anchor.diff:  
     # 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
       "crmn" # requires pcaMethods, and Biobase
       "Crossover" # fails self-test
       "CrypticIBDcheck" # requires rJPSGCS
       "cudaBayesreg" # requres Rmath
  +    "curl" # build is broken
       "curvHDR" # requires flowCore
       "D2C" # requires gRbase
       "DAAGbio" # requires limma
       "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, 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
       "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
  
positive.code:     "msSurv" # requires graph
      "muir" # requires DiagrammeR to build
      "multiDimBio" # requires pcaMethods
      "mutossGUI" # requires mutoss
      "mutoss" # requires multtest
      "MXM" # depends on broken gRbase
      "NBPSeq" # requires qvalue
      "NCmisc" # requires BiocInstaller
      "netClass" # requires samr
      "nettools" # requires WGCNA
      "netweavers" # requires BiocGenerics, Biobase, and limma
      "NLPutils" # requires qdap
      "NORRRM" # can't load SDMTools properly
      "NSA" # requires aroma_core
      "OpenCL" # FIXME: requires CL/opencl.h
      "optBiomarker" # requires rpanel
      "ora" # requires ROracle
      "orQA" # requires genefilter
      "PairViz" # requires graph
      "PANDA" # requires GO.db
      "ParDNAcopy" # requires DNAcopy
      "pathClass" # requires affy, and Biobase
      "PatternClass" # SDMTools.So: Undefined Symbol: X
      "pbdBASE" # requires pbdMPI
      "pbdDEMO" # requires pbdMPI
      "pbdDMAT" # requires pbdMPI
      "pbdSLAP" # requires pbdMPI
      "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
      "PepPrep" # requires biomaRt
      "PerfMeas" # requires limma, graph, and RBGL
      "permGPU" # requires Biobase
      "PhViD" # requires LBE
      "pi0" # requires qvalue
      "plmDE" # requires limma
      "plsRcox" # requires survcomp
      "PMA" # requires impute
      "pmcgd" # depends on broken mixture
      "pmclust" # requires MPI running. HELP WANTED!
      "polyCub" # requires spatstat
      "ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
      "pRF" # requires multtest
      "propOverlap" # requires Biobase
      "protiq" # requires graph, and RBGL
      "PSCBS" # requires DNAcopy
      "pubmed_mineR" # requires SSOAP
      "PubMedWordcloud" # requires GOsummaries
      "qdap" # requires gender
      "qtlnet" # requires pcalg
      "qtpaint" # can't find QtCore libraries
      "QuACN" # requires graph, RBGL
      "quanteda" # fails to build
      "QuasiSeq" # requires edgeR
      "RADami" # requires Biostrings
      "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
      "RbioRXN" # requires fmcsR, and KEGGREST
      "RcmdrPlugin_seeg" # requires seeg
      "Rcplex" # requires cplexAPI
      "RcppAPT" # configure script depends on /bin/sh
      "RcppRedis" # requires Hiredis
      "rDEA" # no such file or directory
      "RDieHarder" # requires libdieharder
      "reader" # requires NCmisc
      "REBayes" # requires Rmosek
      "RefFreeEWAS" # requires isva
      "retistruct" # depends on broken RImageJROI
      "rgp" # fails self-test
      "rgpui" # depends on broken rgp
      "RImageJROI" # requires spatstat
      "rjade" # requires V8 to build
      "rJPSGCS" # requires chopsticks
      "rLindo" # requires LINDO API
      "Rmosek" # requires mosek
      "RnavGraph" # requires graph, and RBGL
      "rneos" # requires XMLRPC
      "RNeXML" # requres taxize
      "RobLoxBioC" # requires Biobase
      "RobLox" # requires Biobase
      "RockFab" # requires EBImage
      "ROI_plugin_symphony" # depends on broken Rsymphony
      "ROracle" # requires OCI
      "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
      "RQuantLib" # requires QuantLib
      "RSAP" # requires SAPNWRFCSDK
      "RSeed" # requires RBGL, and graph
      "rsig" # requires survcomp
      "RSNPset" # requires qvalue
      "Rsymphony" # FIXME: requires SYMPHONY
      "RVideoPoker" # requires Rpanel
      "rysgran" # requires soiltexture
      "samr" # requires impute
      "SDD" # requires rpanel
      "seeg" # requires spatstat
      "selectspm" # depends on broken ecespa
      "semiArtificial" # requires RSNNS
      "SeqFeatR" # requires Biostrings, qvalue, and widgetTools
      "SeqGrapheR" # depends on Biostrings
      "sequenza" # requires copynumber
  
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: {
  