anchor.diff:      "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
  
positive.code: 
    # Packages which cannot be installed due to lack of dependencies or other reasons.
    brokenPackages = [
      "ACNE" # requires aroma_affymetrix
      "Actigraphy" # SDMTools.so: undefined symbol: X
      "adaptsmoFMRI" # requires spatstat
      "ads" # requires spatstat
      "agridat" # requires pcaMethods
      "aLFQ" # requires protiq
      "AntWeb" # requires leafletR
      "aoristic" # requires spatstat
      "apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
      "aroma_affymetrix" # requires aroma_core
      "aroma_cn" # requires PSCBS
      "aroma_core" # requires PSCBS
      "ArrayBin" # requires SAGx
      "babel" # requires edgeR
      "BACA" # requires RDAVIDWebService
      "BcDiag" # requires fabia
      "bdvis" # requres taxize
      "beadarrayFilter" # requires beadarray
      "beadarrayMSV" # requires Biobase, geneplotter, andlimma
      "bigGP" # requires MPI running. HELP WANTED!
      "bigpca" # requires NCmisc
      "Biograph" # requires mvna
      "biotools" # requires rpanel
      "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
      "BLCOP" # depends on broken fPortfolio
      "bmrm" # requires clpAPI
      "branchLars" # requires Rgraphviz
      "BRugs" # requires OpenBUGS
      "calmate" # requires aroma_core
      "CARrampsOcl" # depends on OpenCL
      "CHAT" # requires DNAcopy
      "ChemoSpec" # depends on broken speaq
      "classGraph" # requires graph, and Rgraphviz
      "clpAPI" # requires clp
      "compendiumdb" # requires Biobase
      "CORM" # requires limma
      "cplexAPI" # requires CPLEX
      "crmn" # requires pcaMethods, and Biobase
      "Crossover" # fails self-test
      "CrypticIBDcheck" # requires rJPSGCS
      "cudaBayesreg" # requres Rmath
      "curvHDR" # requires flowCore
      "D2C" # requires gRbase
      "DAAGbio" # requires limma
      "daff" # requires V8 to build
      "dagbag" # requires Rlapack
      "DBKGrad" # requires SDD
      "dbmss" # requires spatstat
      "DCGL" # requires limma
      "dcGOR" # requires dnet
      "demi" # requires affy, affxparser, and oligo
      "DepthProc" # requires samr
      "DiagrammeR" # requires V8 to build
      "DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest'
      "Digiroo2" # requires spatstat
      "dixon" # requires spatstat
      "dnet" # requires supraHex, graph, Rgraphviz, and Biobase
      "doMPI" # requires MPI running. HELP WANTED!
      "dpcR" # requires spatstat
      "DSpat" # requires spatstat
      "ecespa" # requires spatstat
      "ecoengine" # requires leafletR
      "ecospat" # requires spatstat
      "edgeRun" # requires edgeR
      "EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
      "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
      "epoc" # requires graph, and Rgraphviz
      "erpR" # requires rpanel
      "ETAS" # requires spatstat
      "eulerian" # requires graph
      "evobiR" # requres taxiz
      "evora" # requires qvalue
      "ExomeDepth" # requires GenomicRanges, and Rsamtools
      "FAMT" # requires impute
      "fdrDiscreteNull" # requires edgeR
      "FHtest" # requires interval
      "flexCWM" # depends on broken mixture
      "fPortfolio" # requires rneos
      "FunctionalNetworks" # requires breastCancerVDX, and Biobase
      "gamlss_demo" # requires rpanel
      "GeneticTools" # requires snpStats
      "geojsonio" # requires V8 to build
      "GExMap" # requires Biobase and multtest
      "gitter" # requires EBImage
      "glmgraph" # test suite says: "undefined symbol: dgemv_"
      "gmatrix" # depends on proprietary cudatoolkit
      "gMCP" # fails self-test
      "GOGANPA" # requires WGCNA
      "gputools" # depends on proprietary cudatoolkit
      "gRain" # requires gRbase
      "gRapHD" # requires graph
      "gRbase" # requires RBGL, and graph
      "gRc" # requires gRbase
      "gridDebug" # requires gridGraphviz
  
negative.code:     "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
      "xml2" # build is broken
      "ZeligMultilevel" # Requires Nlopt
      "zetadiv" # requires nlopt
      "zoib" # tarball is invalid on server
    ];
  
    otherOverrides = old: new: {
  