From 9489dac1d356ab66d39cb9465cce7b61efdec980 Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Tue, 13 Jan 2015 12:03:48 +0100 Subject: [PATCH] r-modules: update list of broken packages --- pkgs/development/r-modules/default.nix | 364 ++++++++++++++----------- 1 file changed, 202 insertions(+), 162 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 1ec48bcc06f2..be587c2637c4 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -621,23 +621,51 @@ let ]; # Packages which cannot be installed due to lack of dependencies or other reasons. - brokenPackages = [ - # sort -t '#' -k 2 - - "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED! - "MigClim" # SDMTools.So: Undefined Symbol: X - "PatternClass" # SDMTools.So: Undefined Symbol: X - "Actigraphy" # SDMTools.so: undefined symbol: X - "lefse" # SDMTools.so: undefined symbol: X - "raincpc" # SDMTools.so: undefined symbol: X - "rainfreq" # SDMTools.so: undefined symbol: X + brokenPackages = [ # sort -t '#' -k 2 + "birdring" # depends on broken gdal library + "capm" # depends on broken gdal library + "DeducerSpatial" # depends on broken gdal library + "divagis" # depends on broken gdal library + "drsmooth" # depends on broken gdal library + "dynatopmodel" # depends on broken gdal library + "fuzzyMM" # depends on broken gdal library + "gfcanalysis" # depends on broken gdal library + "GSIF" # depends on broken gdal library + "hddtools" # depends on broken gdal library + "lakemorpho" # depends on broken gdal library + "landsat" # depends on broken gdal library + "M3" # depends on broken gdal library + "mgraph" # depends on broken gdal library + "micromap" # depends on broken gdal library + "ModelMap" # depends on broken gdal library + "modiscloud" # depends on broken gdal library + "move" # depends on broken gdal library + "OpasnetUtils" # depends on broken gdal library + "OpenStreetMap" # depends on broken gdal library + "opentraj" # depends on broken gdal library + "paleofire" # depends on broken gdal library + "pgirmess" # depends on broken gdal library + "plotGoogleMaps" # depends on broken gdal library + "plotKML" # depends on broken gdal library + "PopGenReport" # depends on broken gdal library + "prevR" # depends on broken gdal library + "qrfactor" # depends on broken gdal library + "r2dRue" # depends on broken gdal library + "rangeMapper" # depends on broken gdal library + "rAvis" # depends on broken gdal library + "rgdal" # depends on broken gdal library + "rnrfa" # depends on broken gdal library + "spatial_tools" # depends on broken gdal library + "SPODT" # depends on broken gdal library + "taRifx_geo" # depends on broken gdal library + "tmap" # depends on broken gdal library + "trajectories" # depends on broken gdal library + "tripEstimation" # depends on broken gdal library + "UScancer" # depends on broken gdal library + "wrspathrow" # depends on broken gdal library + "wux" # depends on broken gdal library "CARrampsOcl" # depends on OpenCL - "RGA" # jsonlite.so: undefined symbol: XXX - "RSiteCatalyst" # jsonlite.so: undefined symbol: XXX - "RSocrata" # jsonlite.so: undefined symbol: XXX - "SGP" # jsonlite.so: undefined symbol: XXX - "SocialMediaMineR" # jsonlite.so: undefined symbol: XXX - "WikipediR" # jsonlite.so: undefined symbol: XXX + "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED! "alm" # jsonlite.so: undefined symbol: XXX "archivist" # jsonlite.so: undefined symbol: XXX "bold" # jsonlite.so: undefined symbol: XXX @@ -650,222 +678,223 @@ let "pdfetch" # jsonlite.so: undefined symbol: XXX "polidata" # jsonlite.so: undefined symbol: XXX "pollstR" # jsonlite.so: undefined symbol: XXX - "rHealthDataGov" # jsonlite.so: undefined symbol: XXX - "rWBclimate" # jsonlite.so: undefined symbol: XXX "rbison" # jsonlite.so: undefined symbol: XXX + "RGA" # jsonlite.so: undefined symbol: XXX + "rHealthDataGov" # jsonlite.so: undefined symbol: XXX "rinat" # jsonlite.so: undefined symbol: XXX "rjstat" # jsonlite.so: undefined symbol: XXX "rmongodb" # jsonlite.so: undefined symbol: XXX "rnoaa" # jsonlite.so: undefined symbol: XXX + "RSiteCatalyst" # jsonlite.so: undefined symbol: XXX + "RSocrata" # jsonlite.so: undefined symbol: XXX "rsunlight" # jsonlite.so: undefined symbol: XXX + "rWBclimate" # jsonlite.so: undefined symbol: XXX + "SGP" # jsonlite.so: undefined symbol: XXX "slackr" # jsonlite.so: undefined symbol: XXX + "SocialMediaMineR" # jsonlite.so: undefined symbol: XXX "webutils" # jsonlite.so: undefined symbol: XXX + "WikipediR" # jsonlite.so: undefined symbol: XXX + "demi" # requires affy, affxparser, and oligo + "KANT" # requires affy, and Biobase + "pathClass" # requires affy, and Biobase "msarc" # requires AnnotationDbi - "MetaLandSim" # requires Biobase - "RobLox" # requires Biobase - "RobLoxBioC" # requires Biobase + "ACNE" # requires aroma_affymetrix + "aroma_affymetrix" # requires aroma_core + "calmate" # requires aroma_core + "NSA" # requires aroma_core + "beadarrayFilter" # requires beadarray "compendiumdb" # requires Biobase "ktspair" # requires Biobase + "MetaLandSim" # requires Biobase "permGPU" # requires Biobase "propOverlap" # requires Biobase - "GExMap" # requires Biobase and multtest + "RobLoxBioC" # requires Biobase + "RobLox" # requires Biobase "IsoGene" # requires Biobase, and affy "mGSZ" # requires Biobase, and limma + "GExMap" # requires Biobase and multtest "netweavers" # requires BiocGenerics, Biobase, and limma "NCmisc" # requires BiocInstaller "EMDomics" # requires BiocParallel - "RADami" # requires Biostrings + "PepPrep" # requires biomaRt + "snplist" # requires biomaRt "ionflows" # requires Biostrings - "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges + "RADami" # requires Biostrings "SimRAD" # requires Biostrings, and ShortRead "SeqFeatR" # requires Biostrings, qvalue, and widgetTools + "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges + "FunctionalNetworks" # requires breastCancerVDX, and Biobase + "rJPSGCS" # requires chopsticks "OpenCL" # requires CL/opencl.h + "clpAPI" # requires clp + "pcaL1" # requires clp + "bmrm" # requires clpAPI + "sequenza" # requires copynumber "cplexAPI" # requires CPLEX + "Rcplex" # requires cplexAPI "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges "CHAT" # requires DNAcopy - "PSCBS" # requires DNAcopy "ParDNAcopy" # requires DNAcopy + "PSCBS" # requires DNAcopy + "dcGOR" # requires dnet + "bcool" # requires doMPI + "gitter" # requires EBImage "Rcell" # requires EBImage "RockFab" # requires EBImage - "gitter" # requires EBImage + "babel" # requires edgeR + "edgeRun" # requires edgeR + "GSAgm" # requires edgeR + "HTSCluster" # requires edgeR + "QuasiSeq" # requires edgeR + "SimSeq" # requires edgeR + "BcDiag" # requires fabia + "superbiclust" # requires fabia + "curvHDR" # requires flowCore + "RbioRXN" # requires fmcsR, and KEGGREST + "qdap" # requires gender + "orQA" # requires genefilter + "apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light + "ExomeDepth" # requires GenomicRanges, and Rsamtools "rggobi" # requires GGobi + "miRtest" # requires globaltest, GlobalAncova, and limma "PANDA" # requires GO.db "BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db "PubMedWordcloud" # requires GOsummaries - "ExomeDepth" # requires GenomicRanges, and Rsamtools - "HTSDiff" # requires HTSCluster + "eulerian" # requires graph + "gRapHD" # requires graph + "msSurv" # requires graph + "PairViz" # requires graph + "ddepn" # requires graph, and genefilter + "iRefR" # requires graph, and RBGL + "pcalg" # requires graph, and RBGL + "protiq" # requires graph, and RBGL + "RnavGraph" # requires graph, and RBGL + "classGraph" # requires graph, and Rgraphviz + "epoc" # requires graph, and Rgraphviz + "gridGraphviz" # requires graph, and Rgraphviz + "QuACN" # requires graph, RBGL + "D2C" # requires gRbase + "gRain" # requires gRbase + "gRc" # requires gRbase + "gRim" # requires gRbase + "LogisticDx" # requires gRbase + "topologyGSA" # requires gRbase + "gridDebug" # requires gridGraphviz "RAM" # requires Heatplus "RcppRedis" # requires Hiredis + "HTSDiff" # requires HTSCluster + "interval" # requires Icens + "FAMT" # requires impute + "moduleColor" # requires impute + "PMA" # requires impute + "samr" # requires impute + "swamp" # requires impute + "WGCNA" # requires impute + "MetaDE" # requires impute, and Biobase + "FHtest" # requires interval "MSIseq" # requires IRanges "SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools - "interval" # requires Icens + "RefFreeEWAS" # requires isva "PhViD" # requires LBE + "AntWeb" # requires leafletR + "ecoengine" # requires leafletR + "spocc" # requires leafletR + "RDieHarder" # requires libdieharder + "sybilSBML" # requires libSBML + "CORM" # requires limma + "DAAGbio" # requires limma + "DCGL" # requires limma + "metaMA" # requires limma + "plmDE" # requires limma + "SQDA" # requires limma + "RPPanalyzer" # requires limma, and Biobase + "PerfMeas" # requires limma, graph, and RBGL "rLindo" # requires LINDO API "magma" # requires MAGMA "HiPLARM" # requires MAGMA or PLASMA + "MAMA" # requires metaMA + "Rmosek" # requires mosek "bigGP" # requires MPI running. HELP WANTED! "doMPI" # requires MPI running. HELP WANTED! "metaMix" # requires MPI running. HELP WANTED! "pbdMPI" # requires MPI running. HELP WANTED! "pmclust" # requires MPI running. HELP WANTED! "MSeasyTkGUI" # requires MSeasyTkGUI + "hddplot" # requires multtest + "mutoss" # requires multtest + "PCS" # requires multtest + "structSSI" # requires multtest + "TcGSA" # requires multtest + "mutossGUI" # requires mutoss + "Biograph" # requires mvna + "MSeasy" # requires mzR, and xcms "bigpca" # requires NCmisc "reader" # requires NCmisc "ROracle" # requires OCI "BRugs" # requires OpenBUGS - "smart" # requires PMA - "aroma_cn" # requires PSCBS - "aroma_core" # requires PSCBS - "RQuantLib" # requires QuantLib - "RSeed" # requires RBGL, and graph - "gRbase" # requires RBGL, and graph - "ora" # requires ROracle - "semiArtificial" # requires RSNNS - "branchLars" # requires Rgraphviz - "gcExplorer" # requires Rgraphviz - "hasseDiagram" # requires Rgraphviz - "hpoPlot" # requires Rgraphviz - "strum" # requires Rgraphviz - "dagbag" # requires Rlapack - "ltsk" # requires Rlapack and Rblas - "REBayes" # requires Rmosek - "cqrReg" # requires Rmosek - "LinRegInteractive" # requires Rpanel - "RVideoPoker" # requires Rpanel - "ArrayBin" # requires SAGx - "RSAP" # requires SAPNWRFCSDK - "DBKGrad" # requires SDD - "pubmed_mineR" # requires SSOAP - "ENA" # requires WGCNA - "GOGANPA" # requires WGCNA - "nettools" # requires WGCNA - "rneos" # requires XMLRPC - "demi" # requires affy, affxparser, and oligo - "KANT" # requires affy, and Biobase - "pathClass" # requires affy, and Biobase - "ACNE" # requires aroma_affymetrix - "NSA" # requires aroma_core - "aroma_affymetrix" # requires aroma_core - "calmate" # requires aroma_core - "beadarrayFilter" # requires beadarray - "PepPrep" # requires biomaRt - "snplist" # requires biomaRt - "FunctionalNetworks" # requires breastCancerVDX, and Biobase - "rJPSGCS" # requires chopsticks - "clpAPI" # requires clp - "pcaL1" # requires clp - "bmrm" # requires clpAPI - "sequenza" # requires copynumber - "Rcplex" # requires cplexAPI - "dcGOR" # requires dnet - "bcool" # requires doMPI - "GSAgm" # requires edgeR - "HTSCluster" # requires edgeR - "QuasiSeq" # requires edgeR - "SimSeq" # requires edgeR - "babel" # requires edgeR - "edgeRun" # requires edgeR - "BcDiag" # requires fabia - "superbiclust" # requires fabia - "curvHDR" # requires flowCore - "RbioRXN" # requires fmcsR, and KEGGREST - "D2C" # requires gRbase - "LogisticDx" # requires gRbase - "gRain" # requires gRbase - "gRc" # requires gRbase - "gRim" # requires gRbase - "topologyGSA" # requires gRbase - "qdap" # requires gender - "orQA" # requires genefilter - "apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light - "miRtest" # requires globaltest, GlobalAncova, and limma - "PairViz" # requires graph - "eulerian" # requires graph - "gRapHD" # requires graph - "msSurv" # requires graph - "QuACN" # requires graph, RBGL - "RnavGraph" # requires graph, and RBGL - "iRefR" # requires graph, and RBGL - "pcalg" # requires graph, and RBGL - "protiq" # requires graph, and RBGL - "classGraph" # requires graph, and Rgraphviz - "epoc" # requires graph, and Rgraphviz - "gridGraphviz" # requires graph, and Rgraphviz - "ddepn" # requires graph, and genefilter - "gridDebug" # requires gridGraphviz - "FAMT" # requires impute - "PMA" # requires impute - "WGCNA" # requires impute - "moduleColor" # requires impute - "samr" # requires impute - "swamp" # requires impute - "MetaDE" # requires impute, and Biobase - "FHtest" # requires interval - "RefFreeEWAS" # requires isva - "AntWeb" # requires leafletR - "ecoengine" # requires leafletR - "spocc" # requires leafletR - "sybilSBML" # requires libSBML - "RDieHarder" # requires libdieharder - "CORM" # requires limma - "DAAGbio" # requires limma - "DCGL" # requires limma - "SQDA" # requires limma - "metaMA" # requires limma - "plmDE" # requires limma - "RPPanalyzer" # requires limma, and Biobase - "PerfMeas" # requires limma, graph, and RBGL - "MAMA" # requires metaMA - "Rmosek" # requires mosek - "PCS" # requires multtest - "TcGSA" # requires multtest - "hddplot" # requires multtest - "mutoss" # requires multtest - "structSSI" # requires multtest - "mutossGUI" # requires mutoss - "Biograph" # requires mvna - "MSeasy" # requires mzR, and xcms "x_ent" # requires opencpu "pbdBASE" # requires pbdMPI "pbdDEMO" # requires pbdMPI "pbdDMAT" # requires pbdMPI "pbdSLAP" # requires pbdMPI - "LOST" # requires pcaMethods + "qtlnet" # requires pcalg "agridat" # requires pcaMethods + "LOST" # requires pcaMethods "multiDimBio" # requires pcaMethods "crmn" # requires pcaMethods, and Biobase "imputeLCMD" # requires pcaMethods, and impute "MEET" # requires pcaMethods, and seqLogo - "qtlnet" # requires pcalg "SigTree" # requires phyloseq "saps" # requires piano, and survcomp + "smart" # requires PMA "surveillance" # requires polyCub "aLFQ" # requires protiq + "aroma_cn" # requires PSCBS + "aroma_core" # requires PSCBS "NLPutils" # requires qdap - "NBPSeq" # requires qvalue - "RSNPset" # requires qvalue + "RQuantLib" # requires QuantLib "evora" # requires qvalue "isva" # requires qvalue + "NBPSeq" # requires qvalue "pi0" # requires qvalue - "CrypticIBDcheck" # requires rJPSGCS - "PKgraph" # requires rggobi - "SeqGrapheR" # requires rggobi + "RSNPset" # requires qvalue + "gRbase" # requires RBGL, and graph + "RSeed" # requires RBGL, and graph "beadarrayMSV" # requires rggobi "clusterfly" # requires rggobi - "HierO" # requires rneos + "PKgraph" # requires rggobi + "SeqGrapheR" # requires rggobi + "branchLars" # requires Rgraphviz + "gcExplorer" # requires Rgraphviz + "hasseDiagram" # requires Rgraphviz + "hpoPlot" # requires Rgraphviz + "strum" # requires Rgraphviz + "CrypticIBDcheck" # requires rJPSGCS + "dagbag" # requires Rlapack + "ltsk" # requires Rlapack and Rblas + "cqrReg" # requires Rmosek + "REBayes" # requires Rmosek "fPortfolio" # requires rneos - "GUIDE" # requires rpanel - "SDD" # requires rpanel + "HierO" # requires rneos + "ora" # requires ROracle "biotools" # requires rpanel "erpR" # requires rpanel "gamlss_demo" # requires rpanel + "GUIDE" # requires rpanel "lgcp" # requires rpanel "optBiomarker" # requires rpanel + "SDD" # requires rpanel "soilphysics" # requires rpanel "vows" # requires rpanel + "LinRegInteractive" # requires Rpanel + "RVideoPoker" # requires Rpanel + "semiArtificial" # requires RSNNS "PCGSE" # requires safe + "ArrayBin" # requires SAGx "DepthProc" # requires samr "netClass" # requires samr + "RSAP" # requires SAPNWRFCSDK + "DBKGrad" # requires SDD "RcmdrPlugin_seeg" # requires seeg "EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi "GeneticTools" # requires snpStats @@ -873,46 +902,57 @@ let "snpStatsWriter" # requires snpStats "wgsea" # requires snpStats "rysgran" # requires soiltexture - "DSpat" # requires spatstat - "Digiroo2" # requires spatstat - "ETAS" # requires spatstat - "GriegSmith" # requires spatstat - "RImageJROI" # requires spatstat - "SGCS" # requires spatstat - "SpatialVx" # requires spatstat "adaptsmoFMRI" # requires spatstat "ads" # requires spatstat "aoristic" # requires spatstat "dbmss" # requires spatstat + "Digiroo2" # requires spatstat "dixon" # requires spatstat "dpcR" # requires spatstat + "DSpat" # requires spatstat "ecespa" # requires spatstat "ecospat" # requires spatstat + "ETAS" # requires spatstat + "GriegSmith" # requires spatstat "intamapInteractive" # requires spatstat "latticeDensity" # requires spatstat "polyCub" # requires spatstat + "RImageJROI" # requires spatstat "seeg" # requires spatstat + "SGCS" # requires spatstat "siar" # requires spatstat "siplab" # requires spatstat "sparr" # requires spatstat "spatialsegregation" # requires spatstat + "SpatialVx" # requires spatstat "stpp" # requires spatstat "trip" # requires spatstat + "pubmed_mineR" # requires SSOAP "dnet" # requires supraHex, graph, Rgraphviz, and Biobase "plsRcox" # requires survcomp "rsig" # requires survcomp "leapp" # requires sva "ttScreening" # requires sva, and limma - "cudaBayesreg" # requres Rmath + "ENA" # requires WGCNA + "GOGANPA" # requires WGCNA + "nettools" # requires WGCNA + "rneos" # requires XMLRPC "taxize" # requres bold + "cudaBayesreg" # requres Rmath "rsprng" # requres sprng "evobiR" # requres taxiz + "bdvis" # requres taxize "RNeXML" # requres taxize "TR8" # requres taxize - "bdvis" # requres taxize - "h2o" # tries to download some h2o.jar during its build - "jvmr" # tries to download files during its build + "Actigraphy" # SDMTools.so: undefined symbol: X + "lefse" # SDMTools.so: undefined symbol: X + "raincpc" # SDMTools.so: undefined symbol: X + "rainfreq" # SDMTools.so: undefined symbol: X + "MigClim" # SDMTools.So: Undefined Symbol: X + "PatternClass" # SDMTools.So: Undefined Symbol: X "qtbase" # the smokegen binary cannot find libQtCore.so.4 etc. at runtime + "jvmr" # tries to download files during its build + "h2o" # tries to download some h2o.jar during its build ]; otherOverrides = old: new: {