diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index f8f6df9df153..7b805d4d58f6 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -362,6 +362,22 @@ let
     XBRL = [ pkgs.zlib pkgs.libxml2 ];
     xml2 = [ pkgs.libxml2 ];
     XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
+    affyPLM = [ pkgs.zlib ];
+    bamsignals = [ pkgs.zlib ];
+    BitSeq = [ pkgs.zlib ];
+    DiffBind = [ pkgs.zlib ];
+    ShortRead = [ pkgs.zlib ];
+    oligo = [ pkgs.zlib ];
+    gmapR = [ pkgs.zlib ];
+    ncdf = [ pkgs.netcdf ];
+    Rsubread = [ pkgs.zlib ];
+    SemiCompRisks = [ pkgs.gsl_1 ];
+    XVector = [ pkgs.zlib ];
+    Rsamtools = [ pkgs.zlib ];
+    rtracklayer = [ pkgs.zlib ];
+    affyio = [ pkgs.zlib ];
+    VariantAnnotation = [ pkgs.zlib ];
+    snpStats = [ pkgs.zlib ];
   };
 
   packagesWithBuildInputs = {
@@ -681,101 +697,72 @@ let
 
   # Packages which cannot be installed due to lack of dependencies or other reasons.
   brokenPackages = [
-    "a4Base" # depends on broken package annaffy-1.41.1
-    "a4Classif" # broken build
+    "ggiraph" # depends on broken package gdtools
+    "rvg" # depends on broken package gdtools
     "a4Core" # broken build
-    "a4" # depends on broken package annaffy-1.41.1
-    "a4Preproc" # broken build
-    "a4Reporting" # depends on broken package annaffy-1.41.1
+    "arrayMvout" # broken build
+    "affyPara" # broken build
+    "bsubtiliscdf" # broken build
+    "ggpmisc" # depends on broken package polynom
+    "mlt_docreg" # depends on broken package polynom
+    "mlt" # depends on broken package polynom
+    "basefun" # depends on broken package polynom
+    "rtable" # depends on broken package ReporteRs
+    "Mediana" # depends on broken package ReporteRs
+    "ReporteRs" # broken build
+    "a4Classif" # broken build
     "ABAEnrichment" # broken build
     "ABarray" # broken build
     "abd" # depends on broken package nlopt-2.4.2
-    "aCGH" # broken build
     "ACME" # broken build
     "Actigraphy" # Build Is Broken
     "adabag" # depends on broken package nlopt-2.4.2
-    "ADaCGH2" # depends on broken package tilingArray-1.47.0
     "adhoc" # broken build
     "adSplit" # build is broken
     "AER" # depends on broken package nlopt-2.4.2
     "afex" # depends on broken package nlopt-2.4.2
     "AffyCompatible" # broken build
-    "affycomp" # broken build
-    "affyContam" # depends on broken package affyio-1.37.0
-    "affycoretools" # depends on broken package affyio-1.37.0
-    "affy" # depends on broken package affyio-1.37.0
-    "AffyExpress" # depends on broken package affyio-1.37.0
-    "affyILM" # depends on broken package affyio-1.37.0
-    "affyio" # build is broken
-    "affylmGUI" # depends on broken package affyio-1.37.0
-    "affyPara" # depends on broken package affyio-1.37.0
-    "affypdnn" # depends on broken package affyio-1.37.0
-    "affyPLM" # depends on broken package affyio-1.37.0
-    "affyQCReport" # depends on broken package affyio-1.37.0
-    "AffyRNADegradation" # depends on broken package affyio-1.37.0
-    "AffyTiling" # depends on broken package affyio-1.37.0
     "AGDEX" # broken build
-    "AgiMicroRna" # depends on broken package affyio-1.37.0
     "agRee" # depends on broken package nlopt-2.4.2
     "AIMS" # broken build
-    "ALDEx2" # broken build
     "aLFQ" # depends on broken package nlopt-2.4.2
     "algstat" # broken build
-    "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
     "AnalysisPageServer" # broken build
     "animation" # broken build
     "anim_plots" # broken build
-    "annaffy" # build is broken
-    "annmap" # depends on broken package Rsamtools-1.21.8
-    "annotate" # broken build
-    "AnnotationDbi" # broken build
-    "AnnotationForge" # Build Is Broken
     "AnnotationFuncs" # broken build
     "AnnotationHubData" # depends on broken package r-AnnotationForge-1.11.19
-    "AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0
     "annotationTools" # broken build
     "anota" # broken build
     "aods3" # depends on broken package nlopt-2.4.2
     "aop" # broken build
     "apaTables" # depends on broken package r-car-2.1-0
     "apComplex" # build is broken
-    "apex" # depends on broken package Biostrings-2.38.2
     "apmsWAPP" # broken build
     "apt" # depends on broken package nlopt-2.4.2
     "ArfimaMLM" # depends on broken package nlopt-2.4.2
     "arm" # depends on broken package nlopt-2.4.2
     "ArrayBin" # broken build
-    "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
-    "ArrayTV" # depends on broken package affyio-1.37.0
     "ARRmNormalization" # Build Is Broken
     "ART" # depends on broken package ar-car-2.1-0
     "ARTool" # depends on broken package nlopt-2.4.2
     "AssetPricing" # broken build
     "AtelieR" # broken build
-    "attract" # depends on broken package AnnotationForge-1.11.3
     "auRoc" # depends on broken package rjags-4-4
     "AutoModel" # depends on broken package r-car-2.1-0
     "babel" # broken build
     "BACA" # depends on broken package Category-2.35.1
     "backShift" # broken build
     "BAGS" # build is broken
-    "ballgown" # depends on broken package Rsamtools-1.21.8
     "bamdit"
     "bamsignals" # build is broken
     "BANOVA"
     "bapred" # depends on broken package r-lme4-1.1-9
     "bartMachine" # depends on broken package nlopt-2.4.2
-    "Basic4Cseq" # depends on broken package Rsamtools-1.21.8
     "bayescount"
     "bayesDem" # depends on broken package nlopt-2.4.2
     "bayesLife" # depends on broken package nlopt-2.4.2
@@ -794,48 +781,37 @@ let
     "BCRANK" # broken build
     "bcrypt"
     "bdynsys" # depends on broken package car-2.1
-    "beadarray" # broken build
     "beadarrayFilter" # broken build
     "beadarrayMSV" # broken build
     "beadarraySNP" # broken build
-    "BEAT" # depends on broken package Rsamtools-1.21.8
     "BEDMatrix" # broken build
     "bedr" # broken build
     "BEST"
     "betr" # broken build
     "bgmm" # depends on broken package nlopt-2.4.2
-    "bgx" # depends on broken package affyio-1.37.0
     "BicARE" # broken build
     "BIFIEsurvey" # depends on broken package nlopt-2.4.2
     "bigGP" # build is broken
     "BiGGR" # depends on broken package rsbml-2.27.0
     "bigmemoryExtras" # broken build
     "bioassayR" # broken build
-    "Biobase" # broken build
     "biobroom" # depends on broken package r-Biobase-2.30.0
     "BiocCaseStudies" # broken build
     "BiocCheck" # broken build
-    "BiocGenerics" # broken build
     "biocGraph" # broken build
     "biocViews" # broken build
     "bioDist" # broken build
     "BiodiversityR" # depends on broken package nlopt-2.4.2
-    "biomaRt" # broken build
     "biomartr" # broken build
     "BioMVCClass" # broken build
-    "biomvRCNS" # depends on broken package Rsamtools-1.21.8
     "BioNet" # broken build
     "BioSeqClass" # broken build
-    "Biostrings" # broken build
     "biosvd" # broken build
     "biotools" # depends on broken package rpanel-1.1-3
-    "biovizBase" # depends on broken package Rsamtools-1.21.8
     "birta" # broken build
     "birte" # build is broken
     "bisectr" # broken build
     "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
     "blima" # broken build
     "blmeco" # depends on broken package nlopt-2.4.2
@@ -857,14 +833,9 @@ let
     "BrowserVizDemo" # broken build
     "brr" # broken build
     "BRugs" # build is broken
-    "BSgenome" # depends on broken package Rsamtools-1.21.8
-    "bsseq" # broken build
     "BTSPAS"
     "BubbleTree" # depends on broken package r-biovizBase-1.17.2
-    "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
     "cancerclass" # broken build
@@ -873,12 +844,10 @@ let
     "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
-    "Cardinal" # broken build
     "caret" # depends on broken package nlopt-2.4.2
     "caretEnsemble" # depends on broken package nlopt-2.4.2
     "caRpools" # broken build
     "CARrampsOcl" # depends on broken package OpenCL-0.1-3
-    "casper" # depends on broken package Rsamtools-1.21.8
     "cate" # broken build
     "Category" # Build Is Broken
     "categoryCompare" # depends on broken package Category-2.35.1
@@ -889,40 +858,25 @@ let
     "cellHTS2" # depends on broken package Category-2.35.1
     "cellHTS" # broken build
     "CellNOptR" # broken build
-    "CexoR" # depends on broken package Rsamtools-1.21.8
     "CGHbase" # broken build
     "CGHcall" # broken build
     "cghMCR" # broken build
     "CGHnormaliter" # broken build
     "CGHregions" # broken build
     "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
     "ChemmineOB" # broken build
     "ChemmineR" # Build Is Broken
-    "chimera" # depends on broken package Rsamtools-1.21.8
     "ChIPComp" # depends on broken package r-Rsamtools-1.21.18
     "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
     "chroGPS" # broken build
     "chromDraw" # broken build
-    "ChromHeatMap" # depends on broken package Rsamtools-1.21.8
     "classGraph" # broken build
     "classify"
     "ClassifyR" # broken build
-    "cleanUpdTSeq" # depends on broken package Rsamtools-1.21.8
     "cleaver" # broken build
-    "clere" # broken build
     "climwin" # depends on broken package nlopt-2.4.2
     "clippda" # broken build
-    "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
@@ -931,77 +885,53 @@ let
     "clusterStab" # broken build
     "ClustGeo" # depends on broken FactoMineR-1.31.3
     "CMA" # broken build
-    "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
     "CNORdt" # broken build
     "CNORfeeder" # broken build
     "CNORfuzzy" # depends on broken package nlopt-2.4.2
     "CNORode" # broken build
     "CNPBayes" # depends on broken package r-BiocGenerics-0.16.1
     "CNTools" # broken build
-    "cnvGSA" # broken build
     "CNVPanelizer" # depends on broken cn.mops-1.15.1
-    "CNVrd2" # depends on broken package Rsamtools-1.21.8
-    "coalescentMCMC" # depends on broken package Biostrings-2.38.2
-    "cobindR" # depends on broken package Rsamtools-1.21.8
     "CoCiteStats" # Build Is Broken
     "codelink" # broken build
-    "CODEX" # depends on broken package Rsamtools-1.21.8
     "coefplot" # build is broken
     "cogena" # broken build
     "COHCAP" # build is broken
     "colorscience"
-    "coMET" # depends on broken package Rsamtools-1.21.8
-    "CommT" # depends on broken package Biostrings-2.38.2
     "compcodeR" # broken build
     "compendiumdb" # broken build
-    "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
     "convert" # broken build
     "convevol" # broken build
     "copa" # broken build
     "CopulaDTA" # depends on broken package r-rstan-2.8.2
-    "CopyNumber450k" # depends on broken package Rsamtools-1.21.8
     "copynumber" # broken build
-    "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
     "covmat" # depends on broken package r-VIM-4.4.1
     "covr" # broken build
     "cp4p" # broken build
     "cpgen" # depends on broken package r-pedigreemm-0.3-3
     "cplexAPI" # build is broken
-    "cpvSNP" # depends on broken package Rsamtools-1.21.8
     "cquad" # depends on broken package car-2.1-1
     "creditr" # broken build
     "CRImage" # broken build
-    "CRISPRseek" # depends on broken package Rsamtools-1.21.8
-    "crlmm" # depends on broken package affyio-1.37.0
     "crmn" # broken build
     "crmPack" # depends on broken package r-rjags-4-4
     "Crossover" # Build Is Broken
     "CrypticIBDcheck" # depends on broken package nlopt-2.4.2
     "CSAR" # broken build
-    "csaw" # depends on broken package Rsamtools-1.21.8
     "ctsem" # depends on broken package r-OpenMx-2.2.6
     "cudaBayesreg" # build is broken
-    "cummeRbund" # depends on broken package Rsamtools-1.21.8
     "curvHDR" # broken build
-    "customProDB" # depends on broken package Rsamtools-1.21.8
     "cycle" # broken build
     "cytofkit" # broken build
     "D2C" # broken build
     "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
     "DAPAR" # depends on broken package r-imputeLCMD-2.0
     "DASiR" # broken build
@@ -1025,23 +955,17 @@ 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
     "DEGreport" # broken build
-    "demi" # depends on broken package affyio-1.37.0
-    "derfinder" # depends on broken package Rsamtools-1.21.8
     "derfinderHelper" # broken build
-    "derfinderPlot" # depends on broken package Rsamtools-1.21.8
     "DescribeDisplay" # build is broken
     "DESeq2" # broken build
     "DESeq" # broken build
     "DESP" # broken build
     "destiny" # depends on broken package VIM-4.3.0
-    "DEXSeq" # depends on broken package Rsamtools-1.21.8
     "dexus" # broken build
     "DFP" # broken build
     "DiagTest3Grp" # depends on broken package nlopt-2.4.2
-    "DiffBind" # depends on broken package AnnotationForge-1.11.3
     "DiffCorr" # broken build
     "diffHic" # depends on broken package rhdf5-2.13.1
     "difR" # depends on broken package nlopt-2.4.2
@@ -1052,34 +976,26 @@ let
     "diveRsity" # depends on broken package nlopt-2.4.2
     "DJL" # depends on broken package r-car-2.1-0
     "DMRcaller" # broken build
-    "DMRcate" # depends on broken package Rsamtools-1.21.8
-    "DMRforPairs" # depends on broken package Rsamtools-1.21.8
     "dnet" # broken build
     "docxtractr" # broken build
     "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
-    "DrugVsDisease" # depends on broken package affyio-1.37.0
     "DSS" # broken build
-    "dualKS" # depends on broken package affyio-1.37.0
     "dupRadar" # depends on broken package r-Rsubread-1.19.5
     "dyebias" # broken build
     "dynlm" # depends on broken package nlopt-2.4.2
     "easyanova" # depends on broken package nlopt-2.4.2
     "EasyMARK"
-    "easyRNASeq" # depends on broken package Rsamtools-1.21.8
     "EBarrays" # broken build
     "EBcoexpress" # broken build
-    "EBImage" # broken build
     "ecd" # depends on broken package r-polynom-1.3-8
     "ecolitk" # broken build
-    "EDASeq" # depends on broken package Rsamtools-1.21.8
     "EDDA" # broken build
     "edge" # depends on broken package nlopt-2.4.2
     "edgeR" # broken build
@@ -1090,20 +1006,14 @@ let
     "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
     "embryogrowth" # broken build
     "emg" # broken build
     "empiricalFDR_DESeq2" # broken build
-    "ENmix" # depends on broken package affyio-1.37.0
     "EnQuireR" # depends on broken package nlopt-2.4.2
     "EnrichedHeatmap" # broken build
     "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
     "epoc" # broken build
     "epr" # depends on broken package nlopt-2.4.2
     "erccdashboard" # broken build
@@ -1115,10 +1025,6 @@ let
     "euroMix" # build is broken
     "evobiR" # broken build
     "evolqg" # broken build
-    "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
@@ -1129,7 +1035,6 @@ let
     "FactoMineR" # depends on broken package nlopt-2.4.2
     "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
     "fastseg" # broken build
@@ -1137,7 +1042,6 @@ let
     "FDRreg" # depends on broken package nlopt-2.4.2
     "FedData" # broken build
     "FEM" # build is broken
-    "ffpe" # depends on broken package affyio-1.37.0
     "FIACH" # broken build
     "FindMyFriends" # broken build
     "FISHalyseR" # broken build
@@ -1162,7 +1066,6 @@ let
     "flowPeaks" # build is broken
     "flowQB" # broken build
     "flowQ" # build is broken
-    "FlowSOM" # depends on broken package ConsensusClusterPlus-1.23.0
     "flowStats" # depends on broken package ncdfFlow-2.15.2
     "flowTrans" # broken build
     "flowType" # broken build
@@ -1172,18 +1075,13 @@ let
     "flowWorkspace" # depends on broken package ncdfFlow-2.15.2
     "fmcsR" # depends on broken package ChemmineR-2.21.7
     "focalCall" # broken build
-    "FourCSeq" # depends on broken package Rsamtools-1.21.8
     "fPortfolio" # depends on broken package Rsymphony-0.1-20
     "fracprolif" # broken build
     "FreeSortR" # broken build
     "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
     "frmqa" # broken build
     "FSA" # depends on broken package car-2.1-1
     "fscaret" # depends on broken package nlopt-2.4.2
-    "fulltext" # broken build
-    "FunciSNP" # depends on broken package snpStats-1.19.0
     "FunctionalNetworks" # Build Is Broken
     "funcy" # depends on broken package r-car-2.1-0
     "fxregime" # depends on broken package nlopt-2.4.2
@@ -1198,15 +1096,12 @@ let
     "gCMAP" # depends on broken package Category-2.35.1
     "gCMAPWeb" # depends on broken package Category-2.35.1
     "gcmr" # depends on broken package nlopt-2.4.2
-    "gcrma" # depends on broken package affyio-1.37.0
     "GDAtools" # depends on broken package nlopt-2.4.2
     "gdtools" # broken build
     "gemtc"
     "GeneAnswers" # broken build
     "GeneBreak" # depends on broken package r-CGHbase-1.30.0
     "GENE_E" # depends on broken package rhdf5-2.13.1
-    "GeneExpressionSignature" # depends on broken package annaffy-1.41.1
-    "genefilter" # broken build
     "genefu" # broken build
     "GeneMeta" # broken build
     "GeneNetworkBuilder" # broken build
@@ -1218,83 +1113,59 @@ let
     "GeneSelector" # broken build
     "GENESIS" # broken build
     "geNetClassifier" # broken build
-    "GeneticTools" # depends on broken package snpStats-1.19.0
-    "genomation" # depends on broken package Rsamtools-1.21.8
     "GenomeGraphs" # broken build
-    "GenomeInfoDb" # broken build
     "genomeIntervals" # broken build
     "genomes" # broken build
-    "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
-    "GenomicRanges" # broken build
     "GenomicTuples" # broken build
     "Genominator" # broken build
     "genoset" # broken build
     "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
     "GEOmetadb" # broken build
     "geomorph" # broken build
-    "GEOquery" # broken build
     "GEOsearch" # broken build
-    "GEOsubmission" # depends on broken package affyio-1.37.0
     "GERGM"
     "gespeR" # depends on broken package Category-2.35.1
     "GEWIST" # depends on broken package nlopt-2.4.2
     "GExMap" # broken build
     "gfcanalysis" # broken build
-    "GGBase" # depends on broken package snpStats-1.19.0
-    "ggbio" # depends on broken package Rsamtools-1.21.8
     "ggtern" # build is broken
-    "GGtools" # depends on broken package snpStats-1.19.0
     "ggtree" # broken build
     "gimme" # depends on broken package nlopt-2.4.2
-    "girafe" # depends on broken package Rsamtools-1.21.8
     "gitter" # broken build
     "GlobalAncova" # broken build
     "globaltest" # broken build
-    "gmapR" # depends on broken package Rsamtools-1.21.8
     "gmatrix" # depends on broken package cudatoolkit-5.5.22
     "gMCP" # build is broken
     "gmum_r" # broken build
     "GOexpress" # broken build
     "GOFunction" # build is broken
     "GOGANPA" # depends on broken package WGCNA-1.47
-    "GoogleGenomics" # depends on broken package Rsamtools-1.21.8
     "googlesheets" # broken build
     "goProfiles" # build is broken
     "GOSemSim" # Build Is Broken
     "goseq" # build is broken
-    "GOSim" # depends on broken package topGO-2.21.0
     "Goslate" # depends on broken package r-PythonInR-0.1-2
-    "GOstats" # depends on broken package AnnotationForge-1.11.3
-    "GOTHiC" # depends on broken package Rsamtools-1.21.8
     "goTools" # build is broken
     "GPC" # broken build
     "gplm" # depends on broken package nlopt-2.4.2
     "gpuR" # depends on GPU-specific header files
     "gputools" # depends on broken package cudatoolkit-5.5.22
     "gQTLBase" # depends on broken package r-GenomicFiles-1.5.8
-    "gQTLstats" # depends on broken package snpStats-1.19.0
     "gRain" # broken build
     "granova" # depends on broken package nlopt-2.4.2
     "GraphAT" # broken build
-    "graph" # broken build
     "gRapHD" # broken build
     "graphicalVAR" # depends on broken package nlopt-2.4.2
     "graphite" # broken build
     "GraphPAC" # broken build
     "gRbase" # broken build
     "gRc" # broken build
-    "GreyListChIP" # depends on broken package Rsamtools-1.21.8
     "gridDebug" # broken build
     "gridGraphics" # build is broken
     "gridGraphviz" # broken build
     "gRim" # broken build
-    "groHMM" # depends on broken package Rsamtools-1.21.8
     "GSAgm" # broken build
     "GSCA" # depends on broken package rhdf5-2.13.1
     "GSEABase" # broken build
@@ -1306,15 +1177,12 @@ let
     "GUIDEseq" # depends on broken package r-BiocGenerics-0.16.1
     "GUIProfiler" # broken build
     "Guitar" # depends on broken package r-GenomicAlignments-1.5.18
-    "Gviz" # depends on broken package Rsamtools-1.21.8
     "GWAF" # depends on broken package nlopt-2.4.2
-    "gwascat" # depends on broken package interactiveDisplayBase-1.7.0
     "GWASTools" # broken build
     "h2o" # build is broken
     "h5" # build is broken
     "h5vc" # depends on broken package rhdf5-2.13.1
     "hapFabia" # broken build
-    "Harshlight" # depends on broken package affyio-1.37.0
     "hasseDiagram" # broken build
     "hbsae" # depends on broken package nlopt-2.4.2
     "HCsnip" # broken build
@@ -1322,7 +1190,6 @@ let
     "HELP" # broken build
     "HEM" # broken build
     "heplots" # depends on broken package nlopt-2.4.2
-    "hiAnnotator" # depends on broken package Rsamtools-1.21.8
     "HiCfeat" # depends on broken package r-GenomeInfoDb-1.5.16
     "HiDimMaxStable" # broken build
     "hierGWAS"
@@ -1331,21 +1198,16 @@ let
     "HilbertCurve" # broken build
     "HilbertVisGUI" # Build Is Broken
     "HiPLARM" # Build Is Broken
-    "hiReadsProcessor" # depends on broken package Rsamtools-1.21.8
     "hisse" # broken build
     "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
     "HMMcopy" # broken build
     "homomorpheR" # broken build
     "hopach" # broken build
     "hpcwld" # broken build
     "hpoPlot" # broken build
-    "HTqPCR" # depends on broken package affyio-1.37.0
     "HTSanalyzeR" # depends on broken package Category-2.35.1
     "HTSCluster" # broken build
-    "HTSeqGenie" # depends on broken package Rsamtools-1.21.8
-    "htSeqTools" # depends on broken package Rsamtools-1.21.8
     "HTSFilter" # broken build
     "hwwntest" # broken build
     "HybridMTest" # broken build
@@ -1360,7 +1222,6 @@ let
     "iccbeta" # depends on broken package nlopt-2.4.2
     "iCheck" # depends on broken package r-affy-1.48.0
     "iClick" # depends on broken package rugarch-1.3-6
-    "IdeoViz" # depends on broken package Rsamtools-1.21.8
     "idiogram" # broken build
     "IdMappingAnalysis" # broken build
     "IdMappingRetrieval" # broken build
@@ -1375,13 +1236,10 @@ 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
     "inSilicoDb" # broken build
     "inSilicoMerging" # build is broken
     "INSPEcT" # depends on broken GenomicFeatures-1.21.13
-    "intansv" # depends on broken package Rsamtools-1.21.8
     "IntegratedJM" # broken build
-    "interactiveDisplayBase" # build is broken
     "interactiveDisplay" # depends on broken package Category-2.35.1
     "interplot" # depends on broken arm-1.8-5
     "ioncopy" # broken build
@@ -1389,13 +1247,9 @@ let
     "IONiseR" # depends on broken rhdf5-2.13.4
     "iPAC" # broken build
     "iptools"
-    "IRanges" # broken build
     "iRefR" # broken build
     "IsingFit" # depends on broken package nlopt-2.4.2
     "isobar" # broken build
-    "IsoGene" # depends on broken package affyio-1.37.0
-    "IsoGeneGUI" # depends on broken package affyio-1.37.0
-    "ITALICS" # depends on broken package oligo-1.33.0
     "ITEMAN" # depends on broken package r-car-2.1-0
     "iteRates" # broken build
     "iterativeBMA" # broken build
@@ -1410,7 +1264,6 @@ let
     "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
     "KCsmart" # broken build
     "kebabs" # broken build
     "KEGGgraph" # broken build
@@ -1435,7 +1288,6 @@ let
     "lfe" # build is broken
     "lgcp" # depends on broken package rpanel-1.1-3
     "Libra" # broken build
-    "limmaGUI" # depends on broken package affyio-1.37.0
     "LinRegInteractive" # depends on broken package rpanel-1.1-3
     "LiquidAssociation" # build is broken
     "lira"
@@ -1444,26 +1296,19 @@ let
     "lme4" # depends on broken package nlopt-2.4.2
     "LMERConvenienceFunctions" # depends on broken package nlopt-2.4.2
     "lmerTest" # depends on broken package nlopt-2.4.2
-    "LMGene" # depends on broken package affyio-1.37.0
     "lmSupport" # depends on broken package nlopt-2.4.2
     "LogisticDx" # depends on broken package nlopt-2.4.2
     "LOGIT" # depends on broken package r-caret-6.0-58
-    "logitT" # depends on broken package affyio-1.37.0
     "LOLA" # broken build
     "longpower" # depends on broken package nlopt-2.4.2
     "LOST" # broken build
-    "LowMACA" # depends on broken package Rsamtools-1.21.8
     "lpNet" # broken build
     "LPTime" # broken build
-    "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
     "maanova" # broken build
     "macat" # broken build
     "maGUI" # depends on broken package r-affy-1.47.1
     "maigesPack" # broken build
     "MAIT" # depends on broken package nlopt-2.4.2
-    "makecdfenv" # depends on broken package affyio-1.37.0
     "MAMA" # broken build
     "manta" # broken build
     "mAPKL" # build is broken
@@ -1472,7 +1317,6 @@ let
     "marked" # depends on broken package nlopt-2.4.2
     "markophylo" # depends on broken package r-Biostrings-2.38.2
     "maSigPro" # broken build
-    "maskBAD" # depends on broken package affyio-1.37.0
     "massiR" # broken build
     "matchingMarkets" # broken build
     "MatrixRider" # depends on broken package DirichletMultinomial-1.11.1
@@ -1481,16 +1325,13 @@ let
     "MBASED" # broken build
     "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
     "mBvs" # build is broken
-    "mcaGUI" # depends on broken package Rsamtools-1.21.8
     "MCRestimate" # build is broken
     "mdgsa" # build is broken
     "MEAL" # depends on broken package r-Biobase-2.30.0
     "meboot" # depends on broken package nlopt-2.4.2
     "medflex" # depends on broken package r-car-2.1-0
     "mediation" # depends on broken package r-lme4-1.1-8
-    "MEDIPS" # depends on broken package Rsamtools-1.21.8
     "MEDME" # depends on broken package nlopt-2.4.2
     "MEET" # broken build
     "MEIGOR" # broken build
@@ -1507,7 +1348,6 @@ let
     "metacom" # broken build
     "MetaDE" # broken build
     "metagear" # build is broken
-    "metagene" # depends on broken package Rsamtools-1.21.8
     "metagenomeFeatures" # depends on broken package r-Biobase-2.30.0
     "metagenomeSeq" # broken build
     "metaheur" # depends on broken package r-preprocomb-0.2.0
@@ -1519,17 +1359,11 @@ let
     "metaplus" # depends on broken package nlopt-2.4.2
     "metaSEM" # depends on broken package OpenMx-2.2.4
     "metaSeq" # broken build
-    "metaseqR" # depends on broken package affyio-1.37.0
     "Metatron" # depends on broken package nlopt-2.4.2
     "metaX" # depends on broken package r-CAMERA-1.25.2
     "MethTargetedNGS" # broken build
     "methVisual" # broken build
-    "methyAnalysis" # depends on broken package affyio-1.37.0
-    "MethylAid" # depends on broken package Rsamtools-1.21.8
     "methylMnM" # broken build
-    "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
     "Mfuzz" # broken build
     "MGFM" # broken build
     "mGSZ" # broken build
@@ -1543,10 +1377,7 @@ let
     "MigClim" # Build Is Broken
     "migui" # depends on broken package nlopt-2.4.2
     "MIMOSA" # broken build
-    "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
     "MiPP" # broken build
     "MiRaGE" # broken build
     "miRcomp" # depends on broken package r-Biobase-2.30.0
@@ -1556,7 +1387,6 @@ let
     "miRtest" # broken build
     "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
     "MixedPoisson" # broken build
@@ -1566,15 +1396,12 @@ let
     "MLInterfaces" # broken build
     "mlma" # depends on broken package r-lme4-1.1-10
     "mlmRev" # depends on broken package nlopt-2.4.2
-    "MLP" # depends on broken package affyio-1.37.0
     "MLSeq" # depends on broken package nlopt-2.4.2
     "mlVAR" # depends on broken package nlopt-2.4.2
     "MM2S" # broken build
     "MM2Sdata" # broken build
     "MM" # broken build
-    "MMDiff" # depends on broken package AnnotationForge-1.11.3
     "mmnet" # broken build
-    "MmPalateMiRNA" # depends on broken package affyio-1.37.0
     "mogsa" # broken build
     "molaR" # depends on broken package r-geomorph-2.1.7-1
     "mongolite" # build is broken
@@ -1586,10 +1413,6 @@ let
     "mosaic" # depends on broken package nlopt-2.4.2
     "mosaics" # broken build
     "motifbreakR" # depends on broken package r-BSgenome-1.37.5
-    "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
     "mpoly" # broken build
     "mRMRe" # broken build
     "msa" # broken build
@@ -1599,26 +1422,19 @@ let
     "MSGFgui" # depends on broken package MSGFplus-1.3.0
     "MSGFplus" # Build Is Broken
     "MSIseq" # broken build
-    "msmsEDA" # depends on broken package affyio-1.37.0
-    "msmsTests" # depends on broken package affyio-1.37.0
-    "MSnbase" # depends on broken package affyio-1.37.0
-    "MSnID" # depends on broken package affyio-1.37.0
     "MSstats" # depends on broken package nlopt-2.4.2
     "msSurv" # broken build
     "Mulcom" # broken build
     "MultiRR" # depends on broken package nlopt-2.4.2
     "multiscan" # broken build
-    "multtest" # broken build
     "muma" # depends on broken package nlopt-2.4.2
     "munsellinterpol"
     "muscle" # broken build
     "mutoss" # broken build
     "mutossGUI" # build is broken
-    "mvGST" # depends on broken package AnnotationForge-1.11.3
     "mvinfluence" # depends on broken package nlopt-2.4.2
     "mvMORPH" # broken build
     "MXM" # broken build
-    "mygene" # depends on broken package Rsamtools-1.21.8
     "myTAI" # broken build
     "myvariant" # depends on broken package r-VariantAnnotation-1.15.31
     "mzID" # broken build
@@ -1636,7 +1452,6 @@ let
     "netbenchmark" # build is broken
     "netClass" # broken build
     "nethet" # broken build
-    "NetPreProc" # depends on broken package graph-1.48.0
     "netresponse" # broken build
     "NetSAM" # broken build
     "nettools" # depends on broken package WGCNA-1.47
@@ -1648,23 +1463,17 @@ let
     "nlsem" # broken build
     "nlts" # broken build
     "NOISeq" # broken build
-    "nondetects" # depends on broken package affyio-1.37.0
     "nonrandom" # depends on broken package nlopt-2.4.2
-    "NormqPCR" # depends on broken package affyio-1.37.0
     "NORRRM" # build is broken
     "npGSEA" # broken build
     "npIntFactRep" # depends on broken package nlopt-2.4.2
     "NSM3" # broken build
-    "nucleR" # depends on broken package Rsamtools-1.21.8
     "OCplus" # broken build
     "OGSA" # broken build
-    "oligoClasses" # depends on broken package affyio-1.37.0
-    "oligo" # depends on broken package affyio-1.37.0
     "OmicCircos" # broken build
     "omics" # depends on broken package lme4-1.1-10
     "OmicsMarkeR" # depends on broken package nlopt-2.4.2
     "OncoSimulR" # broken build
-    "oneChannelGUI" # depends on broken package affyio-1.37.0
     "OPDOE" # broken build
     "OpenCL" # build is broken
     "opencpu" # broken build
@@ -1678,10 +1487,8 @@ let
     "ordBTL" # depends on broken package nlopt-2.4.2
     "OrderedList" # broken build
     "ordPens" # depends on broken package r-lme4-1.1-9
-    "OrganismDbi" # depends on broken package Rsamtools-1.21.8
     "orQA" # broken build
     "orthopolynom" # broken build
-    "OTUbase" # depends on broken package Rsamtools-1.21.8
     "OutlierD" # broken build
     "OUwie" # depends on broken package nlopt-2.4.2
     "oz" # broken build
@@ -1695,19 +1502,15 @@ let
     "PANDA" # build is broken
     "panelAR" # depends on broken package nlopt-2.4.2
     "PAnnBuilder" # broken build
-    "panp" # depends on broken package affyio-1.37.0
     "papeR" # depends on broken package nlopt-2.4.2
     "PAPi" # broken build
     "parboost" # depends on broken package nlopt-2.4.2
     "parglms" # broken build
     "parma" # depends on broken package nlopt-2.4.2
     "partitions" # broken build
-    "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
     "PBD" # broken build
     "pbdDEMO" # depends on broken package pbdSLAP-0.2-0
@@ -1726,20 +1529,15 @@ let
     "pcot2" # broken build
     "PCpheno" # depends on broken package Category-2.35.1
     "PCS" # broken build
-    "pdInfoBuilder" # depends on broken package affyio-1.37.0
     "pdmclass" # build is broken
     "PDQutils" # broken build
-    "PECA" # depends on broken package affyio-1.37.0
     "pedigreemm" # depends on broken package nlopt-2.4.2
     "pedometrics" # depends on broken package nlopt-2.4.2
     "PepPrep" # broken build
     "pepStat" # broken build
     "pequod" # depends on broken package nlopt-2.4.2
     "PerfMeas" # broken build
-    "PGA" # depends on broken package Rsamtools-1.21.8
     "pglm" # depends on broken package car-2.1-1
-    "PGSEA" # depends on broken package annaffy-1.41.1
-    "phangorn" # depends on broken package Biostrings-2.38.2
     "PharmacoGx"
     "phenoDist" # depends on broken package Category-2.35.1
     "phenoTest" # depends on broken package Category-2.35.1
@@ -1751,35 +1549,28 @@ let
     "PhySortR" # depends on broken package phytools-0.5-10
     "phytools" # broken build
     "piano" # broken build
-    "PICS" # depends on broken package Rsamtools-1.21.8
     "piecewiseSEM" # depends on broken package r-lme4-1.1-10
-    "PING" # depends on broken package Rsamtools-1.21.8
     "pkgDepTools" # broken build
     "plateCore" # depends on broken package ncdfFlow-2.15.2
     "plethy" # broken build
     "plfMA" # broken build
     "plgem" # broken build
-    "plier" # depends on broken package affyio-1.37.0
     "plm" # depends on broken package car-2.1-1
     "PLPE" # broken build
     "plrs" # broken build
     "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
     "polyester" # broken build
     "Polyfit" # broken build
     "polynom" # broken build
     "pomp" # depends on broken package nlopt-2.4.2
     "poppr" # depends on broken package  Biostrings-2.38.2
-    "popprxl" # depends on broken package Biostrings-2.38.2
     "ppiPre" # depends on broken package GOSemSim-1.27.3
     "ppiStats" # depends on broken package Category-2.35.1
     "prada" # broken build
-    "prebs" # depends on broken package affyio-1.37.0
     "PREDA" # broken build
     "predictionet" # broken build
     "predictmeans" # depends on broken package nlopt-2.4.2
@@ -1787,8 +1578,6 @@ let
     "prevalence"
     "pRF" # broken build
     "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
     "PROMISE" # broken build
@@ -1797,31 +1586,21 @@ let
     "Prostar" # depends on broken package r-imputeLCMD-2.0
     "prot2D" # broken build
     "ProteomicsAnnotationHubData" # depends on broken package r-AnnotationHub-2.1.40
-    "proteoQC" # depends on broken package affyio-1.37.0
-    "ProtGenerics" # broken build
     "protiq" # broken build
     "provenance" # broken build
     "PSAboot" # depends on broken package nlopt-2.4.2
     "PSEA" # broken build
     "PSICQUIC" # broken build
     "ptw" # depends on broken nloptr-1.0.4
-    "puma" # depends on broken package affyio-1.37.0
     "PurBayes"
     "purge" # depends on broken package r-lme4-1.1-9
-    "pvac" # depends on broken package affyio-1.37.0
     "PVAClone"
     "pvca" # depends on broken package nlopt-2.4.2
-    "Pviz" # depends on broken package Rsamtools-1.21.8
     "PWMEnrich" # broken build
-    "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
@@ -1829,16 +1608,11 @@ let
     "QuACN" # broken build
     "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
     "QuartPAC" # broken build
     "QuasiSeq" # broken build
-    "QuasR" # depends on broken package Rsamtools-1.21.8
     "qusage" # broken build
     "R2jags"
     "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
     "RADami" # broken build
     "rain" # broken build
     "raincpc" # build is broken
@@ -1846,11 +1620,8 @@ let
     "RAM" # broken build
     "RamiGO" # depends on broken package RCytoscape-1.19.0
     "randPack" # broken build
-    "RANKS" # depends on broken package graph-1.48.0
     "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
     "rase" # broken build
     "rationalfun" # broken build
@@ -1862,7 +1633,6 @@ let
     "Rblpapi" # broken build
     "rbsurv" # broken build
     "rbundler" # broken build
-    "Rcade" # depends on broken package Rsamtools-1.21.8
     "rcellminer" # broken build
     "rCGH" # depends on broken package r-affy-1.47.1
     "Rchemcpp" # depends on broken package ChemmineR-2.21.7
@@ -1923,44 +1693,29 @@ let
     "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
     "reb" # broken build
     "recluster" # broken build
-    "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
     "refund_shiny" # depends on broken package r-refund-0.1-13
-    "regioneR" # depends on broken package Rsamtools-1.21.8
-    "regionReport" # depends on broken package Rsamtools-1.21.8
     "regRSM" # broken build
     "REndo" # depends on broken package AER-1.2-4
     "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
     "rerddap" # broken build
     "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
     "RGalaxy" # broken build
     "rgbif" # depends on broken package V8-0.6
     "Rgnuplot"
     "rgp" # build is broken
     "rgpui" # depends on broken package rgp-0.4-1
-    "Rgraphviz" # broken build
     "rGREAT" # broken build
     "RGSEA" # broken build
     "rgsepd" # depends on broken package goseq-1.21.1
     "rhdf5" # build is broken
-    "rHVDM" # depends on broken package affyio-1.37.0
     "RiboProfiling" # depends on broken package r-BiocGenerics-0.16.1
     "riboSeqR" # broken build
-    "Ringo" # depends on broken package affyio-1.37.0
-    "RIPSeeker" # depends on broken package Rsamtools-1.21.8
-    "Risa" # depends on broken package affyio-1.37.0
     "rjade" # depends on broken package V8-0.6
     "rjags"
     "rJPSGCS" # build is broken
@@ -1978,51 +1733,39 @@ let
     "RMySQL" # broken build
     "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
     "rnetcarto" # broken build
-    "Rnits" # depends on broken package affyio-1.37.0
     "rNOMADS" # broken build
-    "roar" # depends on broken package Rsamtools-1.21.8
-    "RobLoxBioC" # depends on broken package affyio-1.37.0
     "RobLox" # broken build
     "robustlmm" # depends on broken package nlopt-2.4.2
     "rockchalk" # depends on broken package nlopt-2.4.2
     "RockFab" # broken build
     "ROI_plugin_symphony" # depends on broken package Rsymphony-0.1-20
     "Roleswitch" # broken build
-    "Rolexa" # depends on broken package Rsamtools-1.21.8
     "rols" # build is broken
     "ROntoTools" # broken build
     "ROracle" # Build Is Broken
-    "RPA" # depends on broken package affyio-1.37.0
     "rpanel" # build is broken
     "Rphylopars" # broken build
     "Rpoppler" # broken build
     "RPPanalyzer" # broken build
     "RpsiXML" # broken build
     "rpubchem" # depends on broken package nlopt-2.4.2
-    "Rqc" # depends on broken package Rsamtools-1.21.8
     "RQuantLib" # build is broken
     "rqubic" # broken build
     "rr" # depends on broken package nlopt-2.4.2
     "rRDP" # broken build
     "RRreg" # depends on broken package r-lme4-1.1-10
-    "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
     "RSeed" # broken build
-    "rSFFreader" # depends on broken package Rsamtools-1.21.8
     "Rsomoclu"
     "rstan" # build is broken
     "RStoolbox" # depends on broken package r-caret-6.0-52
     "Rsubread" # Build Is Broken
-    "RSVSim" # depends on broken package Rsamtools-1.21.8
     "Rsymphony" # build is broken
     "rTableICC" # broken build
     "rTANDEM" # build is broken
@@ -2030,22 +1773,17 @@ let
     "RTCGA" # depends on broken package r-rvest-0.3.0
     "RTN" # depends on broken package nlopt-2.4.2
     "RTopper" # broken build
-    "rtracklayer" # depends on broken package Rsamtools-1.21.8
     "Rtreemix" # broken build
     "rTRM" # broken build
-    "rTRMui" # depends on broken package Rsamtools-1.21.8
     "rugarch" # depends on broken package nlopt-2.4.2
     "rUnemploymentData" # broken build
-    "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
     "rvest" # broken build
     "RVFam" # depends on broken package nlopt-2.4.2
     "RVideoPoker" # depends on broken package rpanel-1.1-3
     "RWebServices" # broken build
     "ryouready" # depends on broken package nlopt-2.4.2
-    "S4Vectors" # broken build
     "sadists" # broken build
     "safe" # broken build
     "SAGx" # broken build
@@ -2053,7 +1791,6 @@ let
     "sangerseqR" # broken build
     "sapFinder" # depends on broken package rTANDEM-1.9.0
     "saps" # broken build
-    "SCAN_UPC" # depends on broken package affyio-1.37.0
     "scholar" # depends on broken package r-rvest-0.3.1
     "ScISI" # depends on broken package apComplex-2.35.0
     "scmamp" # broken build
@@ -2062,7 +1799,6 @@ let
     "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
     "sejmRP" # depends on broken package r-rvest-0.3.0
     "Sejong" # broken build
     "SELEX" # broken build
@@ -2073,26 +1809,18 @@ let
     "semPlot" # depends on broken package nlopt-2.4.2
     "SensMixed" # depends on broken package r-lme4-1.1-9
     "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
     "SeqFeatR" # broken build
     "SeqGrapheR" # Build Is Broken
     "SeqGSEA" # broken build
     "seqHMM" # depends on broken package nloptr-1.0.4
     "seqPattern" # broken build
-    "seqplots" # depends on broken package Rsamtools-1.21.8
     "seqTools" # build is broken
     "sequenza" # broken build
-    "SeqVarTools" # depends on broken package Rsamtools-1.21.8
-    "SGSeq" # depends on broken package Rsamtools-1.21.8
     "SharpeR" # broken build
     "sharx"
-    "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
     "Shrinkage" # depends on broken package r-multtest-2.25.2
     "SIBER"
     "SICtools" # depends on broken package r-Biostrings-2.38.2
@@ -2100,17 +1828,12 @@ let
     "sigaR" # broken build
     "SigCheck" # broken build
     "SigFuge" # broken build
-    "siggenes" # broken build
     "sigsquared" # broken build
     "SigTree" # broken build
     "SIMAT" # depends on broken package mzR-2.3.1
-    "SimBindProfiles" # depends on broken package affyio-1.37.0
     "SIM" # broken build
-    "similaRpeak" # depends on broken package Rsamtools-1.21.8
     "simmr"
-    "simpleaffy" # depends on broken package affyio-1.37.0
     "simPop" # depends on broken package r-VIM-4.4.1
-    "SimRAD" # depends on broken package Rsamtools-1.21.8
     "simr" # depends on broken package r-lme4-1.1-10
     "SimReg" # broken build
     "simulatorZ" # broken build
@@ -2118,25 +1841,16 @@ let
     "SISPA" # depends on broken package r-GSVA-1.18.0
     "SJava" # broken build
     "sjPlot" # depends on broken package nlopt-2.4.2
-    "skewr" # depends on broken package affyio-1.37.0
     "SLGI" # depends on broken package apComplex-2.35.0
     "smacof" # broken build
     "SNAGEE" # build is broken
-    "snapCGH" # depends on broken package tilingArray-1.47.0
     "snm" # depends on broken package nlopt-2.4.2
-    "SNPchip" # depends on broken package affyio-1.37.0
-    "snpEnrichment" # depends on broken package snpStats-1.19.0
     "SNPhood" # depends on broken package r-BiocGenerics-0.16.1
     "snplist" # broken build
-    "snpStats" # build is broken
-    "snpStatsWriter" # depends on broken package snpStats-1.19.0
-    "SNPtools" # depends on broken package Rsamtools-1.21.8
     "SOD" # depends on broken package cudatoolkit-5.5.22
     "sodium" # broken build
-    "soGGi" # depends on broken package Rsamtools-1.21.8
     "soilphysics" # depends on broken package rpanel-1.1-3
     "SomatiCA" # broken build
-    "SomaticSignatures" # depends on broken package Rsamtools-1.21.8
     "sortinghat" # broken build
     "SoyNAM" # depends on broken package r-lme4-1.1-8
     "SpacePAC" # broken build
@@ -2151,23 +1865,17 @@ let
     "SPIA" # broken build
     "spkTools" # broken build
     "splicegear" # broken build
-    "spliceR" # depends on broken package Rsamtools-1.21.8
     "spliceSites" # broken build
-    "SplicingGraphs" # depends on broken package Rsamtools-1.21.8
     "splm" # depends on broken package car-2.1-1
     "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
     "SRAdb" # broken build
     "srd" # broken build
-    "sscore" # depends on broken package affyio-1.37.0
     "ssizeRNA" # broken build
     "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
     "StatMethRank"
     "Statomica" # broken build
     "stepp" # depends on broken package nlopt-2.4.2
@@ -2179,19 +1887,14 @@ let
     "structSSI" # broken build
     "strum" # broken build
     "subSeq" # depends on broken package r-Biobase-2.30.0
-    "SummarizedExperiment" # broken build
     "superbiclust" # broken build
     "Surrogate" # depends on broken package nlopt-2.4.2
     "Sushi" # broken build
-    "sva" # broken build
     "svglite" # depends on broken package gdtools-0.0.6
-    "SVM2CRM" # depends on broken package Rsamtools-1.21.8
     "sybilSBML" # build is broken
-    "synapter" # depends on broken package affyio-1.37.0
     "synchronicity" # build is broken
     "synthpop" # build is broken
     "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
     "TarSeqQC" # depends on broken package r-BiocGenerics-0.16.1
     "TCC" # broken build
@@ -2201,38 +1904,26 @@ let
     "TDARACNE" # broken build
     "TDMR" # depends on broken package nlopt-2.4.2
     "TED" # broken build
-    "TEQC" # depends on broken package Rsamtools-1.21.8
     "TextoMineR"  # depends on broken package FactoMineR-1.31.4
     "TFBSTools" # depends on broken package DirichletMultinomial-1.11.1
     "tigerstats" # depends on broken package nlopt-2.4.2
     "tigre" # broken build
-    "tilingArray" # depends on broken package affyio-1.37.0
     "timecourse" # broken build
     "timeSeq" # broken build
-    "timetree" # depends on broken package Biostrings-2.38.2
     "TIN" # depends on broken package WGCNA-1.47
-    "TitanCNA" # depends on broken package Rsamtools-1.21.8
     "TKF" # broken build
     "TLBC" # depends on broken package r-caret-6.0-58
     "tmle" # broken build
     "tnam" # depends on broken package r-lme4-1.1-9
     "tolBasis" # depends on broken package r-polynom-1.3-8
-    "ToPASeq" # depends on broken package Rsamtools-1.21.8
-    "topGO" # build is broken
-    "topologyGSA" # depends on broken package Rsamtools-1.21.8
     "TPP" # broken build
-    "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"
-    "treescape" # depends on broken package Biostrings-2.38.2
     "triform" # broken build
     "trigger" # broken build
     "TriMatch" # depends on broken package nlopt-2.4.2
     "triplex" # broken build
-    "TROM" # depends on broken package topGO-2.21.0
     "TRONCO" # broken build
     "TSdist" # broken build
     "TSMySQL" # broken build
@@ -2240,42 +1931,28 @@ let
     "tspair" # broken build
     "TSSi" # broken build
     "ttScreening" # broken build
-    "TurboNorm" # depends on broken package affyio-1.37.0
     "tweeDEseq" # broken build
     "twilight" # broken build
     "UBCRM" # broken build
     "umx" # depends on broken package r-OpenMx-2.2.6
     "UNDO" # broken build
-    "unifiedWMWqPCR" # depends on broken package affyio-1.37.0
     "uniftest" # broken build
     "UniProt_ws" # broken build
     "untb" # broken build
     "userfriendlyscience" # depends on broken package nlopt-2.4.2
     "V8" # build is broken
-    "VanillaICE" # depends on broken package affyio-1.37.0
     "varComp" # depends on broken package r-lme4-1.1-9
     "varian" # build is broken
     "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
     "VBmix" # broken build
     "VegaMC" # broken build
     "VIM" # depends on broken package nlopt-2.4.2
     "VIMGUI" # depends on broken package nlopt-2.4.2
-    "viper" # broken build
     "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
     "webp" # build is broken
     "wfe" # depends on broken package nlopt-2.4.2
     "WGCNA" # build is broken
-    "wgsea" # depends on broken package snpStats-1.19.0
     "wikipediatrend" # broken build
     "wordbankr" # depends on broken package r-RMySQL-0.10.7
     "XBSeq" # broken build
@@ -2284,9 +1961,6 @@ let
     "x_ent" # broken build
     "xergm" # depends on broken package nlopt-2.4.2
     "xps" # build is broken
-    "XVector" # broken build
-    "yaqcaffy" # depends on broken package affyio-1.37.0
-    "yCrypticRNAs" # depends on broken package biomaRt-2.26.1
     "ZeligChoice" # depends on broken package r-AER-1.2-4
     "Zelig" # depends on broken package r-AER-1.2-4
     "zetadiv" # depends on broken package nlopt-2.4.2