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r-modules: update list of broken packages

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This commit is contained in:
Peter Simons 2015-01-13 12:03:48 +01:00
parent 844828afad
commit 9489dac1d3
1 changed files with 202 additions and 162 deletions
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364
pkgs/development/r-modules/default.nix
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@ -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: {