.4.2 + "CoverageView" # depends on broken package Rsamtools-1.21.8 "cplexAPI" # build is broken + "cpvSNP" # depends on broken package Rsamtools-1.21.8 + "CRISPRseek" # depends on broken package Rsamtools-1.21.8 "crlmm" # depends on broken package affyio-1.37.0 + "Crossover" # Build Is Broken "CrypticIBDcheck" # depends on broken package nlopt-2.4.2 + "csaw" # depends on broken package Rsamtools-1.21.8 + "cudaBayesreg" # build is broken + "cummeRbund" # depends on broken package Rsamtools-1.21.8 + "customProDB" # depends on broken package Rsamtools-1.21.8 + "daff" # depends on broken package V8-0.6 + "dagbag" # build is broken + "dagLogo" # depends on broken package Rsamtools-1.21.8 "DAMisc" # depends on broken package nlopt-2.4.2 + "DBKGrad" # depends on broken package rpanel-1.1-3 "Deducer" # depends on broken package nlopt-2.4.2 "DeducerExtras" # depends on broken package nlopt-2.4.2 "DeducerPlugInExample" # depends on broken package nlopt-2.4.2 @@ -1039,8 +851,13 @@ let "DeducerSpatial" # depends on broken package nlopt-2.4.2 "DeducerSurvival" # depends on broken package nlopt-2.4.2 "DeducerText" # depends on broken package nlopt-2.4.2 + "deepSNV" # depends on broken package Rsamtools-1.21.8 "DEGraph" # depends on broken package RCytoscape-1.19.0 "demi" # depends on broken package affyio-1.37.0 + "derfinder" # depends on broken package Rsamtools-1.21.8 + "derfinderPlot" # depends on broken package Rsamtools-1.21.8 + "destiny" # depends on broken package VIM-4.3.0 + "DEXSeq" # depends on broken package Rsamtools-1.21.8 "DiagTest3Grp" # depends on broken package nlopt-2.4.2 "DiffBind" # depends on broken package AnnotationForge-1.11.3 "diffHic" # depends on broken package rhdf5-2.13.1 @@ -1049,10 +866,14 @@ let "discSurv" # depends on broken package nlopt-2.4.2 "DistatisR" # depends on broken package nlopt-2.4.2 "diveRsity" # depends on broken package nlopt-2.4.2 + "DMRcate" # depends on broken package Rsamtools-1.21.8 + "DMRforPairs" # depends on broken package Rsamtools-1.21.8 "domainsignatures" # build is broken "doMPI" # build is broken + "DOQTL" # depends on broken package Rsamtools-1.21.8 "DOSE" # depends on broken package GOSemSim-1.27.3 "dpa" # depends on broken package nlopt-2.4.2 + "dpcR" # depends on broken nloptr-1.0.4 "drc" # depends on broken package nlopt-2.4.2 "drfit" # depends on broken package nlopt-2.4.2 "drsmooth" # depends on broken package nlopt-2.4.2 @@ -1060,20 +881,32 @@ let "dualKS" # depends on broken package affyio-1.37.0 "dynlm" # depends on broken package nlopt-2.4.2 "easyanova" # depends on broken package nlopt-2.4.2 + "easyRNASeq" # depends on broken package Rsamtools-1.21.8 + "EDASeq" # depends on broken package Rsamtools-1.21.8 "edge" # depends on broken package nlopt-2.4.2 "eeptools" # depends on broken package nlopt-2.4.2 "EffectLiteR" # depends on broken package nlopt-2.4.2 "effects" # depends on broken package nlopt-2.4.2 "eiR" # depends on broken package ChemmineR-2.21.7 "eisa" # depends on broken package Category-2.35.1 + "ELMER" # depends on broken package Rsamtools-1.21.8 "EMA" # depends on broken package nlopt-2.4.2 "ENmix" # depends on broken package affyio-1.37.0 "EnQuireR" # depends on broken package nlopt-2.4.2 + "EnrichmentBrowser" # depends on broken package r-EDASeq-2.3.2 "ensembldb" # depends on broken package interactiveDisplayBase-1.7.0 + "ensemblVEP" # depends on broken package Rsamtools-1.21.8 + "epigenomix" # depends on broken package Rsamtools-1.21.8 "episplineDensity" # depends on broken package nlopt-2.4.2 + "epivizr" # depends on broken package Rsamtools-1.21.8 "epr" # depends on broken package nlopt-2.4.2 "erer" # depends on broken package nlopt-2.4.2 + "erma" # depends on broken GenomicFiles-1.5.4 + "erpR" # depends on broken package rpanel-1.1-3 "ExiMiR" # depends on broken package affyio-1.37.0 + "exomeCopy" # depends on broken package Rsamtools-1.21.8 + "ExomeDepth" # depends on broken package Rsamtools-1.21.8 + "exomePeak" # depends on broken package Rsamtools-1.21.8 "ExpressionView" # depends on broken package Category-2.35.1 "extRemes" # depends on broken package nlopt-2.4.2 "ez" # depends on broken package nlopt-2.4.2 @@ -1082,10 +915,12 @@ let "Factoshiny" # depends on broken package nlopt-2.4.2 "faoutlier" # depends on broken package nlopt-2.4.2 "farms" # depends on broken package affyio-1.37.0 + "fastLiquidAssociation" # depends on broken package LiquidAssociation-1.23.0 "fastR" # depends on broken package nlopt-2.4.2 "FDRreg" # depends on broken package nlopt-2.4.2 "FEM" # build is broken "ffpe" # depends on broken package affyio-1.37.0 + "flagme" # depends on broken package mzR-2.3.1 "flowDensity" # depends on broken package nlopt-2.4.2 "flowPeaks" # build is broken "flowQ" # build is broken @@ -1094,13 +929,17 @@ let "flowVS" # depends on broken package ncdfFlow-2.15.2 "flowWorkspace" # depends on broken package ncdfFlow-2.15.2 "fmcsR" # depends on broken package ChemmineR-2.21.7 + "FourCSeq" # depends on broken package Rsamtools-1.21.8 + "fPortfolio" # depends on broken package Rsymphony-0.1-20 "freqweights" # depends on broken package nlopt-2.4.2 "frma" # depends on broken package affyio-1.37.0 "frmaTools" # depends on broken package affyio-1.37.0 "fscaret" # depends on broken package nlopt-2.4.2 "FunciSNP" # depends on broken package snpStats-1.19.0 + "FunctionalNetworks" # Build Is Broken "fxregime" # depends on broken package nlopt-2.4.2 "gamclass" # depends on broken package nlopt-2.4.2 + "gamlss_demo" # depends on broken package rpanel-1.1-3 "gamm4" # depends on broken package nlopt-2.4.2 "gCMAP" # depends on broken package Category-2.35.1 "gCMAPWeb" # depends on broken package Category-2.35.1 @@ -1110,20 +949,35 @@ let "GENE_E" # depends on broken package rhdf5-2.13.1 "GeneExpressionSignature" # depends on broken package annaffy-1.41.1 "GeneticTools" # depends on broken package snpStats-1.19.0 + "genomation" # depends on broken package Rsamtools-1.21.8 + "GenomicAlignments" # depends on broken package Rsamtools-1.21.8 + "GenomicFeatures" # depends on broken package Rsamtools-1.21.8 + "GenomicFiles" # depends on broken package Rsamtools-1.21.8 + "GenomicInteractions" # depends on broken package Rsamtools-1.21.8 + "genotypeeval" # depends on broken package r-rtracklayer-1.29.12 + "GenoView" # depends on broken package Rsamtools-1.21.8 "genridge" # depends on broken package nlopt-2.4.2 + "geojsonio" # depends on broken package V8-0.6 "GEOsubmission" # depends on broken package affyio-1.37.0 "gespeR" # depends on broken package Category-2.35.1 "GEWIST" # depends on broken package nlopt-2.4.2 "GGBase" # depends on broken package snpStats-1.19.0 + "ggbio" # depends on broken package Rsamtools-1.21.8 "GGtools" # depends on broken package snpStats-1.19.0 "gimme" # depends on broken package nlopt-2.4.2 + "girafe" # depends on broken package Rsamtools-1.21.8 + "gmapR" # depends on broken package Rsamtools-1.21.8 "gmatrix" # depends on broken package cudatoolkit-5.5.22 + "gMCP" # build is broken "GOFunction" # build is broken + "GOGANPA" # depends on broken package WGCNA-1.47 + "GoogleGenomics" # depends on broken package Rsamtools-1.21.8 "goProfiles" # build is broken "GOSemSim" # Build Is Broken "goseq" # build is broken "GOSim" # depends on broken package topGO-2.21.0 "GOstats" # depends on broken package AnnotationForge-1.11.3 + "GOTHiC" # depends on broken package Rsamtools-1.21.8 "goTools" # build is broken "gplm" # depends on broken package nlopt-2.4.2 "gputools" # depends on broken package cudatoolkit-5.5.22 @@ -1131,24 +985,40 @@ let "granova" # depends on broken package nlopt-2.4.2 "graphicalVAR" # depends on broken package nlopt-2.4.2 "GraphPCA" # depends on broken package nlopt-2.4.2 + "GreyListChIP" # depends on broken package Rsamtools-1.21.8 + "groHMM" # depends on broken package Rsamtools-1.21.8 "GSCA" # depends on broken package rhdf5-2.13.1 + "GUIDE" # depends on broken package rpanel-1.1-3 + "Gviz" # depends on broken package Rsamtools-1.21.8 "GWAF" # depends on broken package nlopt-2.4.2 "gwascat" # depends on broken package interactiveDisplayBase-1.7.0 "h2o" # build is broken + "h5" # build is broken "h5vc" # depends on broken package rhdf5-2.13.1 "Harshlight" # depends on broken package affyio-1.37.0 "hbsae" # depends on broken package nlopt-2.4.2 "heplots" # depends on broken package nlopt-2.4.2 + "hiAnnotator" # depends on broken package Rsamtools-1.21.8 + "hierGWAS" + "HierO" # Build Is Broken + "highriskzone" "HilbertVisGUI" # Build Is Broken + "HiPLARM" # Build Is Broken + "hiReadsProcessor" # depends on broken package Rsamtools-1.21.8 "HistDAWass" # depends on broken package nlopt-2.4.2 + "HiTC" # depends on broken package Rsamtools-1.21.8 "HLMdiag" # depends on broken package nlopt-2.4.2 "HTqPCR" # depends on broken package affyio-1.37.0 "HTSanalyzeR" # depends on broken package Category-2.35.1 + "HTSeqGenie" # depends on broken package Rsamtools-1.21.8 + "htSeqTools" # depends on broken package Rsamtools-1.21.8 "hysteresis" # depends on broken package nlopt-2.4.2 "IATscores" # depends on broken package nlopt-2.4.2 "ibd" # depends on broken package nlopt-2.4.2 "ibh" # build is broken "iccbeta" # depends on broken package nlopt-2.4.2 + "IdeoViz" # depends on broken package Rsamtools-1.21.8 + "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 "immunoClust" # build is broken @@ -1156,9 +1026,15 @@ let "in2extRemes" # depends on broken package nlopt-2.4.2 "inferference" # depends on broken package nlopt-2.4.2 "influence_ME" # depends on broken package nlopt-2.4.2 + "InPAS" # depends on broken package Rsamtools-1.21.8 "inSilicoMerging" # build is broken + "INSPEcT" # depends on broken GenomicFeatures-1.21.13 + "intansv" # depends on broken package Rsamtools-1.21.8 "interactiveDisplayBase" # build is broken "interactiveDisplay" # depends on broken package Category-2.35.1 + "interplot" # depends on broken arm-1.8-5 + "IONiseR" # depends on broken rhdf5-2.13.4 + "iptools" "IsingFit" # depends on broken package nlopt-2.4.2 "IsoGene" # depends on broken package affyio-1.37.0 "IsoGeneGUI" # depends on broken package affyio-1.37.0 @@ -1166,14 +1042,21 @@ let "IVAS" # depends on broken package nlopt-2.4.2 "ivpack" # depends on broken package nlopt-2.4.2 "JAGUAR" # depends on broken package nlopt-2.4.2 + "jetset" "joda" # depends on broken package nlopt-2.4.2 "jomo" # build is broken + "js" # depends on broken package V8-0.6 "KANT" # depends on broken package affyio-1.37.0 "keggorthology" # build is broken + "KEGGprofile" # Build Is Broken + "lawn" # depends on broken package V8-0.6 "learnstats" # depends on broken package nlopt-2.4.2 + "lefse" # build is broken "lessR" # depends on broken package nlopt-2.4.2 "lfe" # build is broken + "lgcp" # depends on broken package rpanel-1.1-3 "limmaGUI" # depends on broken package affyio-1.37.0 + "LinRegInteractive" # depends on broken package rpanel-1.1-3 "LiquidAssociation" # build is broken "lmdme" # build is broken "lme4" # depends on broken package nlopt-2.4.2 @@ -1184,8 +1067,10 @@ let "LogisticDx" # depends on broken package nlopt-2.4.2 "logitT" # depends on broken package affyio-1.37.0 "longpower" # depends on broken package nlopt-2.4.2 + "LowMACA" # depends on broken package Rsamtools-1.21.8 "lumi" # depends on broken package affyio-1.37.0 "LVSmiRNA" # depends on broken package affyio-1.37.0 + "M3D" # depends on broken package Rsamtools-1.21.8 "MAIT" # depends on broken package nlopt-2.4.2 "makecdfenv" # depends on broken package affyio-1.37.0 "mAPKL" # build is broken @@ -1195,27 +1080,46 @@ let "MatrixRider" # depends on broken package DirichletMultinomial-1.11.1 "MaxPro" # depends on broken package nlopt-2.4.2 "mbest" # depends on broken package nlopt-2.4.2 + "MBmca" # depends on broken nloptr-1.0.4 "mBPCR" # depends on broken package affyio-1.37.0 + "mcaGUI" # depends on broken package Rsamtools-1.21.8 "MCRestimate" # build is broken "mdgsa" # build is broken "meboot" # depends on broken package nlopt-2.4.2 + "mediation" # depends on broken package r-lme4-1.1-8 + "MEDIPS" # depends on broken package Rsamtools-1.21.8 "MEDME" # depends on broken package nlopt-2.4.2 "MEMSS" # depends on broken package nlopt-2.4.2 "meshr" # depends on broken package Category-2.35.1 + "Metab" # depends on broken package mzR-2.3.1 "metagear" # build is broken + "metagene" # depends on broken package Rsamtools-1.21.8 + "metaMix" # build is broken + "metaMS" # depends on broken package mzR-2.3.1 "metaplus" # depends on broken package nlopt-2.4.2 + "metaSEM" # depends on broken package OpenMx-2.2.4 "metaseqR" # depends on broken package affyio-1.37.0 "Metatron" # depends on broken package nlopt-2.4.2 "methyAnalysis" # depends on broken package affyio-1.37.0 + "MethylAid" # depends on broken package Rsamtools-1.21.8 + "methylPipe" # depends on broken package Rsamtools-1.21.8 + "MethylSeekR" # depends on broken package Rsamtools-1.21.8 + "methylumi" # depends on broken package Rsamtools-1.21.8 "miceadds" # depends on broken package nlopt-2.4.2 "micEconAids" # depends on broken package nlopt-2.4.2 "micEconCES" # depends on broken package nlopt-2.4.2 "micEconSNQP" # depends on broken package nlopt-2.4.2 "mi" # depends on broken package nlopt-2.4.2 + "MigClim" # Build Is Broken "migui" # depends on broken package nlopt-2.4.2 "MineICA" # depends on broken package AnnotationForge-1.11.3 + "minfi" # depends on broken package Rsamtools-1.21.8 + "minimist" # depends on broken package V8-0.6 "MinimumDistance" # depends on broken package affyio-1.37.0 + "mirIntegrator" # build is broken + "missDeaths" "missMDA" # depends on broken package nlopt-2.4.2 + "missMethyl" # depends on broken package Rsamtools-1.21.8 "mitoODE" # build is broken "mixAK" # depends on broken package nlopt-2.4.2 "mixlm" # depends on broken package nlopt-2.4.2 @@ -1229,6 +1133,12 @@ let "mongolite" # build is broken "monocle" # build is broken "mosaic" # depends on broken package nlopt-2.4.2 + "MotifDb" # depends on broken package Rsamtools-1.21.8 + "motifRG" # depends on broken package Rsamtools-1.21.8 + "motifStack" # depends on broken package Rsamtools-1.21.8 + "MotIV" # depends on broken package Rsamtools-1.21.8 + "MSeasy" # depends on broken package mzR-2.3.1 + "MSeasyTkGUI" # depends on broken package mzR-2.3.1 "MSGFgui" # depends on broken package MSGFplus-1.3.0 "MSGFplus" # Build Is Broken "msmsEDA" # depends on broken package affyio-1.37.0 @@ -1239,15 +1149,19 @@ let "multiDimBio" # depends on broken package nlopt-2.4.2 "MultiRR" # depends on broken package nlopt-2.4.2 "muma" # depends on broken package nlopt-2.4.2 + "munsellinterpol" "mutossGUI" # build is broken "mvGST" # depends on broken package AnnotationForge-1.11.3 "mvinfluence" # depends on broken package nlopt-2.4.2 + "mygene" # depends on broken package Rsamtools-1.21.8 "mzR" # build is broken "NanoStringQCPro" # build is broken "nCal" # depends on broken package nlopt-2.4.2 "ncdfFlow" # build is broken "NCIgraph" # depends on broken package RCytoscape-1.19.0 "netbenchmark" # build is broken + "nettools" # depends on broken package WGCNA-1.47 + "NGScopy" "NHPoisson" # depends on broken package nlopt-2.4.2 "nloptr" # depends on broken package nlopt-2.4.2 "nondetects" # depends on broken package affyio-1.37.0 @@ -1255,6 +1169,7 @@ let "NormqPCR" # depends on broken package affyio-1.37.0 "NORRRM" # build is broken "npIntFactRep" # depends on broken package nlopt-2.4.2 + "nucleR" # depends on broken package Rsamtools-1.21.8 "oligoClasses" # depends on broken package affyio-1.37.0 "oligo" # depends on broken package affyio-1.37.0 "OmicsMarkeR" # depends on broken package nlopt-2.4.2 @@ -1263,7 +1178,11 @@ let "openCyto" # depends on broken package ncdfFlow-2.15.2 "OpenMx" # build is broken "OperaMate" # depends on broken package Category-2.35.1 + "optBiomarker" # depends on broken package rpanel-1.1-3 + "ora" # depends on broken package ROracle-1.1-12 "ordBTL" # depends on broken package nlopt-2.4.2 + "OrganismDbi" # depends on broken package Rsamtools-1.21.8 + "OTUbase" # depends on broken package Rsamtools-1.21.8 "OUwie" # depends on broken package nlopt-2.4.2 "PADOG" # build is broken "pamm" # depends on broken package nlopt-2.4.2 @@ -1273,15 +1192,22 @@ let "papeR" # depends on broken package nlopt-2.4.2 "parboost" # depends on broken package nlopt-2.4.2 "parma" # depends on broken package nlopt-2.4.2 + "Pasha" # depends on broken package GenomicAlignments-1.5.12 "pathClass" # depends on broken package affyio-1.37.0 "pathRender" # build is broken + "pathview" # build is broken "PatternClass" # build is broken "Pbase" # depends on broken package affyio-1.37.0 + "pbdBASE" # depends on broken package pbdSLAP-0.2-0 + "pbdDEMO" # depends on broken package pbdSLAP-0.2-0 + "pbdDMAT" # depends on broken package pbdSLAP-0.2-0 "pbdSLAP" # build is broken "PBImisc" # depends on broken package nlopt-2.4.2 "pbkrtest" # depends on broken package nlopt-2.4.2 "PBSddesolve" # build is broken "PBSmapping" # build is broken + "pcaBootPlot" # depends on broken FactoMineR-1.31.3 + "pcaL1" # build is broken "PCpheno" # depends on broken package Category-2.35.1 "pdInfoBuilder" # depends on broken package affyio-1.37.0 "pdmclass" # build is broken @@ -1289,20 +1215,27 @@ let "pedigreemm" # depends on broken package nlopt-2.4.2 "pedometrics" # depends on broken package nlopt-2.4.2 "pequod" # depends on broken package nlopt-2.4.2 + "permGPU" # build is broken + "PGA" # depends on broken package Rsamtools-1.21.8 "PGSEA" # depends on broken package annaffy-1.41.1 + "PharmacoGx" "phenoDist" # depends on broken package Category-2.35.1 "phenoTest" # depends on broken package Category-2.35.1 "PhenStat" # depends on broken package nlopt-2.4.2 "phia" # depends on broken package nlopt-2.4.2 "phylocurve" # depends on broken package nlopt-2.4.2 "phyloTop" # depends on broken package nlopt-2.4.2 + "PICS" # depends on broken package Rsamtools-1.21.8 + "PING" # depends on broken package Rsamtools-1.21.8 "plateCore" # depends on broken package ncdfFlow-2.15.2 "plier" # depends on broken package affyio-1.37.0 "plsRbeta" # depends on broken package nlopt-2.4.2 "plsRcox" # depends on broken package nlopt-2.4.2 "plsRglm" # depends on broken package nlopt-2.4.2 "plw" # depends on broken package affyio-1.37.0 + "pmclust" # build is broken "pmm" # depends on broken package nlopt-2.4.2 + "podkat" # depends on broken package Rsamtools-1.21.8 "polytomous" # depends on broken package nlopt-2.4.2 "pomp" # depends on broken package nlopt-2.4.2 "ppiPre" # depends on broken package GOSemSim-1.27.3 @@ -1310,28 +1243,51 @@ let "prebs" # depends on broken package affyio-1.37.0 "predictmeans" # depends on broken package nlopt-2.4.2 "prLogistic" # depends on broken package nlopt-2.4.2 + "proBAMr" # depends on broken package Rsamtools-1.21.8 "ProCoNA" # depends on broken package AnnotationForge-1.11.3 "pRoloc" # depends on broken package nlopt-2.4.2 "pRolocGUI" # depends on broken package nlopt-2.4.2 "proteoQC" # depends on broken package affyio-1.37.0 "PSAboot" # depends on broken package nlopt-2.4.2 + "ptw" # depends on broken nloptr-1.0.4 "puma" # depends on broken package affyio-1.37.0 "pvac" # depends on broken package affyio-1.37.0 "pvca" # depends on broken package nlopt-2.4.2 + "Pviz" # depends on broken package Rsamtools-1.21.8 "pwOmics" # depends on broken package interactiveDisplayBase-1.7.0 + "PythonInR" "qcmetrics" # build is broken + "QDNAseq" # depends on broken package Rsamtools-1.21.8 + "QFRM" "qgraph" # depends on broken package nlopt-2.4.2 "qpcrNorm" # depends on broken package affyio-1.37.0 + "qpgraph" # depends on broken package Rsamtools-1.21.8 + "qrqc" # depends on broken package Rsamtools-1.21.8 + "qtbase" # build is broken "qtlnet" # depends on broken package nlopt-2.4.2 + "qtpaint" # depends on broken package qtbase-1.0.9 + "qtutils" # depends on broken package qtbase-1.0.9 "QUALIFIER" # depends on broken package ncdfFlow-2.15.2 "quantification" # depends on broken package nlopt-2.4.2 + "quantro" # depends on broken package Rsamtools-1.21.8 + "QuasR" # depends on broken package Rsamtools-1.21.8 "R2STATS" # depends on broken package nlopt-2.4.2 + "R3CPET" # depends on broken package Rsamtools-1.21.8 + "r3Cseq" # depends on broken package Rsamtools-1.21.8 + "R453Plus1Toolbox" # depends on broken package Rsamtools-1.21.8 "radiant" # depends on broken package nlopt-2.4.2 "raincpc" # build is broken "rainfreq" # build is broken "RamiGO" # depends on broken package RCytoscape-1.19.0 + "RapidPolygonLookup" # depends on broken package PBSmapping-2.69.76 + "RAPIDR" # depends on broken package Rsamtools-1.21.8 + "RareVariantVis" # depends on broken VariantAnnotation-1.15.19 + "Rariant" # depends on broken package Rsamtools-1.21.8 "rasclass" # depends on broken package nlopt-2.4.2 + "RBerkeley" "RbioRXN" # depends on broken package ChemmineR-2.21.7 + "Rcade" # depends on broken package Rsamtools-1.21.8 + "rCGH" # depends on broken package r-affy-1.47.1 "Rchemcpp" # depends on broken package ChemmineR-2.21.7 "Rcmdr" # depends on broken package nlopt-2.4.2 "RcmdrMisc" # depends on broken package nlopt-2.4.2 @@ -1373,27 +1329,47 @@ let "RcmdrPlugin_temis" # depends on broken package nlopt-2.4.2 "RcmdrPlugin_UCA" # depends on broken package nlopt-2.4.2 "Rcpi" # depends on broken package ChemmineR-2.21.7 + "Rcplex" # Build Is Broken + "RcppAPT" # Build Is Broken "RcppOctave" # build is broken "RcppRedis" # build is broken "RCytoscape" # Build Is Broken "RDAVIDWebService" # depends on broken package Category-2.35.1 "rdd" # depends on broken package nlopt-2.4.2 + "rddtools" # depends on broken package r-AER-1.2-4 + "rDEA" # build is broken "RDieHarder" # build is broken "ReactomePA" # depends on broken package GOSemSim-1.27.3 "ReadqPCR" # depends on broken package affyio-1.37.0 + "REBayes" # depends on broken package Rmosek-1.2.5.1 + "REDseq" # depends on broken package Rsamtools-1.21.8 "referenceIntervals" # depends on broken package nlopt-2.4.2 "RefNet" # depends on broken package interactiveDisplayBase-1.7.0 "RefPlus" # depends on broken package affyio-1.37.0 "refund" # depends on broken package nlopt-2.4.2 + "regioneR" # depends on broken package Rsamtools-1.21.8 + "regionReport" # depends on broken package Rsamtools-1.21.8 + "repijson" # depends on broken package V8-0.6 "Repitools" # depends on broken package affyio-1.37.0 "ReportingTools" # depends on broken package Category-2.35.1 + "ReQON" # depends on broken package Rsamtools-1.21.8 "REST" # depends on broken package nlopt-2.4.2 + "rfPred" # depends on broken package Rsamtools-1.21.8 + "rGADEM" # depends on broken package Rsamtools-1.21.8 + "rgbif" # depends on broken package V8-0.6 + "Rgnuplot" "rgp" # build is broken + "rgpui" # depends on broken package rgp-0.4-1 "rgsepd" # depends on broken package goseq-1.21.1 "rhdf5" # build is broken "rHVDM" # depends on broken package affyio-1.37.0 "Ringo" # depends on broken package affyio-1.37.0 + "RIPSeeker" # depends on broken package Rsamtools-1.21.8 "Risa" # depends on broken package affyio-1.37.0 + "rjade" # depends on broken package V8-0.6 + "rJPSGCS" # build is broken + "rLindo" # build is broken + "RMassBank" # depends on broken package mzR-2.3.1 "rMAT" # build is broken "rmgarch" # depends on broken package nlopt-2.4.2 "rminer" # depends on broken package nlopt-2.4.2 @@ -1401,37 +1377,56 @@ let "Rmosek" # build is broken "RNAinteract" # depends on broken package Category-2.35.1 "RNAither" # depends on broken package nlopt-2.4.2 + "RNAprobR" # depends on broken package Rsamtools-1.21.8 + "rnaSeqMap" # depends on broken package Rsamtools-1.21.8 + "RnaSeqSampleSize" # Build Is Broken "RnavGraph" # build is broken + "RnBeads" # depends on broken package Rsamtools-1.21.8 "Rnits" # depends on broken package affyio-1.37.0 + "roar" # depends on broken package Rsamtools-1.21.8 "RobLoxBioC" # depends on broken package affyio-1.37.0 "robustlmm" # depends on broken package nlopt-2.4.2 "rockchalk" # depends on broken package nlopt-2.4.2 + "ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20 + "Rolexa" # depends on broken package Rsamtools-1.21.8 "rols" # build is broken + "ROracle" # Build Is Broken "RPA" # depends on broken package affyio-1.37.0 "rpanel" # build is broken "rpubchem" # depends on broken package nlopt-2.4.2 + "Rqc" # depends on broken package Rsamtools-1.21.8 "RQuantLib" # build is broken "rr" # depends on broken package nlopt-2.4.2 + "Rsamtools" # Build Is Broken "RSAP" # build is broken "rsbml" # build is broken "rscala" # build is broken "RSDA" # depends on broken package nlopt-2.4.2 + "rSFFreader" # depends on broken package Rsamtools-1.21.8 "Rsubread" # Build Is Broken + "RSVSim" # depends on broken package Rsamtools-1.21.8 "Rsymphony" # build is broken "rTANDEM" # build is broken "RTN" # depends on broken package nlopt-2.4.2 + "rtracklayer" # depends on broken package Rsamtools-1.21.8 + "rTRMui" # depends on broken package Rsamtools-1.21.8 "rugarch" # depends on broken package nlopt-2.4.2 "RUVcorr" # build is broken "RUVnormalize" # Build Is Broken + "RUVSeq" # depends on broken package Rsamtools-1.21.8 "RVAideMemoire" # depends on broken package nlopt-2.4.2 "RVFam" # depends on broken package nlopt-2.4.2 + "RVideoPoker" # depends on broken package rpanel-1.1-3 "ryouready" # depends on broken package nlopt-2.4.2 "sampleSelection" # depends on broken package nlopt-2.4.2 + "sapFinder" # depends on broken package rTANDEM-1.9.0 "SCAN_UPC" # depends on broken package affyio-1.37.0 "ScISI" # depends on broken package apComplex-2.35.0 "sdcMicro" # depends on broken package nlopt-2.4.2 "sdcMicroGUI" # depends on broken package nlopt-2.4.2 + "SDD" # depends on broken package rpanel-1.1-3 "seeg" # depends on broken package nlopt-2.4.2 + "segmentSeq" # depends on broken package Rsamtools-1.21.8 "sem" # depends on broken package nlopt-2.4.2 "semdiag" # depends on broken package nlopt-2.4.2 "SemDist" # Build Is Broken @@ -1439,9 +1434,23 @@ let "semPlot" # depends on broken package nlopt-2.4.2 "SensoMineR" # depends on broken package nlopt-2.4.2 "SEPA" # depends on broken package topGO-2.21.0 + "seq2pathway" # depends on broken package WGCNA-1.47 + "SeqArray" # depends on broken package Rsamtools-1.21.8 + "seqbias" # depends on broken package Rsamtools-1.21.8 + "seqCNA" # build is broken + "SeqGrapheR" # Build Is Broken + "seqplots" # depends on broken package Rsamtools-1.21.8 "seqTools" # build is broken + "SeqVarTools" # depends on broken package Rsamtools-1.21.8 + "SGSeq" # depends on broken package Rsamtools-1.21.8 + "shinyMethyl" # depends on broken package Rsamtools-1.21.8 + "shinyTANDEM" # depends on broken package rTANDEM-1.9.0 + "ShortRead" # depends on broken package Rsamtools-1.21.8 + "SIMAT" # depends on broken package mzR-2.3.1 "SimBindProfiles" # depends on broken package affyio-1.37.0 + "similaRpeak" # depends on broken package Rsamtools-1.21.8 "simpleaffy" # depends on broken package affyio-1.37.0 + "SimRAD" # depends on broken package Rsamtools-1.21.8 "sirt" # depends on broken package nlopt-2.4.2 "sjPlot" # depends on broken package nlopt-2.4.2 "skewr" # depends on broken package affyio-1.37.0 @@ -1453,11 +1462,23 @@ let "snpEnrichment" # depends on broken package snpStats-1.19.0 "snpStats" # build is broken "snpStatsWriter" # depends on broken package snpStats-1.19.0 + "SNPtools" # depends on broken package Rsamtools-1.21.8 "SOD" # depends on broken package cudatoolkit-5.5.22 + "soGGi" # depends on broken package Rsamtools-1.21.8 + "soilphysics" # depends on broken package rpanel-1.1-3 + "SomaticSignatures" # depends on broken package Rsamtools-1.21.8 + "SoyNAM" # depends on broken package r-lme4-1.1-8 "spacom" # depends on broken package nlopt-2.4.2 "specificity" # depends on broken package nlopt-2.4.2 + "spliceR" # depends on broken package Rsamtools-1.21.8 + "SplicingGraphs" # depends on broken package Rsamtools-1.21.8 + "spocc" # depends on broken package V8-0.6 + "spoccutils" # depends on broken spocc-0.3.0 + "spsann" # depends on broken package r-pedometrics-0.6-2 "sscore" # depends on broken package affyio-1.37.0 "ssmrob" # depends on broken package nlopt-2.4.2 + "ssviz" # depends on broken package Rsamtools-1.21.8 + "stagePop" # depends on broken package PBSddesolve-1.11.29 "staRank" # depends on broken package Category-2.35.1 "Starr" # depends on broken package affyio-1.37.0 "STATegRa" # depends on broken package affyio-1.37.0 @@ -1465,16 +1486,29 @@ let "stepp" # depends on broken package nlopt-2.4.2 "stringgaussnet" # build is broken "Surrogate" # depends on broken package nlopt-2.4.2 + "SVM2CRM" # depends on broken package Rsamtools-1.21.8 + "sybilSBML" # build is broken "synapter" # depends on broken package affyio-1.37.0 "systemfit" # depends on broken package nlopt-2.4.2 "systemPipeR" # depends on broken package AnnotationForge-1.11.3 + "TargetSearch" # depends on broken package mzR-2.3.1 "TcGSA" # depends on broken package nlopt-2.4.2 "TDMR" # depends on broken package nlopt-2.4.2 + "TEQC" # depends on broken package Rsamtools-1.21.8 "TFBSTools" # depends on broken package DirichletMultinomial-1.11.1 "tigerstats" # depends on broken package nlopt-2.4.2 "tilingArray" # depends on broken package affyio-1.37.0 + "TIN" # depends on broken package WGCNA-1.47 + "TitanCNA" # depends on broken package Rsamtools-1.21.8 + "ToPASeq" # depends on broken package Rsamtools-1.21.8 "topGO" # build is broken + "topologyGSA" # depends on broken package Rsamtools-1.21.8 + "tracktables" # depends on broken package Rsamtools-1.21.8 + "trackViewer" # depends on broken package Rsamtools-1.21.8 + "translateSPSS2R" # depends on broken car-2.0-25 "tRanslatome" # depends on broken package GOSemSim-1.27.3 + "TransView" # depends on broken package Rsamtools-1.21.8 + "traseR" "TriMatch" # depends on broken package nlopt-2.4.2 "TROM" # depends on broken package topGO-2.21.0 "TurboNorm" # depends on broken package affyio-1.37.0 @@ -1482,47 +1516,30 @@ let "userfriendlyscience" # depends on broken package nlopt-2.4.2 "V8" # build is broken "VanillaICE" # depends on broken package affyio-1.37.0 + "variancePartition" # depends on broken package lme4-1.1-8 + "VariantAnnotation" # depends on broken package Rsamtools-1.21.8 + "VariantFiltering" # depends on broken package Rsamtools-1.21.8 + "VariantTools" # depends on broken package Rsamtools-1.21.8 "VIM" # depends on broken package nlopt-2.4.2 "VIMGUI" # depends on broken package nlopt-2.4.2 + "vmsbase" # depends on broken package PBSmapping-2.69.76 "vows" # depends on broken package nlopt-2.4.2 "vsn" # depends on broken package affyio-1.37.0 "vtpnet" # depends on broken package interactiveDisplayBase-1.7.0 "wateRmelon" # depends on broken package affyio-1.37.0 + "wavClusteR" # depends on broken package Rsamtools-1.21.8 "waveTiling" # depends on broken package affyio-1.37.0 "webbioc" # depends on broken package affyio-1.37.0 "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 + "xcms" # depends on broken package mzR-2.3.1 "xergm" # depends on broken package nlopt-2.4.2 "xps" # build is broken "yaqcaffy" # depends on broken package affyio-1.37.0 "ZeligMultilevel" # depends on broken package nlopt-2.4.2 "zetadiv" # depends on broken package nlopt-2.4.2 - "CNVPanelizer" # depends on broken cn.mops-1.15.1 - "ClustGeo" # depends on broken FactoMineR-1.31.3 - "INSPEcT" # depends on broken GenomicFeatures-1.21.13 - "IONiseR" # depends on broken rhdf5-2.13.4 - "MBmca" # depends on broken nloptr-1.0.4 - "RareVariantVis" # depends on broken VariantAnnotation-1.15.19 - "alsace" # depends on broken nloptr-1.0.4 - "chipPCR" # depends on broken nloptr-1.0.4 - "clusterSEs" # depends on broken AER-1.2-4 - "dpcR" # depends on broken nloptr-1.0.4 - "erma" # depends on broken GenomicFiles-1.5.4 - "interplot" # depends on broken arm-1.8-5 - "pcaBootPlot" # depends on broken FactoMineR-1.31.3 - "ptw" # depends on broken nloptr-1.0.4 - "spoccutils" # depends on broken spocc-0.3.0 - "translateSPSS2R" # depends on broken car-2.0-25 - "EnrichmentBrowser" # depends on broken package r-EDASeq-2.3.2 - "SoyNAM" # depends on broken package r-lme4-1.1-8 - "genotypeeval" # depends on broken package r-rtracklayer-1.29.12 - "ifaTools" # depends on broken package r-OpenMx-2.2.6 - "mediation" # depends on broken package r-lme4-1.1-8 - "rCGH" # depends on broken package r-affy-1.47.1 - "rddtools" # depends on broken package r-AER-1.2-4 - "spsann" # depends on broken package r-pedometrics-0.6-2 ]; otherOverrides = old: new: {