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r-modules: disable broken packages to avoid Hydra evaluation errors

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This commit is contained in:
Peter Simons 2015-06-16 10:44:52 +02:00
parent c9743be445
commit d4c810cccd
1 changed files with 273 additions and 5 deletions
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pkgs/development/r-modules/default.nix
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@ -649,97 +649,191 @@ let
# Packages which cannot be installed due to lack of dependencies or other reasons. # Packages which cannot be installed due to lack of dependencies or other reasons.
brokenPackages = [ brokenPackages = [
"abd" # requires nlopt
"ACNE" # requires aroma_affymetrix "ACNE" # requires aroma_affymetrix
"Actigraphy" # SDMTools.so: undefined symbol: X "Actigraphy" # SDMTools.so: undefined symbol: X
"adabag" # requires nlopt
"adaptsmoFMRI" # requires spatstat "adaptsmoFMRI" # requires spatstat
"ads" # requires spatstat "ads" # requires spatstat
"AER" # REQUIRES NLOPT
"afex" # requires nlopt
"agRee" # requires nlopt
"agridat" # requires pcaMethods "agridat" # requires pcaMethods
"aLFQ" # requires protiq "aLFQ" # requires protiq
"alr3" # requires nlopt
"alr4" # requires nlopt
"anacor" # requires nlopt
"AntWeb" # requires leafletR "AntWeb" # requires leafletR
"aods3" # requires nlopt
"aoristic" # requires spatstat "aoristic" # requires spatstat
"apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light "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_affymetrix" # requires aroma_core
"aroma_cn" # requires PSCBS "aroma_cn" # requires PSCBS
"aroma_core" # requires PSCBS "aroma_core" # requires PSCBS
"ArrayBin" # requires SAGx "ArrayBin" # requires SAGx
"ARTool" # Requires Nlopt
"babel" # requires edgeR "babel" # requires edgeR
"BACA" # requires RDAVIDWebService "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 "BcDiag" # requires fabia
"bdvis" # requres taxize "bdvis" # requres taxize
"beadarrayFilter" # requires beadarray "beadarrayFilter" # requires beadarray
"beadarrayMSV" # requires Biobase, geneplotter, andlimma "beadarrayMSV" # requires Biobase, geneplotter, andlimma
"bgmm" # requires nlopt
"BIFIEsurvey" # requires DiagrammeR to build
"bigGP" # requires MPI running. HELP WANTED! "bigGP" # requires MPI running. HELP WANTED!
"bigpca" # requires NCmisc "bigpca" # requires NCmisc
"BiodiversityR" # Requires Nlopt
"Biograph" # requires mvna "Biograph" # requires mvna
"biotools" # requires rpanel "biotools" # requires rpanel
"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
"BLCOP" # depends on broken fPortfolio "BLCOP" # depends on broken fPortfolio
"blmeco" # requires nlopt
"blme" # requires nlopt
"bmd" # requires nlopt
"bmem" # requires DiagrammeR to build
"bmrm" # requires clpAPI "bmrm" # requires clpAPI
"bootnet" # requires IsingFit
"boss" # requires nlopt
"BradleyTerry2" # Requires Nlopt
"branchLars" # requires Rgraphviz "branchLars" # requires Rgraphviz
"BRugs" # requires OpenBUGS "BRugs" # requires OpenBUGS
"CADFtest" # Requires Nlopt
"cAIC4" # requires nlopt
"calmate" # requires aroma_core "calmate" # requires aroma_core
"candisc" # requires nlopt
"carcass" # requires nlopt
"caretEnsemble" # requires nlopt
"caret" # requires nlopt
"CARrampsOcl" # depends on OpenCL "CARrampsOcl" # depends on OpenCL
"car" # requires nlopt
"CCpop" # Requires Nlopt
"ChainLadder" # Requires Nlopt
"CHAT" # requires DNAcopy "CHAT" # requires DNAcopy
"ChemoSpec" # depends on broken speaq "ChemoSpec" # depends on broken speaq
"classGraph" # requires graph, and Rgraphviz "classGraph" # requires graph, and Rgraphviz
"climwin" # requires nlopt
"CLME" # REQUIRES NLOPT
"clpAPI" # requires clp "clpAPI" # requires clp
"clusterPower" # requires nlopt
"compendiumdb" # requires Biobase "compendiumdb" # requires Biobase
"conformal" # requires nlopt
"corHMM" # requires nlopt
"CORM" # requires limma "CORM" # requires limma
"CosmoPhotoz" # Requires Nlopt
"cp4p" # build is broken
"cplexAPI" # requires CPLEX "cplexAPI" # requires CPLEX
"crmn" # requires pcaMethods, and Biobase "crmn" # requires pcaMethods, and Biobase
"Crossover" # fails self-test "Crossover" # fails self-test
"CrypticIBDcheck" # requires rJPSGCS "CrypticIBDcheck" # requires rJPSGCS
"cudaBayesreg" # requres Rmath "cudaBayesreg" # requres Rmath
"curl" # build is broken
"curvHDR" # requires flowCore "curvHDR" # requires flowCore
"D2C" # requires gRbase "D2C" # requires gRbase
"DAAGbio" # requires limma "DAAGbio" # requires limma
"daff" # requires V8 to build "daff" # requires V8 to build
"dagbag" # requires Rlapack "dagbag" # requires Rlapack
"DAMisc" # Requires Nlopt
"DBKGrad" # requires SDD "DBKGrad" # requires SDD
"dbmss" # requires spatstat "dbmss" # requires spatstat
"DCGL" # requires limma "DCGL" # requires limma
"dcGOR" # requires dnet "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 "demi" # requires affy, affxparser, and oligo
"DepthProc" # requires samr "DepthProc" # requires samr
"DiagrammeR" # requires V8 to build "DiagrammeR" # requires V8 to build
"DiagTest3Grp" # Requires Nlopt
"DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest' "DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest'
"difR" # requires nlopt
"Digiroo2" # requires spatstat "Digiroo2" # requires spatstat
"discSurv" # requires nlopt
"DistatisR" # Requires Nlopt
"diveRsity" # requires DiagrammeR to build
"dixon" # requires spatstat "dixon" # requires spatstat
"dnet" # requires supraHex, graph, Rgraphviz, and Biobase "dnet" # requires supraHex, graph, Rgraphviz, and Biobase
"doMPI" # requires MPI running. HELP WANTED! "doMPI" # requires MPI running. HELP WANTED!
"dpa" # requires DiagrammeR to build
"dpcR" # requires spatstat "dpcR" # requires spatstat
"drc" # requires nlopt
"drfit" # requires nlopt
"drsmooth" # requires nlopt
"DSpat" # requires spatstat "DSpat" # requires spatstat
"dynlm" # requires nlopt
"easyanova" # requires nlopt
"ecespa" # requires spatstat "ecespa" # requires spatstat
"ecoengine" # requires leafletR "ecoengine" # requires leafletR
"ecospat" # requires spatstat "ecospat" # requires spatstat
"edgeRun" # requires edgeR "edgeRun" # requires edgeR
"eeptools" # requires nlopt
"EffectLiteR" # Requires Nlopt
"effects" # requires nlopt
"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi "EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
"EnQuireR" # Requires Nlopt
"episplineDensity" # requires nlopt
"epoc" # requires graph, and Rgraphviz "epoc" # requires graph, and Rgraphviz
"epr" # requires nlopt
"erer" # requires nlopt
"erpR" # requires rpanel "erpR" # requires rpanel
"ETAS" # requires spatstat "ETAS" # requires spatstat
"eulerian" # requires graph "eulerian" # requires graph
"evobiR" # requres taxiz "evobiR" # requres taxiz
"evora" # requires qvalue "evora" # requires qvalue
"ExomeDepth" # requires GenomicRanges, and Rsamtools "ExomeDepth" # requires GenomicRanges, and Rsamtools
"extRemes" # requires nlopt
"ez" # requires nlopt
"FactoMineR" # Requires Nlopt
"Factoshiny" # Requires Nlopt
"FAMT" # requires impute "FAMT" # requires impute
"faoutlier" # requires DiagrammeR to build
"fastR" # requires nlopt
"fdrDiscreteNull" # requires edgeR "fdrDiscreteNull" # requires edgeR
"FDRreg" # Requires Nlopt
"FHtest" # requires interval "FHtest" # requires interval
"flexCWM" # depends on broken mixture "flexCWM" # depends on broken mixture
"fPortfolio" # requires rneos "fPortfolio" # requires rneos
"freqweights" # requires nlopt
"fscaret" # requires nlopt
"FunctionalNetworks" # requires breastCancerVDX, and Biobase "FunctionalNetworks" # requires breastCancerVDX, and Biobase
"fxregime" # requires nlopt
"gamclass" # requires nlopt
"gamlss_demo" # requires rpanel "gamlss_demo" # requires rpanel
"gamm4" # requires nlopt
"gcmr" # requires nlopt
"GDAtools" # Requires Nlopt
"GeneticTools" # requires snpStats "GeneticTools" # requires snpStats
"genridge" # requires nlopt
"geojsonio" # requires V8 to build "geojsonio" # requires V8 to build
"GExMap" # requires Biobase and multtest "GExMap" # requires Biobase and multtest
"gimme" # requires DiagrammeR to build
"gitter" # requires EBImage "gitter" # requires EBImage
"glmgraph" # test suite says: "undefined symbol: dgemv_" "glmgraph" # test suite says: "undefined symbol: dgemv_"
"gmatrix" # depends on proprietary cudatoolkit "gmatrix" # depends on proprietary cudatoolkit
"gMCP" # fails self-test "gMCP" # fails self-test
"GOGANPA" # requires WGCNA "GOGANPA" # requires WGCNA
"gplm" # requires nlopt
"gputools" # depends on proprietary cudatoolkit "gputools" # depends on proprietary cudatoolkit
"gRain" # requires gRbase "gRain" # requires gRbase
"granova" # requires nlopt
"gRapHD" # requires graph "gRapHD" # requires graph
"graphicalVAR" # requires DiagrammeR to build
"GraphPCA" # Requires Nlopt
"gRbase" # requires RBGL, and graph "gRbase" # requires RBGL, and graph
"gRc" # requires gRbase "gRc" # requires gRbase
"gridDebug" # requires gridGraphviz "gridDebug" # requires gridGraphviz
@ -748,51 +842,101 @@ let
"gRim" # requires gRbase "gRim" # requires gRbase
"GSAgm" # requires edgeR "GSAgm" # requires edgeR
"GUIDE" # requires rpanel "GUIDE" # requires rpanel
"GWAF" # REQUIRES NLOPT
"h2o" # tries to download some h2o.jar during its build "h2o" # tries to download some h2o.jar during its build
"h5" # depends on missing h5 system library
"hasseDiagram" # requires Rgraphviz "hasseDiagram" # requires Rgraphviz
"hbsae" # requires nlopt
"hddplot" # requires multtest "hddplot" # requires multtest
"heplots" # requires nlopt
"HH" # REQUIRES NLOPT
"HierO" # requires rneos "HierO" # requires rneos
"HiPLARM" # requires MAGMA or PLASMA "HiPLARM" # requires MAGMA or PLASMA
"HistDAWass" # Requires Nlopt
"HLMdiag" # Requires Nlopt
"hpoPlot" # requires Rgraphviz "hpoPlot" # requires Rgraphviz
"hsdar" # fails to build "hsdar" # fails to build
"HTSCluster" # requires edgeR "HTSCluster" # requires edgeR
"hysteresis" # requires nlopt
"IATscores" # requires DiagrammeR to build
"ibd" # requires nlopt
"iccbeta" # requires nlopt
"iFes" # depends on proprietary cudatoolkit "iFes" # depends on proprietary cudatoolkit
"imputeLCMD" # requires pcaMethods, and impute "imputeLCMD" # requires pcaMethods, and impute
"imputeR" # requires nlopt
"in2extRemes" # requires nlopt
"incReg" # requires nlopt
"inferference" # requires nlopt
"influence_ME" # requires nlopt
"intamapInteractive" # requires spatstat "intamapInteractive" # requires spatstat
"interval" # requires Icens "interval" # requires Icens
"ionflows" # requires Biostrings "ionflows" # requires Biostrings
"iRefR" # requires graph, and RBGL "iRefR" # requires graph, and RBGL
"IsingFit" # requires DiagrammeR to build
"IsoGene" # requires Biobase, and affy "IsoGene" # requires Biobase, and affy
"isva" # requires qvalue "isva" # requires qvalue
"ivpack" # requires nlopt
"JAGUAR" # REQUIRES NLOPT
"jomo" # linking errors "jomo" # linking errors
"js" # requires broken V8 "js" # requires broken V8
"KANT" # requires affy, and Biobase "KANT" # requires affy, and Biobase
"ktspair" # requires Biobase "ktspair" # requires Biobase
"latticeDensity" # requires spatstat "latticeDensity" # requires spatstat
"lawn" # requires DiagrammeR to build
"lawn" # requires V8 to build
"leapp" # requires sva "leapp" # requires sva
"learnstats" # requires nlopt
"lefse" # SDMTools.so: undefined symbol: X "lefse" # SDMTools.so: undefined symbol: X
"lessR" # requires nlopt
"lfe" # fails to compile "lfe" # fails to compile
"lgcp" # requires rpanel "lgcp" # requires rpanel
"LinRegInteractive" # requires Rpanel "LinRegInteractive" # requires Rpanel
"lme4" # requires nlopt
"LMERConvenienceFunctions" # Requires Nlopt
"lmerTest" # requires nlopt
"lmSupport" # requires nlopt
"LogisticDx" # requires gRbase "LogisticDx" # requires gRbase
"longpower" # requires nlopt
"LOST" # requires pcaMethods "LOST" # requires pcaMethods
"ltsk" # requires Rlapack and Rblas "ltsk" # requires Rlapack and Rblas
"magma" # requires MAGMA
"MAMA" # requires metaMA "MAMA" # requires metaMA
"marked" # requires nlopt
"MaxPro" # Requires Nlopt
"mbest" # requires nlopt
"meboot" # requires nlopt
"MEET" # requires pcaMethods, and seqLogo "MEET" # requires pcaMethods, and seqLogo
"MEMSS" # REQUIRES NLOPT
"metabolomics" # depends on broken crmn "metabolomics" # depends on broken crmn
"MetaDE" # requires impute, and Biobase "MetaDE" # requires impute, and Biobase
"metagear" # build is broken
"MetaLandSim" # requires Biobase "MetaLandSim" # requires Biobase
"metaMA" # requires limma "metaMA" # requires limma
"metaMix" # requires MPI running. HELP WANTED! "metaMix" # requires MPI running. HELP WANTED!
"metaplus" # requires nlopt
"metaSEM" # requires OpenMx
"Metatron" # Requires Nlopt
"mGSZ" # requires Biobase, and limma "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 "MigClim" # SDMTools.So: Undefined Symbol: X
"migui" # requires nlopt
"minimist" # requires broken V8 "minimist" # requires broken V8
"mi" # requires nlopt
"miRtest" # requires globaltest, GlobalAncova, and limma "miRtest" # requires globaltest, GlobalAncova, and limma
"missMDA" # requires nlopt
"mixAK" # requires nlopt
"MixGHD" # requires mixture to build "MixGHD" # requires mixture to build
"mixlm" # requires nlopt
"MixMAP" # Requires Nlopt
"mixture" # mixture.so: undefined symbol: dtrmm_ "mixture" # mixture.so: undefined symbol: dtrmm_
"mlmRev" # requires nlopt
"mlVAR" # requires DiagrammeR to build
"MM2S" # BUILD IS BROKEN
"moduleColor" # requires impute "moduleColor" # requires impute
"mongolite" # doesn't find OpenSSL "mongolite" # doesn't find OpenSSL
"mosaic" # requires nlopt
"msarc" # requires AnnotationDbi "msarc" # requires AnnotationDbi
"MSeasy" # requires mzR, and xcms "MSeasy" # requires mzR, and xcms
"MSeasyTkGUI" # requires MSeasyTkGUI "MSeasyTkGUI" # requires MSeasyTkGUI
@ -800,106 +944,209 @@ let
"msSurv" # requires graph "msSurv" # requires graph
"muir" # requires DiagrammeR to build "muir" # requires DiagrammeR to build
"multiDimBio" # requires pcaMethods "multiDimBio" # requires pcaMethods
"MultiRR" # Requires Nlopt
"muma" # requires nlopt
"mutossGUI" # requires mutoss "mutossGUI" # requires mutoss
"mutoss" # requires multtest "mutoss" # requires multtest
"mvinfluence" # requires nlopt
"MXM" # depends on broken gRbase "MXM" # depends on broken gRbase
"NBPSeq" # requires qvalue "NBPSeq" # requires qvalue
"nCal" # requires nlopt
"NCmisc" # requires BiocInstaller "NCmisc" # requires BiocInstaller
"netClass" # requires samr "netClass" # requires samr
"nettools" # requires WGCNA "nettools" # requires WGCNA
"netweavers" # requires BiocGenerics, Biobase, and limma "netweavers" # requires BiocGenerics, Biobase, and limma
"NHPoisson" # Requires Nlopt
"nloptr" # requires nlopt
"NLPutils" # requires qdap "NLPutils" # requires qdap
"nonrandom" # requires nlopt
"NORRRM" # can't load SDMTools properly "NORRRM" # can't load SDMTools properly
"npIntFactRep" # requires nlopt
"NSA" # requires aroma_core "NSA" # requires aroma_core
"OpenCL" # FIXME: requires CL/opencl.h "OpenCL" # FIXME: requires CL/opencl.h
"OpenMx" # Build Is Broken
"optBiomarker" # requires rpanel "optBiomarker" # requires rpanel
"ora" # requires ROracle "ora" # requires ROracle
"ordBTL" # requires nlopt
"orQA" # requires genefilter "orQA" # requires genefilter
"OUwie" # Requires Nlopt
"PairViz" # requires graph "PairViz" # requires graph
"pamm" # requires nlopt
"PANDA" # requires GO.db "PANDA" # requires GO.db
"pander" # build is broken
"panelAR" # requires nlopt
"papeR" # requires nlopt
"parboost" # requires nlopt
"ParDNAcopy" # requires DNAcopy "ParDNAcopy" # requires DNAcopy
"parma" # requires nlopt
"pathClass" # requires affy, and Biobase "pathClass" # requires affy, and Biobase
"PatternClass" # SDMTools.So: Undefined Symbol: X "PatternClass" # SDMTools.So: Undefined Symbol: X
"pbdBASE" # requires pbdMPI "pbdBASE" # requires pbdMPI
"pbdDEMO" # requires pbdMPI "pbdDEMO" # requires pbdMPI
"pbdDMAT" # requires pbdMPI "pbdDMAT" # requires pbdMPI
"pbdSLAP" # requires pbdMPI "pbdSLAP" # requires pbdMPI
"PBImisc" # Requires Nlopt
"pbkrtest" # requires nlopt
"PBSddesolve" # fails its test suite for unclear reasons "PBSddesolve" # fails its test suite for unclear reasons
"PBSmapping" # fails its test suite for unclear reasons "PBSmapping" # fails its test suite for unclear reasons
"pcaL1" # requires clp "pcaL1" # requires clp
"pcalg" # requires graph, and RBGL "pcalg" # requires graph, and RBGL
"PCGSE" # requires safe "PCGSE" # requires safe
"PCS" # requires multtest "PCS" # requires multtest
"pedigreemm" # requires nlopt
"pedometrics" # requires nlopt
"PepPrep" # requires biomaRt "PepPrep" # requires biomaRt
"pequod" # requires nlopt
"PerfMeas" # requires limma, graph, and RBGL "PerfMeas" # requires limma, graph, and RBGL
"permGPU" # requires Biobase "permGPU" # requires Biobase
"phia" # requires nlopt
"PhViD" # requires LBE "PhViD" # requires LBE
"phylocurve" # requires nlopt
"phyloTop" # requires nlopt
"pi0" # requires qvalue "pi0" # requires qvalue
"plmDE" # requires limma "plmDE" # requires limma
"plsRbeta" # requires nlopt
"plsRcox" # requires survcomp "plsRcox" # requires survcomp
"plsRglm" # requires nlopt
"PMA" # requires impute "PMA" # requires impute
"pmcgd" # depends on broken mixture "pmcgd" # depends on broken mixture
"pmclust" # requires MPI running. HELP WANTED! "pmclust" # requires MPI running. HELP WANTED!
"polyCub" # requires spatstat "polyCub" # requires spatstat
"polytomous" # requires nlopt
"pomp" # requires nlopt
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db "ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
"predictmeans" # requires nlopt
"pRF" # requires multtest "pRF" # requires multtest
"prLogistic" # requires nlopt
"propOverlap" # requires Biobase "propOverlap" # requires Biobase
"protiq" # requires graph, and RBGL "protiq" # requires graph, and RBGL
"PSAboot" # Requires Nlopt
"PSCBS" # requires DNAcopy "PSCBS" # requires DNAcopy
"pubmed_mineR" # requires SSOAP "pubmed_mineR" # requires SSOAP
"PubMedWordcloud" # requires GOsummaries "PubMedWordcloud" # requires GOsummaries
"qdap" # requires gender "qdap" # requires gender
"qgraph" # requires DiagrammeR to build
"qtbase" # build is broken
"qtlnet" # requires pcalg "qtlnet" # requires pcalg
"qtpaint" # can't find QtCore libraries "qtpaint" # can't find QtCore libraries
"qtutils" # requires qtbase
"QuACN" # requires graph, RBGL "QuACN" # requires graph, RBGL
"quanteda" # fails to build "quanteda" # fails to build
"quantification" # requires nlopt
"QuasiSeq" # requires edgeR "QuasiSeq" # requires edgeR
"R2STATS" # REQUIRES NLOPT
"RADami" # requires Biostrings "RADami" # requires Biostrings
"radiant" # requires nlopt
"raincpc" # SDMTools.so: undefined symbol: X "raincpc" # SDMTools.so: undefined symbol: X
"rainfreq" # SDMTools.so: undefined symbol: X "rainfreq" # SDMTools.so: undefined symbol: X
"RAM" # requires Heatplus "RAM" # requires Heatplus
"RapidPolygonLookup" # depends on broken PBSmapping "RapidPolygonLookup" # depends on broken PBSmapping
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
"rasclass" # requires nlopt
"RbioRXN" # requires fmcsR, and KEGGREST "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_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 "Rcplex" # requires cplexAPI
"RcppAPT" # configure script depends on /bin/sh "RcppAPT" # configure script depends on /bin/sh
"RcppOctave" # Build Is Broken
"RcppRedis" # requires Hiredis "RcppRedis" # requires Hiredis
"rdd" # requires nlopt
"rDEA" # no such file or directory "rDEA" # no such file or directory
"RDieHarder" # requires libdieharder "RDieHarder" # requires libdieharder
"reader" # requires NCmisc "reader" # requires NCmisc
"REBayes" # requires Rmosek "REBayes" # requires Rmosek
"referenceIntervals" # requires nlopt
"RefFreeEWAS" # requires isva "RefFreeEWAS" # requires isva
"refund" # requires nlopt
"REST" # REQUIRES NLOPT
"retistruct" # depends on broken RImageJROI "retistruct" # depends on broken RImageJROI
"rgbif" # requires V8 to build
"rgp" # fails self-test "rgp" # fails self-test
"rgpui" # depends on broken rgp "rgpui" # depends on broken rgp
"RImageJROI" # requires spatstat "RImageJROI" # requires spatstat
"rjade" # requires V8 to build "rjade" # requires V8 to build
"rJPSGCS" # requires chopsticks "rJPSGCS" # requires chopsticks
"rLindo" # requires LINDO API "rLindo" # requires LINDO API
"rmgarch" # requires nlopt
"rminer" # requires nlopt
"Rmosek" # requires mosek "Rmosek" # requires mosek
"RnavGraph" # requires graph, and RBGL "RnavGraph" # requires graph, and RBGL
"rneos" # requires XMLRPC "rneos" # requires XMLRPC
"RNeXML" # requres taxize "RNeXML" # requres taxize
"RobLoxBioC" # requires Biobase "RobLoxBioC" # requires Biobase
"RobLox" # requires Biobase "RobLox" # requires Biobase
"robustlmm" # requires nlopt
"rockchalk" # requires nlopt
"RockFab" # requires EBImage "RockFab" # requires EBImage
"ROI_plugin_symphony" # depends on broken Rsymphony "ROI_plugin_symphony" # depends on broken Rsymphony
"ROracle" # requires OCI "ROracle" # requires OCI
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED! "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
"rpubchem" # requires nlopt
"RQuantLib" # requires QuantLib "RQuantLib" # requires QuantLib
"rr" # requires nlopt
"RSAP" # requires SAPNWRFCSDK "RSAP" # requires SAPNWRFCSDK
"rscala" # build is broken
"RSDA" # REQUIRES NLOPT
"RSeed" # requires RBGL, and graph "RSeed" # requires RBGL, and graph
"rsig" # requires survcomp "rsig" # requires survcomp
"RSNPset" # requires qvalue "RSNPset" # requires qvalue
"Rsymphony" # FIXME: requires SYMPHONY "Rsymphony" # FIXME: requires SYMPHONY
"rugarch" # requires nlopt
"RVAideMemoire" # Requires Nlopt
"RVFam" # Requires Nlopt
"RVideoPoker" # requires Rpanel "RVideoPoker" # requires Rpanel
"ryouready" # requires nlopt
"rysgran" # requires soiltexture "rysgran" # requires soiltexture
"sampleSelection" # requires nlopt
"samr" # requires impute "samr" # requires impute
"sdcMicroGUI" # requires nlopt
"sdcMicro" # requires nlopt
"SDD" # requires rpanel "SDD" # requires rpanel
"seeg" # requires spatstat "seeg" # requires spatstat
"selectspm" # depends on broken ecespa "selectspm" # depends on broken ecespa
"semdiag" # requires DiagrammeR to build
"semGOF" # requires DiagrammeR to build
"semiArtificial" # requires RSNNS "semiArtificial" # requires RSNNS
"semPlot" # requires DiagrammeR to build
"sem" # requires DiagrammeR to build
"SensoMineR" # Requires Nlopt
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools "SeqFeatR" # requires Biostrings, qvalue, and widgetTools
"SeqGrapheR" # depends on Biostrings "SeqGrapheR" # depends on Biostrings
"sequenza" # requires copynumber "sequenza" # requires copynumber
@ -909,6 +1156,8 @@ let
"SimRAD" # requires Biostrings, and ShortRead "SimRAD" # requires Biostrings, and ShortRead
"SimSeq" # requires edgeR "SimSeq" # requires edgeR
"siplab" # requires spatstat "siplab" # requires spatstat
"sirt" # requires DiagrammeR to build
"sjPlot" # requires nlopt
"smart" # requires PMA "smart" # requires PMA
"snpEnrichment" # requires snpStats "snpEnrichment" # requires snpStats
"snplist" # requires biomaRt "snplist" # requires biomaRt
@ -916,41 +1165,60 @@ let
"SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools "SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
"SOD" # depends on proprietary cudatoolkit "SOD" # depends on proprietary cudatoolkit
"soilphysics" # requires rpanel "soilphysics" # requires rpanel
"spacom" # requires nlopt
"sparr" # requires spatstat "sparr" # requires spatstat
"spatialsegregation" # requires spatstat "spatialsegregation" # requires spatstat
"SpatialVx" # requires spatstat "SpatialVx" # requires spatstat
"speaq" # requires MassSpecWavelet "speaq" # requires MassSpecWavelet
"specificity" # requires nlopt
"spocc" # requires leafletR "spocc" # requires leafletR
"SQDA" # requires limma "SQDA" # requires limma
"ssizeRNA" # depends on missing 'Biobase', 'edgeR', 'limma', 'qvalue'
"ssmrob" # requires nlopt
"stagePop" # depends on broken PBSddesolve "stagePop" # depends on broken PBSddesolve
"statar" # depends on broken lfe "statar" # depends on broken lfe
"Statomica" # requires Biobase, multtest "Statomica" # requires Biobase, multtest
"stcm" # requires nlopt
"stepp" # requires nlopt
"stpp" # requires spatstat "stpp" # requires spatstat
"structSSI" # requires multtest "structSSI" # requires multtest
"strum" # requires Rgraphviz "strum" # requires Rgraphviz
"superbiclust" # requires fabia "superbiclust" # requires fabia
"Surrogate" # Requires Nlopt
"surveillance" # requires polyCub "surveillance" # requires polyCub
"survJamda" # depends on missing survcomp
"swamp" # requires impute "swamp" # requires impute
"switchr" # build is broken
"switchrGist" # requires switchr
"sybilSBML" # requires libSBML "sybilSBML" # requires libSBML
"systemfit" # requires nlopt
"taxize" # requres bold "taxize" # requres bold
"TcGSA" # requires multtest "TcGSA" # requires multtest
"TDMR" # REQUIRES NLOPT
"tigerstats" # requires nlopt
"timeSeq" # depends on missing edgeR
"topologyGSA" # requires gRbase "topologyGSA" # requires gRbase
"TR8" # requres taxize "TR8" # requres taxize
"TriMatch" # Requires Nlopt
"trip" # requires spatstat "trip" # requires spatstat
"TROM" # misses undeclared dependencies topGO', 'AnnotationDbi', 'GO.db' "TROM" # misses undeclared dependencies topGO', 'AnnotationDbi', 'GO.db'
"ttScreening" # requires sva, and limma "ttScreening" # requires sva, and limma
"userfriendlyscience" # requires nlopt
"V8" # compilation error "V8" # compilation error
"VIMGUI" # REQUIRES NLOPT
"VIM" # REQUIRES NLOPT
"vmsbase" # depends on broken PBSmapping "vmsbase" # depends on broken PBSmapping
"vows" # requires rpanel "vows" # requires rpanel
"wfe" # requires nlopt
"WGCNA" # requires impute "WGCNA" # requires impute
"wgsea" # requires snpStats "wgsea" # requires snpStats
"WideLM" # depends on proprietary cudatoolkit "WideLM" # depends on proprietary cudatoolkit
"x_ent" # requires opencpu "x_ent" # requires opencpu
"xergm" # requires nlopt
"xml2" # build is broken
"ZeligMultilevel" # Requires Nlopt
"zetadiv" # requires nlopt
"zoib" # tarball is invalid on server "zoib" # tarball is invalid on server
"timeSeq" # depends on missing edgeR
"survJamda" # depends on missing survcomp
"ssizeRNA" # depends on missing 'Biobase', 'edgeR', 'limma', 'qvalue'
"h5" # depends on missing h5 system library
]; ];
otherOverrides = old: new: { otherOverrides = old: new: {