R: improve support for CRAN and Bioconductor package sets

 - Update the instructions for re-generating each of the package set files.
 - Provide test-evaluation.nix expression to verify that the package sets evaluates.
 - Update list of known broken packages.

1 files changed, 979 insertions, 707 deletions

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index fb1975455716..34dbf4cba523 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -205,8 +205,8 @@ let
   # `self` is `_self` with overridden packages;
   # packages in `_self` may depends on overridden packages.
   self = (defaultOverrides _self self) // overrides;
-  _self = import ./cran-packages.nix { inherit self; derive = deriveCran; }
-       // import ./bioc-packages.nix { inherit self; derive = deriveBioc; };
+  _self = import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
+          import ./cran-packages.nix { inherit self; derive = deriveCran; };
 
   # tweaks for the individual packages and "in self" follow
 
@@ -223,12 +223,16 @@ let
     BayesVarSel = [ pkgs.gsl ];
     BayesXsrc = [ pkgs.readline pkgs.ncurses ];
     bigGP = [ pkgs.openmpi ];
+    BiocCheck = [ pkgs.which ];
+    Biostrings = [ pkgs.zlib ];
     bnpmr = [ pkgs.gsl ];
     BNSP = [ pkgs.gsl ];
     cairoDevice = [ pkgs.gtk2 ];
     Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
+    Cardinal = [ pkgs.which ];
     CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
     chebpol = [ pkgs.fftw ];
+    ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ];
     cit = [ pkgs.gsl ];
     curl = [ pkgs.curl ];
     devEMF = [ pkgs.xlibs.libXft ];
@@ -239,11 +243,13 @@ let
     Formula = [ pkgs.gmp ];
     geoCount = [ pkgs.gsl ];
     git2r = [ pkgs.zlib pkgs.openssl ];
+    GLAD = [ pkgs.gsl ];
     glpkAPI = [ pkgs.gmp pkgs.glpk ];
     gmp = [ pkgs.gmp ];
     graphscan = [ pkgs.gsl ];
     gsl = [ pkgs.gsl ];
     HiCseg = [ pkgs.gsl ];
+    iBMQ = [ pkgs.gsl ];
     igraph = [ pkgs.gmp ];
     JavaGD = [ pkgs.jdk ];
     jpeg = [ pkgs.libjpeg ];
@@ -271,8 +277,8 @@ let
     R2GUESS = [ pkgs.gsl ];
     R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
     RAppArmor = [ pkgs.libapparmor ];
-    rapport = [ pkgs.which ];
     rapportools = [ pkgs.which ];
+    rapport = [ pkgs.which ];
     rbamtools = [ pkgs.zlib ];
     RCA = [ pkgs.gmp ];
     rcdd = [ pkgs.gmp ];
@@ -287,6 +293,7 @@ let
     Rglpk = [ pkgs.glpk ];
     RGtk2 = [ pkgs.gtk2 ];
     Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
+    Rhtslib = [ pkgs.zlib ];
     ridge = [ pkgs.gsl ];
     RJaCGH = [ pkgs.zlib ];
     rjags = [ pkgs.jags ];
@@ -391,251 +398,242 @@ let
   };
 
   packagesRequireingX = [
-    "AnalyzeFMRI"
-    "AnnotLists"
-    "AnthropMMD"
-    "AtelieR"
-    "BAT"
-    "BCA"
-    "BEQI2"
-    "BHMSMAfMRI"
-    "BioGeoBEARS"
-    "BiodiversityR"
-    "CCTpack"
-    "CommunityCorrelogram"
-    "ConvergenceConcepts"
-    "DALY"
-    "DSpat"
-    "Deducer"
-    "DeducerExtras"
-    "DeducerPlugInExample"
-    "DeducerPlugInScaling"
-    "DeducerSpatial"
-    "DeducerSurvival"
-    "HomoPolymer"
-    "MetSizeR"
-    "DeducerText"
-    "Demerelate"
-    "DescTools"
-    "DivMelt"
-    "ENiRG"
-    "EcoVirtual"
-    "EnQuireR"
-    "FAiR"
-    "FD"
-    "FFD"
-    "FeedbackTS"
-    "FreeSortR"
-    "GGEBiplotGUI"
-    "GPCSIV"
-    "GUniFrac"
-    "Geneland"
-    "GeoGenetix"
-    "GeoXp"
-    "GrammR"
-    "GrapheR"
-    "GroupSeq"
-    "HH"
-    "HiveR"
-    "IsotopeR"
-    "JGR"
-    "KappaGUI"
-    "LS2Wstat"
-    "MAR1"
-    "MTurkR"
-    "MareyMap"
-    "MergeGUI"
-    "Meth27QC"
-    "MicroStrategyR"
-    "MissingDataGUI"
-    "MplusAutomation"
-    "OligoSpecificitySystem"
-    "OpenRepGrid"
-    "PBSadmb"
-    "PBSmodelling"
-    "PCPS"
-    "PKgraph"
-    "PopGenReport"
-    "PredictABEL"
-    "PrevMap"
-    "ProbForecastGOP"
-    "QCAGUI"
-    "R2STATS"
-    "RHRV"
-    "RNCEP"
-    "RQDA"
-    "RSDA"
-    "RSurvey"
-    "RandomFields"
-    "Rcmdr"
-    "RcmdrPlugin_BCA"
-    "RcmdrPlugin_DoE"
-    "RcmdrPlugin_EACSPIR"
-    "RcmdrPlugin_EBM"
-    "RcmdrPlugin_EZR"
-    "RcmdrPlugin_EcoVirtual"
-    "RcmdrPlugin_FactoMineR"
-    "RcmdrPlugin_HH"
-    "RcmdrPlugin_IPSUR"
-    "RcmdrPlugin_KMggplot2"
-    "RcmdrPlugin_MA"
-    "RcmdrPlugin_MPAStats"
-    "RcmdrPlugin_ROC"
-    "RcmdrPlugin_SCDA"
-    "RcmdrPlugin_SLC"
-    "RcmdrPlugin_SM"
-    "RcmdrPlugin_StatisticalURV"
-    "RcmdrPlugin_TeachingDemos"
-    "RcmdrPlugin_UCA"
-    "RcmdrPlugin_coin"
-    "RcmdrPlugin_depthTools"
-    "RcmdrPlugin_doex"
-    "RcmdrPlugin_epack"
-    "RcmdrPlugin_lfstat"
-    "RcmdrPlugin_mosaic"
-    "RcmdrPlugin_orloca"
-    "RcmdrPlugin_plotByGroup"
-    "RcmdrPlugin_pointG"
-    "RcmdrPlugin_qual"
-    "RcmdrPlugin_sampling"
-    "RcmdrPlugin_sos"
-    "RcmdrPlugin_steepness"
-    "RcmdrPlugin_survival"
-    "RcmdrPlugin_temis"
-    "RenextGUI"
-    "RunuranGUI"
-    "SOLOMON"
-    "SPACECAP"
-    "SRRS"
-    "SSDforR"
-    "STEPCAM"
-    "SYNCSA"
-    "Simile"
-    "SimpleTable"
-    "StatDA"
-    "SyNet"
-    "TDMR"
-    "TED"
-    "TIMP"
-    "TTAinterfaceTrendAnalysis"
-    "TestScorer"
-    "VIMGUI"
-    "VecStatGraphs3D"
-    "WMCapacity"
     "accrual"
     "ade4TkGUI"
     "adehabitat"
     "analogue"
     "analogueExtra"
+    "AnalyzeFMRI"
+    "AnnotLists"
+    "AnthropMMD"
     "aplpack"
     "aqfig"
     "arf3DS4"
     "asbio"
+    "AtelieR"
+    "BAT"
     "bayesDem"
+    "BCA"
+    "BEQI2"
     "betapart"
     "betaper"
+    "BHMSMAfMRI"
+    "BiodiversityR"
+    "BioGeoBEARS"
     "bio_infer"
     "bipartite"
     "biplotbootGUI"
     "blender"
     "cairoDevice"
+    "CCTpack"
     "cncaGUI"
     "cocorresp"
+    "CommunityCorrelogram"
     "confidence"
     "constrainedKriging"
+    "ConvergenceConcepts"
     "cpa"
+    "DALY"
     "dave"
     "debug"
+    "Deducer"
+    "DeducerExtras"
+    "DeducerPlugInExample"
+    "DeducerPlugInScaling"
+    "DeducerSpatial"
+    "DeducerSurvival"
+    "DeducerText"
+    "Demerelate"
+    "DescTools"
     "detrendeR"
     "dgmb"
+    "DivMelt"
     "dpa"
-    "dynBiplotGUI"
+    "DSpat"
     "dynamicGraph"
+    "dynBiplotGUI"
+    "EasyqpcR"
+    "EcoVirtual"
+    "ENiRG"
+    "EnQuireR"
     "eVenn"
     "exactLoglinTest"
-    "fSRM"
+    "FAiR"
     "fat2Lpoly"
     "fbati"
+    "FD"
     "feature"
+    "FeedbackTS"
+    "FFD"
     "fgui"
     "fisheyeR"
     "fit4NM"
     "forams"
     "forensim"
+    "FreeSortR"
     "fscaret"
-    "gWidgets2RGtk2"
-    "gWidgets2tcltk"
-    "gWidgetsRGtk2"
-    "gWidgetstcltk"
+    "fSRM"
     "gcmr"
+    "Geneland"
+    "GeoGenetix"
+    "geomorph"
     "geoR"
     "geoRglm"
-    "geomorph"
     "georob"
+    "GeoXp"
+    "GGEBiplotGUI"
     "gnm"
+    "GPCSIV"
+    "GrammR"
+    "GrapheR"
+    "GroupSeq"
     "gsubfn"
+    "GUniFrac"
+    "gWidgets2RGtk2"
+    "gWidgets2tcltk"
+    "gWidgetsRGtk2"
+    "gWidgetstcltk"
+    "HH"
+    "HiveR"
+    "HomoPolymer"
     "iBUGS"
-    "iDynoR"
     "ic50"
+    "iDynoR"
     "in2extRemes"
     "iplots"
     "isopam"
+    "IsotopeR"
+    "JGR"
+    "KappaGUI"
     "likeLTD"
     "loe"
     "logmult"
+    "LS2Wstat"
+    "MAR1"
+    "MareyMap"
     "memgene"
+    "MergeGUI"
     "metacom"
+    "Meth27QC"
+    "MetSizeR"
+    "MicroStrategyR"
     "migui"
     "miniGUI"
+    "MissingDataGUI"
     "mixsep"
     "mlDNA"
+    "MplusAutomation"
     "mpmcorrelogram"
     "mritc"
+    "MTurkR"
     "multgee"
     "multibiplotGUI"
     "nodiv"
+    "OligoSpecificitySystem"
     "onemap"
+    "OpenRepGrid"
     "palaeoSig"
     "paleoMAS"
     "pbatR"
+    "PBSadmb"
+    "PBSmodelling"
+    "PCPS"
     "pez"
     "phylotools"
     "picante"
+    "PKgraph"
     "playwith"
     "plotSEMM"
     "plsRbeta"
     "plsRglm"
     "pmg"
+    "PopGenReport"
     "poppr"
     "powerpkg"
+    "PredictABEL"
     "prefmod"
+    "PrevMap"
+    "ProbForecastGOP"
+    "QCAGUI"
     "qtbase"
     "qtpaint"
     "qtutils"
+    "R2STATS"
     "r4ss"
-    "rAverage"
+    "RandomFields"
     "rareNMtests"
+    "rAverage"
+    "Rcmdr"
+    "RcmdrPlugin_BCA"
+    "RcmdrPlugin_coin"
+    "RcmdrPlugin_depthTools"
+    "RcmdrPlugin_DoE"
+    "RcmdrPlugin_doex"
+    "RcmdrPlugin_EACSPIR"
+    "RcmdrPlugin_EBM"
+    "RcmdrPlugin_EcoVirtual"
+    "RcmdrPlugin_epack"
+    "RcmdrPlugin_EZR"
+    "RcmdrPlugin_FactoMineR"
+    "RcmdrPlugin_HH"
+    "RcmdrPlugin_IPSUR"
+    "RcmdrPlugin_KMggplot2"
+    "RcmdrPlugin_lfstat"
+    "RcmdrPlugin_MA"
+    "RcmdrPlugin_mosaic"
+    "RcmdrPlugin_MPAStats"
+    "RcmdrPlugin_orloca"
+    "RcmdrPlugin_plotByGroup"
+    "RcmdrPlugin_pointG"
+    "RcmdrPlugin_qual"
+    "RcmdrPlugin_ROC"
+    "RcmdrPlugin_sampling"
+    "RcmdrPlugin_SCDA"
+    "RcmdrPlugin_SLC"
+    "RcmdrPlugin_SM"
+    "RcmdrPlugin_sos"
+    "RcmdrPlugin_StatisticalURV"
+    "RcmdrPlugin_steepness"
+    "RcmdrPlugin_survival"
+    "RcmdrPlugin_TeachingDemos"
+    "RcmdrPlugin_temis"
+    "RcmdrPlugin_UCA"
     "recluster"
     "relax"
     "relimp"
+    "RenextGUI"
     "reportRx"
     "reshapeGUI"
     "rgl"
+    "RHRV"
     "rich"
     "ringscale"
     "rioja"
     "ripa"
     "rite"
     "rnbn"
+    "RNCEP"
+    "RQDA"
+    "RSDA"
     "rsgcc"
+    "RSurvey"
+    "RunuranGUI"
     "sdcMicroGUI"
     "sharpshootR"
     "simba"
+    "Simile"
+    "SimpleTable"
+    "SOLOMON"
     "soundecology"
+    "SPACECAP"
     "spacodiR"
     "spatsurv"
     "sqldf"
+    "SRRS"
+    "SSDforR"
     "statcheck"
+    "StatDA"
+    "STEPCAM"
     "stosim"
     "strvalidator"
     "stylo"
@@ -643,17 +641,27 @@ let
     "svIDE"
     "svSocket"
     "svWidgets"
+    "SYNCSA"
+    "SyNet"
     "tcltk2"
+    "TDMR"
+    "TED"
+    "TestScorer"
+    "TIMP"
     "titan"
     "tkrgl"
     "tkrplot"
     "tmap"
     "tspmeta"
+    "TTAinterfaceTrendAnalysis"
     "twiddler"
     "vcdExtra"
+    "VecStatGraphs3D"
     "vegan"
     "vegan3d"
     "vegclust"
+    "VIMGUI"
+    "WMCapacity"
     "x12GUI"
     "xergm"
   ];
@@ -667,572 +675,832 @@ let
 
   # Packages which cannot be installed due to lack of dependencies or other reasons.
   brokenPackages = [
-    "abd" # requires nlopt
-    "ACNE" # requires aroma_affymetrix
-    "Actigraphy" # SDMTools.so: undefined symbol: X
-    "adabag" # requires nlopt
-    "adaptsmoFMRI" # requires spatstat
-    "ads" # requires spatstat
-    "AER" # REQUIRES NLOPT
-    "afex" # requires nlopt
-    "agRee" # requires nlopt
-    "agridat" # requires pcaMethods
-    "aLFQ" # requires protiq
-    "alr3" # requires nlopt
-    "alr4" # requires nlopt
-    "anacor" # requires nlopt
-    "AntWeb" # requires leafletR
-    "aods3" # requires nlopt
-    "aoristic" # requires spatstat
-    "apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
-    "apt" # requires nlopt
-    "ArfimaMLM" # Requires Nlopt
-    "arm" # requires nlopt
-    "aroma_affymetrix" # requires aroma_core
-    "aroma_cn" # requires PSCBS
-    "aroma_core" # requires PSCBS
-    "ArrayBin" # requires SAGx
-    "ARTool" # Requires Nlopt
-    "babel" # requires edgeR
-    "BACA" # requires RDAVIDWebService
-    "backShift" # requires pcalg to build
-    "bartMachine" # requires nlopt
-    "bayesDem" # requires nlopt
-    "bayesLife" # requires nlopt
-    "bayesPop" # requires nlopt
-    "Bayesthresh" # Requires Nlopt
-    "BBRecapture" # Requires Nlopt
-    "BCA" # REQUIRES NLOPT
-    "BcDiag" # requires fabia
-    "bdvis" # requres taxize
-    "beadarrayFilter" # requires beadarray
-    "beadarrayMSV" # requires Biobase, geneplotter, andlimma
-    "bgmm" # requires nlopt
-    "BIFIEsurvey" # requires DiagrammeR to build
-    "bigGP" # requires MPI running. HELP WANTED!
-    "bigpca" # requires NCmisc
-    "BiodiversityR" # Requires Nlopt
-    "Biograph" # requires mvna
-    "biotools" # requires rpanel
-    "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
-    "BLCOP" # depends on broken fPortfolio
-    "blmeco" # requires nlopt
-    "blme" # requires nlopt
-    "bmd" # requires nlopt
-    "bmem" # requires DiagrammeR to build
-    "bmrm" # requires clpAPI
-    "bootnet" # requires IsingFit
-    "boss" # requires nlopt
-    "BradleyTerry2" # Requires Nlopt
-    "branchLars" # requires Rgraphviz
-    "BRugs" # requires OpenBUGS
-    "CADFtest" # Requires Nlopt
-    "cAIC4" # requires nlopt
-    "calmate" # requires aroma_core
-    "candisc" # requires nlopt
-    "carcass" # requires nlopt
-    "caretEnsemble" # requires nlopt
-    "caret" # requires nlopt
-    "CARrampsOcl" # depends on OpenCL
-    "car" # requires nlopt
-    "CCpop" # Requires Nlopt
-    "ChainLadder" # Requires Nlopt
-    "CHAT" # requires DNAcopy
-    "ChemoSpec" # depends on broken speaq
-    "classGraph" # requires graph, and Rgraphviz
-    "climwin" # requires nlopt
-    "CLME" # REQUIRES NLOPT
-    "clpAPI" # requires clp
-    "clusterPower" # requires nlopt
-    "compendiumdb" # requires Biobase
-    "conformal" # requires nlopt
-    "corHMM" # requires nlopt
-    "CORM" # requires limma
-    "CosmoPhotoz" # Requires Nlopt
-    "cp4p" # build is broken
-    "cplexAPI" # requires CPLEX
-    "Crossover" # fails self-test
-    "cudaBayesreg" # requres Rmath
-    "daff" # requires V8 to build
-    "dagbag" # requires Rlapack
-    "DAMisc" # Requires Nlopt
-    "DBKGrad" # requires SDD
-    "dbmss" # requires spatstat
-    "DCGL" # requires limma
-    "dcGOR" # requires dnet
-    "DeducerExtras" # Requires Nlopt
-    "DeducerPlugInExample" # Requires Nlopt
-    "DeducerPlugInScaling" # Requires Nlopt
-    "Deducer" # Requires Nlopt
-    "DeducerSpatial" # Requires Nlopt
-    "DeducerSurvival" # Requires Nlopt
-    "DeducerText" # Requires Nlopt
-    "demi" # requires affy, affxparser, and oligo
-    "DepthProc" # requires samr
-    "DiagrammeR" # requires V8 to build
-    "DiagTest3Grp" # Requires Nlopt
-    "DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest'
-    "difR" # requires nlopt
-    "Digiroo2" # requires spatstat
-    "discSurv" # requires nlopt
-    "DistatisR" # Requires Nlopt
-    "diveRsity" # requires DiagrammeR to build
-    "dixon" # requires spatstat
-    "dnet" # requires supraHex, graph, Rgraphviz, and Biobase
-    "doMPI" # requires MPI running. HELP WANTED!
-    "dpa" # requires DiagrammeR to build
-    "dpcR" # requires spatstat
-    "drc" # requires nlopt
-    "drfit" # requires nlopt
-    "drsmooth" # requires nlopt
-    "DSpat" # requires spatstat
-    "dynlm" # requires nlopt
-    "easyanova" # requires nlopt
-    "ecespa" # requires spatstat
-    "ecoengine" # requires leafletR
-    "ecospat" # requires spatstat
-    "edgeRun" # requires edgeR
-    "eeptools" # requires nlopt
-    "EffectLiteR" # Requires Nlopt
-    "effects" # requires nlopt
-    "EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
-    "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
-    "EnQuireR" # Requires Nlopt
-    "episplineDensity" # requires nlopt
-    "epoc" # requires graph, and Rgraphviz
-    "epr" # requires nlopt
-    "erer" # requires nlopt
-    "erpR" # requires rpanel
-    "ETAS" # requires spatstat
-    "eulerian" # requires graph
-    "evobiR" # requres taxiz
-    "evora" # requires qvalue
-    "ExomeDepth" # requires GenomicRanges, and Rsamtools
-    "extRemes" # requires nlopt
-    "ez" # requires nlopt
-    "FactoMineR" # Requires Nlopt
-    "Factoshiny" # Requires Nlopt
-    "FAMT" # requires impute
-    "faoutlier" # requires DiagrammeR to build
-    "fastR" # requires nlopt
-    "fdrDiscreteNull" # requires edgeR
-    "FDRreg" # Requires Nlopt
-    "FHtest" # requires interval
-    "flexCWM" # depends on broken mixture
-    "fPortfolio" # requires rneos
-    "freqweights" # requires nlopt
-    "fscaret" # requires nlopt
-    "FunctionalNetworks" # requires breastCancerVDX
-    "FunctionalNetworks" # requires breastCancerVDX, and Biobase
-    "fxregime" # requires nlopt
-    "gamclass" # requires nlopt
-    "gamlss_demo" # requires rpanel
-    "gamm4" # requires nlopt
-    "gcmr" # requires nlopt
-    "GDAtools" # Requires Nlopt
-    "GeneticTools" # requires snpStats
-    "genridge" # requires nlopt
-    "geojsonio" # requires V8 to build
-    "GExMap" # requires Biobase and multtest
-    "gimme" # requires DiagrammeR to build
-    "gitter" # requires EBImage
-    "glmgraph" # test suite says: "undefined symbol: dgemv_"
-    "gmatrix" # depends on proprietary cudatoolkit
-    "gmatrix" # requires CUDA runtime
-    "gMCP" # fails self-test
-    "GOGANPA" # requires WGCNA
-    "gplm" # requires nlopt
-    "gputools" # depends on proprietary cudatoolkit
-    "gRain" # requires gRbase
-    "granova" # requires nlopt
-    "gRapHD" # requires graph
-    "graphicalVAR" # requires DiagrammeR to build
-    "GraphPCA" # Requires Nlopt
-    "gRbase" # requires RBGL, and graph
-    "gRc" # requires gRbase
-    "gridDebug" # requires gridGraphviz
-    "gridGraphviz" # requires graph, and Rgraphviz
-    "GriegSmith" # requires spatstat
-    "gRim" # requires gRbase
-    "GSAgm" # requires edgeR
-    "GUIDE" # requires rpanel
-    "GWAF" # REQUIRES NLOPT
-    "h2o" # tries to download some h2o.jar during its build
-    "h5" # depends on missing h5 system library
-    "hasseDiagram" # requires Rgraphviz
-    "hbsae" # requires nlopt
-    "hddplot" # requires multtest
-    "heplots" # requires nlopt
-    "HH" # REQUIRES NLOPT
-    "HierO" # requires rneos
-    "HiPLARM" # requires MAGMA or PLASMA
-    "HistDAWass" # Requires Nlopt
-    "HLMdiag" # Requires Nlopt
-    "hpoPlot" # requires Rgraphviz
-    "hsdar" # fails to build
-    "HTSCluster" # requires edgeR
-    "hysteresis" # requires nlopt
-    "IATscores" # requires DiagrammeR to build
-    "ibd" # requires nlopt
-    "iccbeta" # requires nlopt
-    "iFes" # depends on proprietary cudatoolkit
-    "imputeLCMD" # requires pcaMethods, and impute
-    "imputeR" # requires nlopt
-    "in2extRemes" # requires nlopt
-    "incReg" # requires nlopt
-    "inferference" # requires nlopt
-    "influence_ME" # requires nlopt
-    "intamapInteractive" # requires spatstat
-    "interval" # requires Icens
-    "ionflows" # requires Biostrings
-    "iRefR" # requires graph, and RBGL
-    "IsingFit" # requires DiagrammeR to build
-    "IsoGene" # requires Biobase, and affy
-    "isva" # requires qvalue
-    "ivpack" # requires nlopt
-    "JAGUAR" # REQUIRES NLOPT
-    "jomo" # linking errors
-    "js" # requires broken V8
-    "KANT" # requires affy, and Biobase
-    "ktspair" # requires Biobase
-    "latticeDensity" # requires spatstat
-    "lawn" # requires DiagrammeR to build
-    "lawn" # requires V8 to build
-    "leapp" # requires sva
-    "learnstats" # requires nlopt
-    "lefse" # SDMTools.so: undefined symbol: X
-    "lessR" # requires nlopt
-    "lfe" # fails to compile
-    "lgcp" # requires rpanel
-    "LinRegInteractive" # requires Rpanel
-    "lme4" # requires nlopt
-    "LMERConvenienceFunctions" # Requires Nlopt
-    "lmerTest" # requires nlopt
-    "lmSupport" # requires nlopt
-    "LogisticDx" # requires gRbase
-    "longpower" # requires nlopt
-    "LOST" # requires pcaMethods
-    "ltsk" # requires Rlapack and Rblas
-    "magma" # requires MAGMA
-    "MAMA" # requires metaMA
-    "marked" # requires nlopt
-    "MaxPro" # Requires Nlopt
-    "mbest" # requires nlopt
-    "meboot" # requires nlopt
-    "MEET" # requires pcaMethods, and seqLogo
-    "MEMSS" # REQUIRES NLOPT
-    "metabolomics" # depends on broken crmn
-    "MetaDE" # requires impute, and Biobase
-    "metagear" # build is broken
-    "MetaLandSim" # requires Biobase
-    "metaMA" # requires limma
-    "metaMix" # requires MPI running. HELP WANTED!
-    "metaplus" # requires nlopt
-    "metaSEM" # requires OpenMx
-    "Metatron" # Requires Nlopt
-    "mGSZ" # requires Biobase, and limma
-    "miceadds" # requires DiagrammeR to build
-    "micEconAids" # requires nlopt
-    "micEconCES" # requires nlopt
-    "micEconSNQP" # requires nlopt
-    "MigClim" # SDMTools.So: Undefined Symbol: X
-    "migui" # requires nlopt
-    "minimist" # requires broken V8
-    "mi" # requires nlopt
-    "miRtest" # requires globaltest, GlobalAncova, and limma
-    "missMDA" # requires nlopt
-    "mixAK" # requires nlopt
-    "MixGHD" # requires mixture to build
-    "mixlm" # requires nlopt
-    "MixMAP" # Requires Nlopt
-    "mixture" # mixture.so: undefined symbol: dtrmm_
-    "mlmRev" # requires nlopt
-    "mlVAR" # requires DiagrammeR to build
-    "MM2S" # BUILD IS BROKEN
-    "moduleColor" # requires impute
-    "mongolite" # doesn't find OpenSSL
-    "mosaic" # requires nlopt
-    "msarc" # requires AnnotationDbi
-    "MSeasy" # requires mzR, and xcms
-    "MSeasyTkGUI" # requires MSeasyTkGUI
-    "MSIseq" # requires IRanges
-    "msSurv" # requires graph
-    "muir" # requires DiagrammeR to build
-    "multiDimBio" # requires pcaMethods
-    "MultiRR" # Requires Nlopt
-    "muma" # requires nlopt
-    "mutossGUI" # requires mutoss
-    "mutoss" # requires multtest
-    "mvinfluence" # requires nlopt
-    "MXM" # depends on broken gRbase
-    "NBPSeq" # requires qvalue
-    "nCal" # requires nlopt
-    "NCmisc" # requires BiocInstaller
-    "netClass" # requires samr
-    "nettools" # requires WGCNA
-    "netweavers" # requires BiocGenerics, Biobase, and limma
-    "NHPoisson" # Requires Nlopt
-    "nloptr" # requires nlopt
-    "NLPutils" # requires qdap
-    "nonrandom" # requires nlopt
-    "NORRRM" # can't load SDMTools properly
-    "npIntFactRep" # requires nlopt
-    "NSA" # requires aroma_core
-    "OpenCL" # FIXME: requires CL/opencl.h
-    "OpenMx" # Build Is Broken
-    "optBiomarker" # requires rpanel
-    "ora" # requires ROracle
-    "ordBTL" # requires nlopt
-    "orQA" # requires genefilter
-    "OUwie" # Requires Nlopt
-    "PairViz" # requires graph
-    "pamm" # requires nlopt
-    "PANDA" # requires GO.db
-    "panelAR" # requires nlopt
-    "papeR" # requires nlopt
-    "parboost" # requires nlopt
-    "ParDNAcopy" # requires DNAcopy
-    "parma" # requires nlopt
-    "pathClass" # requires affy, and Biobase
-    "PatternClass" # SDMTools.So: Undefined Symbol: X
-    "pbdBASE" # requires pbdMPI
-    "pbdDEMO" # requires pbdMPI
-    "pbdDMAT" # requires pbdMPI
-    "pbdSLAP" # requires pbdMPI
-    "PBImisc" # Requires Nlopt
-    "pbkrtest" # requires nlopt
-    "PBSddesolve" # fails its test suite for unclear reasons
-    "PBSmapping" # fails its test suite for unclear reasons
-    "pcaL1" # requires clp
-    "pcalg" # requires graph, and RBGL
-    "PCGSE" # requires safe
-    "PCS" # requires multtest
-    "pedigreemm" # requires nlopt
-    "pedometrics" # requires nlopt
-    "PepPrep" # requires biomaRt
-    "pequod" # requires nlopt
-    "PerfMeas" # requires limma, graph, and RBGL
-    "permGPU" # requires Biobase
-    "phia" # requires nlopt
-    "PhViD" # requires LBE
-    "phylocurve" # requires nlopt
-    "phyloTop" # requires nlopt
-    "pi0" # requires qvalue
-    "plmDE" # requires limma
-    "plsRbeta" # requires nlopt
-    "plsRcox" # requires survcomp
-    "plsRglm" # requires nlopt
-    "PMA" # requires impute
-    "pmcgd" # depends on broken mixture
-    "pmclust" # requires MPI running. HELP WANTED!
-    "polyCub" # requires spatstat
-    "polytomous" # requires nlopt
-    "pomp" # requires nlopt
-    "ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
-    "ppiPre" # requires GO.db
-    "predictmeans" # requires nlopt
-    "pRF" # requires multtest
-    "prLogistic" # requires nlopt
-    "propOverlap" # requires Biobase
-    "protiq" # requires graph, and RBGL
-    "PSAboot" # Requires Nlopt
-    "PSCBS" # requires DNAcopy
-    "pubmed_mineR" # requires SSOAP
-    "PubMedWordcloud" # requires GOsummaries
-    "qdap" # requires gender
-    "qgraph" # requires DiagrammeR to build
+    "a4Base" # depends on broken package annaffy-1.41.1
+    "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
+    "adabag" # depends on broken package nlopt-2.4.2
+    "ADaCGH2" # depends on broken package tilingArray-1.47.0
+    "adSplit" # build is broken
+    "AER" # depends on broken package nlopt-2.4.2
+    "afex" # depends on broken package nlopt-2.4.2
+    "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
+    "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
+    "alr3" # depends on broken package nlopt-2.4.2
+    "alr4" # depends on broken package nlopt-2.4.2
+    "altcdfenvs" # depends on broken package affyio-1.37.0
+    "anacor" # depends on broken package nlopt-2.4.2
+    "annaffy" # build is broken
+    "AnnotationForge" # Build Is Broken
+    "AnnotationHub" # depends on broken package interactiveDisplayBase-1.7.0
+    "aods3" # depends on broken package nlopt-2.4.2
+    "apComplex" # build is broken
+    "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
+    "ArrayExpress" # depends on broken package affyio-1.37.0
+    "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
+    "ARTool" # depends on broken package nlopt-2.4.2
+    "attract" # depends on broken package AnnotationForge-1.11.3
+    "BACA" # depends on broken package Category-2.35.1
+    "BAGS" # build is broken
+    "bartMachine" # depends on broken package nlopt-2.4.2
+    "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
+    "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
+    "BiGGR" # depends on broken package rsbml-2.27.0
+    "BiodiversityR" # depends on broken package nlopt-2.4.2
+    "birte" # build is broken
+    "BiSEp" # depends on broken package GOSemSim-1.27.3
+    "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
+    "bmem" # depends on broken package nlopt-2.4.2
+    "bootnet" # depends on broken package nlopt-2.4.2
+    "boss" # depends on broken package nlopt-2.4.2
+    "BradleyTerry2" # depends on broken package nlopt-2.4.2
+    "BRugs" # build is broken
+    "CADFtest" # depends on broken package nlopt-2.4.2
+    "CAFE" # depends on broken package affyio-1.37.0
+    "cAIC4" # depends on broken package nlopt-2.4.2
+    "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
+    "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
+    "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
+    "chipenrich" # build is broken
+    "ChIPQC" # depends on broken package AnnotationForge-1.11.3
+    "ChIPXpress" # depends on broken package affyio-1.37.0
+    "climwin" # depends on broken package nlopt-2.4.2
+    "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
-    "qtlnet" # requires pcalg
-    "qtpaint" # can't find QtCore libraries
-    "qtutils" # requires qtbase
-    "QuACN" # requires graph, RBGL
-    "quanteda" # fails to build
-    "quantification" # requires nlopt
-    "QuasiSeq" # requires edgeR
-    "R2STATS" # REQUIRES NLOPT
-    "RADami" # requires Biostrings
-    "radiant" # requires nlopt
-    "raincpc" # SDMTools.so: undefined symbol: X
-    "rainfreq" # SDMTools.so: undefined symbol: X
-    "RAM" # requires Heatplus
-    "RapidPolygonLookup" # depends on broken PBSmapping
-    "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
-    "rasclass" # requires nlopt
-    "RbioRXN" # requires fmcsR, and KEGGREST
-    "RcmdrMisc" # Requires Nlopt
-    "RcmdrPlugin_BCA" # Requires Nlopt
-    "RcmdrPlugin_coin" # requires nlopt
-    "RcmdrPlugin_depthTools" # requires nlopt
-    "RcmdrPlugin_DoE" # Requires Nlopt
-    "RcmdrPlugin_doex" # requires nlopt
-    "RcmdrPlugin_EACSPIR" # Requires Nlopt
-    "RcmdrPlugin_EBM" # Requires Nlopt
-    "RcmdrPlugin_EcoVirtual" # Requires Nlopt
-    "RcmdrPlugin_epack" # requires nlopt
-    "RcmdrPlugin_EZR" # Requires Nlopt
-    "RcmdrPlugin_FactoMineR" # Requires Nlopt
-    "RcmdrPlugin_HH" # Requires Nlopt
-    "RcmdrPlugin_IPSUR" # Requires Nlopt
-    "RcmdrPlugin_KMggplot2" # Requires Nlopt
-    "RcmdrPlugin_lfstat" # requires nlopt
-    "RcmdrPlugin_MA" # Requires Nlopt
-    "RcmdrPlugin_mosaic" # requires nlopt
-    "RcmdrPlugin_MPAStats" # Requires Nlopt
-    "RcmdrPlugin_NMBU" # Requires Nlopt
-    "RcmdrPlugin_orloca" # requires nlopt
-    "RcmdrPlugin_plotByGroup" # requires nlopt
-    "RcmdrPlugin_pointG" # requires nlopt
-    "RcmdrPlugin_qual" # requires nlopt
-    "RcmdrPlugin_RMTCJags" # Requires Nlopt
-    "RcmdrPlugin_ROC" # Requires Nlopt
-    "RcmdrPlugin_sampling" # requires nlopt
-    "RcmdrPlugin_SCDA" # Requires Nlopt
-    "RcmdrPlugin_seeg" # requires seeg
-    "RcmdrPlugin_SLC" # Requires Nlopt
-    "RcmdrPlugin_SM" # Requires Nlopt
-    "RcmdrPlugin_sos" # requires nlopt
-    "RcmdrPlugin_StatisticalURV" # Requires Nlopt
-    "RcmdrPlugin_steepness" # requires nlopt
-    "RcmdrPlugin_survival" # requires nlopt
-    "RcmdrPlugin_TeachingDemos" # Requires Nlopt
-    "RcmdrPlugin_temis" # requires nlopt
-    "RcmdrPlugin_UCA" # Requires Nlopt
-    "Rcmdr" # Requires Nlopt
-    "Rcplex" # requires cplexAPI
-    "RcppAPT" # configure script depends on /bin/sh
-    "RcppOctave" # Build Is Broken
-    "RcppRedis" # requires Hiredis
-    "rdd" # requires nlopt
-    "rDEA" # no such file or directory
-    "RDieHarder" # requires libdieharder
-    "reader" # requires NCmisc
-    "REBayes" # requires Rmosek
-    "referenceIntervals" # requires nlopt
-    "RefFreeEWAS" # requires isva
-    "refund" # requires nlopt
-    "REST" # REQUIRES NLOPT
-    "retistruct" # depends on broken RImageJROI
-    "rgbif" # requires V8 to build
-    "rgp" # fails self-test
-    "rgpui" # depends on broken rgp
-    "rjade" # requires V8 to build
-    "rJPSGCS" # requires chopsticks
-    "rLindo" # requires LINDO API
-    "rmgarch" # requires nlopt
-    "rminer" # requires nlopt
-    "Rmosek" # requires mosek
-    "RnavGraph" # requires graph, and RBGL
-    "rneos" # requires XMLRPC
-    "RNeXML" # requres taxize
-    "RobLoxBioC" # requires Biobase
-    "RobLox" # requires Biobase
-    "robustlmm" # requires nlopt
-    "rockchalk" # requires nlopt
-    "RockFab" # requires EBImage
-    "ROI_plugin_symphony" # depends on broken Rsymphony
-    "ROracle" # requires OCI
-    "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
-    "rpubchem" # requires nlopt
-    "RQuantLib" # requires QuantLib
-    "rr" # requires nlopt
-    "RSAP" # requires SAPNWRFCSDK
+    "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
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+    "mvinfluence" # depends on broken package nlopt-2.4.2
+    "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
+    "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
+    "nonrandom" # depends on broken package nlopt-2.4.2
+    "NormqPCR" # depends on broken package affyio-1.37.0
+    "NORRRM" # build is broken
+    "npIntFactRep" # depends on broken package nlopt-2.4.2
+    "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
+    "oneChannelGUI" # depends on broken package affyio-1.37.0
+    "OpenCL" # build is broken
+    "openCyto" # depends on broken package ncdfFlow-2.15.2
+    "OpenMx" # build is broken
+    "OperaMate" # depends on broken package Category-2.35.1
+    "ordBTL" # depends on broken package nlopt-2.4.2
+    "OUwie" # depends on broken package nlopt-2.4.2
+    "PADOG" # build is broken
+    "pamm" # depends on broken package nlopt-2.4.2
+    "PANDA" # build is broken
+    "panelAR" # depends on broken package nlopt-2.4.2
+    "panp" # depends on broken package affyio-1.37.0
+    "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
+    "pathClass" # depends on broken package affyio-1.37.0
+    "pathRender" # build is broken
+    "PatternClass" # build is broken
+    "Pbase" # depends on broken package affyio-1.37.0
+    "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
+    "PCpheno" # depends on broken package Category-2.35.1
+    "pdInfoBuilder" # depends on broken package affyio-1.37.0
+    "pdmclass" # build is broken
+    "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
+    "pequod" # depends on broken package nlopt-2.4.2
+    "PGSEA" # depends on broken package annaffy-1.41.1
+    "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
+    "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
+    "pmm" # depends on broken package nlopt-2.4.2
+    "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
+    "ppiStats" # depends on broken package Category-2.35.1
+    "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
+    "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
+    "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
+    "pwOmics" # depends on broken package interactiveDisplayBase-1.7.0
+    "qcmetrics" # build is broken
+    "qgraph" # depends on broken package nlopt-2.4.2
+    "qpcrNorm" # depends on broken package affyio-1.37.0
+    "qtlnet" # depends on broken package nlopt-2.4.2
+    "QUALIFIER" # depends on broken package ncdfFlow-2.15.2
+    "quantification" # depends on broken package nlopt-2.4.2
+    "R2STATS" # depends on broken package nlopt-2.4.2
+    "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
+    "rasclass" # depends on broken package nlopt-2.4.2
+    "RbioRXN" # depends on broken package ChemmineR-2.21.7
+    "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
+    "RcmdrPlugin_BCA" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_coin" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_depthTools" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_DoE" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_doex" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_EACSPIR" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_EBM" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_EcoVirtual" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_epack" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_EZR" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_FactoMineR" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_HH" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_IPSUR" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_KMggplot2" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_lfstat" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_MA" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_mosaic" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_MPAStats" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_NMBU" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_orloca" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_plotByGroup" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_pointG" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_qual" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_RMTCJags" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_ROC" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_sampling" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_SCDA" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_seeg" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_SLC" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_SM" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_sos" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_StatisticalURV" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_steepness" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_survival" # depends on broken package nlopt-2.4.2
+    "RcmdrPlugin_TeachingDemos" # depends on broken package nlopt-2.4.2
+    "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
+    "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
+    "RDieHarder" # build is broken
+    "ReactomePA" # depends on broken package GOSemSim-1.27.3
+    "ReadqPCR" # depends on broken package affyio-1.37.0
+    "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
+    "Repitools" # depends on broken package affyio-1.37.0
+    "ReportingTools" # depends on broken package Category-2.35.1
+    "REST" # depends on broken package nlopt-2.4.2
+    "rgp" # build is broken
+    "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
+    "Risa" # depends on broken package affyio-1.37.0
+    "rMAT" # build is broken
+    "rmgarch" # depends on broken package nlopt-2.4.2
+    "rminer" # depends on broken package nlopt-2.4.2
+    "RmiR" # Build Is Broken
+    "Rmosek" # build is broken
+    "RNAinteract" # depends on broken package Category-2.35.1
+    "RNAither" # depends on broken package nlopt-2.4.2
+    "RnavGraph" # build is broken
+    "Rnits" # depends on broken package affyio-1.37.0
+    "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
+    "rols" # 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
+    "RQuantLib" # build is broken
+    "rr" # depends on broken package nlopt-2.4.2
+    "RSAP" # build is broken
+    "rsbml" # build is broken
     "rscala" # build is broken
-    "RSDA" # REQUIRES NLOPT
-    "RSeed" # requires RBGL, and graph
-    "rsig" # requires survcomp
-    "RSNPset" # requires qvalue
-    "rsprng" # requres sprng
-    "Rsymphony" # FIXME: requires SYMPHONY
-    "rugarch" # requires nlopt
-    "RVAideMemoire" # Requires Nlopt
-    "RVFam" # Requires Nlopt
-    "RVideoPoker" # requires Rpanel
-    "ryouready" # requires nlopt
-    "rysgran" # requires soiltexture
-    "sampleSelection" # requires nlopt
-    "samr" # requires impute
-    "sdcMicroGUI" # requires nlopt
-    "sdcMicro" # requires nlopt
-    "SDD" # requires rpanel
-    "seeg" # requires spatstat
-    "selectspm" # depends on broken ecespa
-    "semdiag" # requires DiagrammeR to build
-    "semGOF" # requires DiagrammeR to build
-    "semiArtificial" # requires RSNNS
-    "semPlot" # requires DiagrammeR to build
-    "sem" # requires DiagrammeR to build
-    "SensoMineR" # Requires Nlopt
-    "SeqFeatR" # requires Biostrings, qvalue, and widgetTools
-    "SeqGrapheR" # depends on Biostrings
-    "sequenza" # requires copynumber
-    "SGCS" # requires spatstat
-    "siar" # requires spatstat
-    "SID" # requires pcalg
-    "SimRAD" # requires Biostrings, and ShortRead
-    "SimSeq" # requires edgeR
-    "siplab" # requires spatstat
-    "sirt" # requires DiagrammeR to build
-    "sjPlot" # requires nlopt
-    "smart" # requires PMA
-    "snpEnrichment" # requires snpStats
-    "snplist" # requires biomaRt
-    "snpStatsWriter" # requires snpStats
-    "SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
-    "SOD" # depends on proprietary cudatoolkit
-    "soilphysics" # requires rpanel
-    "spacom" # requires nlopt
-    "sparr" # requires spatstat
-    "spatialsegregation" # requires spatstat
-    "SpatialVx" # requires spatstat
-    "speaq" # requires MassSpecWavelet
-    "specificity" # requires nlopt
-    "spocc" # requires leafletR
-    "SQDA" # requires limma
-    "ssizeRNA" # depends on missing 'Biobase', 'edgeR', 'limma', 'qvalue'
-    "ssmrob" # requires nlopt
-    "stagePop" # depends on broken PBSddesolve
-    "statar" # depends on broken lfe
-    "Statomica" # requires Biobase, multtest
-    "stcm" # requires nlopt
-    "stepp" # requires nlopt
-    "stpp" # requires spatstat
-    "structSSI" # requires multtest
-    "strum" # requires Rgraphviz
-    "superbiclust" # requires fabia
-    "Surrogate" # Requires Nlopt
-    "surveillance" # requires polyCub
-    "survJamda" # depends on missing survcomp
-    "swamp" # requires impute
-    "switchr" # build is broken
-    "switchrGist" # requires switchr
-    "sybilSBML" # requires libSBML
-    "systemfit" # requires nlopt
-    "taxize" # requres bold
-    "TcGSA" # requires multtest
-    "TDMR" # REQUIRES NLOPT
-    "tigerstats" # requires nlopt
-    "timeSeq" # depends on missing edgeR
-    "topologyGSA" # requires gRbase
-    "TR8" # requres taxize
-    "TriMatch" # Requires Nlopt
-    "trip" # requires spatstat
-    "TROM" # misses undeclared dependencies topGO', 'AnnotationDbi', 'GO.db'
-    "ttScreening" # requires sva, and limma
-    "userfriendlyscience" # requires nlopt
-    "V8" # compilation error
-    "VIMGUI" # REQUIRES NLOPT
-    "VIM" # REQUIRES NLOPT
-    "vmsbase" # depends on broken PBSmapping
-    "vows" # requires rpanel
-    "wfe" # requires nlopt
-    "WGCNA" # requires impute
-    "wgsea" # requires snpStats
-    "WideLM" # depends on proprietary cudatoolkit
-    "x_ent" # requires opencpu
-    "xergm" # requires nlopt
-    "ZeligMultilevel" # Requires Nlopt
-    "zetadiv" # requires nlopt
-    "zoib" # tarball is invalid on server
+    "RSDA" # depends on broken package nlopt-2.4.2
+    "Rsubread" # Build Is Broken
+    "Rsymphony" # build is broken
+    "rTANDEM" # build is broken
+    "RTN" # depends on broken package nlopt-2.4.2
+    "rugarch" # depends on broken package nlopt-2.4.2
+    "RUVcorr" # build is broken
+    "RUVnormalize" # Build Is Broken
+    "RVAideMemoire" # depends on broken package nlopt-2.4.2
+    "RVFam" # depends on broken package nlopt-2.4.2
+    "ryouready" # depends on broken package nlopt-2.4.2
+    "sampleSelection" # depends on broken package nlopt-2.4.2
+    "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
+    "seeg" # depends on broken package nlopt-2.4.2
+    "sem" # depends on broken package nlopt-2.4.2
+    "semdiag" # depends on broken package nlopt-2.4.2
+    "SemDist" # Build Is Broken
+    "semGOF" # depends on broken package nlopt-2.4.2
+    "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
+    "seqTools" # build is broken
+    "SimBindProfiles" # depends on broken package affyio-1.37.0
+    "simpleaffy" # depends on broken package affyio-1.37.0
+    "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
+    "SLGI" # depends on broken package apComplex-2.35.0
+    "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
+    "snpStats" # build is broken
+    "snpStatsWriter" # depends on broken package snpStats-1.19.0
+    "SOD" # depends on broken package cudatoolkit-5.5.22
+    "spacom" # depends on broken package nlopt-2.4.2
+    "specificity" # depends on broken package nlopt-2.4.2
+    "sscore" # depends on broken package affyio-1.37.0
+    "ssmrob" # depends on broken package nlopt-2.4.2
+    "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
+    "stcm" # depends on broken package nlopt-2.4.2
+    "stepp" # depends on broken package nlopt-2.4.2
+    "stringgaussnet" # build is broken
+    "Surrogate" # depends on broken package nlopt-2.4.2
+    "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
+    "TcGSA" # depends on broken package nlopt-2.4.2
+    "TDMR" # depends on broken package nlopt-2.4.2
+    "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
+    "topGO" # build is broken
+    "tRanslatome" # depends on broken package GOSemSim-1.27.3
+    "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
+    "unifiedWMWqPCR" # depends on broken package affyio-1.37.0
+    "userfriendlyscience" # depends on broken package nlopt-2.4.2
+    "V8" # build is broken
+    "VanillaICE" # depends on broken package affyio-1.37.0
+    "VIM" # depends on broken package nlopt-2.4.2
+    "VIMGUI" # depends on broken package nlopt-2.4.2
+    "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
+    "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
+    "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
   ];
 
   otherOverrides = old: new: {
@@ -1391,6 +1659,10 @@ let
       ];
     });
 
+    V8 = old.V8.overrideDerivation (attrs: {
+      preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
+    });
+
   };
 in
   self