From d4c810cccda570df54adcc51329f07dca69db65a Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Tue, 16 Jun 2015 10:44:52 +0200 Subject: [PATCH] r-modules: disable broken packages to avoid Hydra evaluation errors --- pkgs/development/r-modules/default.nix | 278 ++++++++++++++++++++++++- 1 file changed, 273 insertions(+), 5 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 2f8c22fe8658..34e50d08413d 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -649,97 +649,191 @@ 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 "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 @@ -748,51 +842,101 @@ let "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 @@ -800,106 +944,209 @@ let "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 + "pander" # build is broken + "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 + "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 + "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 "RImageJROI" # requires spatstat "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 + "rscala" # build is broken + "RSDA" # REQUIRES NLOPT "RSeed" # requires RBGL, and graph "rsig" # requires survcomp "RSNPset" # requires qvalue "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 @@ -909,6 +1156,8 @@ let "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 @@ -916,41 +1165,60 @@ let "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 - "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: {