Disable some broken R packages.

This commit is contained in:
Peter Simons 2015-02-22 17:45:12 +01:00
parent d5017499a2
commit 80101c8329
2 changed files with 262 additions and 259 deletions

View file

@ -6323,5 +6323,5 @@ zoo = derive { name="zoo"; version="1.7-11"; sha256="0fp726rp9mqsfmm391bmckk76lq
zooimage = derive { name="zooimage"; version="3.0-5"; sha256="1r3slmyw0dyqfa40dr5xga814z09ibhmmby8p1cii5lh61xm4c39"; depends=[svMisc svDialogs mlearning filehash jpeg png]; };
zoom = derive { name="zoom"; version="2.0.4"; sha256="03f5rxfr6ncf1j6vpn7pip21q7ylj4bx0a5xphqb6x6i33lxf1g5"; depends=[]; };
ztable = derive { name="ztable"; version="0.1.5"; sha256="1jfqnqy9544gfvz3bsb48v4177nwp4b4n9l2743asq8sbq305b5r"; depends=[]; };
zyp = derive { name="zyp"; version="0.10-1"; sha256="0f1fqqxysf3psnvn08s5qly2c958h1hhznjjj8mvpjr5g6hqlr1k"; depends=[Kendall]; };
zyp = derive { name="zyp"; version="0.10-1"; sha256="0f1fqqxysf3psnvn08s5qly2c958h1hhznjjj8mvpjr5g6hqlr1k"; depends=[Kendall]; };
}

View file

@ -647,286 +647,289 @@ let
];
# Packages which cannot be installed due to lack of dependencies or other reasons.
brokenPackages = [ # sort -t '#' -k 2
"V8" # compilation error
"metabolomics" # depends on broken crmn
"selectspm" # depends on broken ecespa
"BLCOP" # depends on broken fPortfolio
"MXM" # depends on broken gRbase
"bamboo" # depends on broken jvmr
"flexCWM" # depends on broken mixture
"pmcgd" # depends on broken mixture
"retistruct" # depends on broken RImageJROI
"ROI_plugin_symphony" # depends on broken Rsymphony
"ChemoSpec" # depends on broken speaq
"CARrampsOcl" # depends on OpenCL
"gmatrix" # depends on proprietary cudatoolkit
"gputools" # depends on proprietary cudatoolkit
"iFes" # depends on proprietary cudatoolkit
"SOD" # depends on proprietary cudatoolkit
"WideLM" # depends on proprietary cudatoolkit
"OpenCL" # FIXME: requires CL/opencl.h
"Rsymphony" # FIXME: requires SYMPHONY
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
"jomo" # linking errors
"mixture" # mixture.so: undefined symbol: dtrmm_
"rDEA" # no such file or directory
"demi" # requires affy, affxparser, and oligo
"KANT" # requires affy, and Biobase
"pathClass" # requires affy, and Biobase
"msarc" # requires AnnotationDbi
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
brokenPackages = [
"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
"RobLoxBioC" # requires Biobase
"RobLox" # requires Biobase
"IsoGene" # requires Biobase, and affy
"mGSZ" # requires Biobase, and limma
"GExMap" # requires Biobase and multtest
"Statomica" # requires Biobase, multtest
"netweavers" # requires BiocGenerics, Biobase, and limma
"NCmisc" # requires BiocInstaller
"EMDomics" # requires BiocParallel
"PepPrep" # requires biomaRt
"snplist" # requires biomaRt
"ionflows" # requires Biostrings
"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
"js" # requires broken V8
"minimist" # requires broken V8
"rJPSGCS" # requires chopsticks
"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
"ParDNAcopy" # requires DNAcopy
"PSCBS" # requires DNAcopy
"dcGOR" # requires dnet
"gitter" # requires EBImage
"Rcell" # requires EBImage
"RockFab" # requires EBImage
"babel" # requires edgeR
"edgeRun" # requires edgeR
"fdrDiscreteNull" # 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
"eulerian" # requires graph
"gRapHD" # requires graph
"msSurv" # requires graph
"PairViz" # requires graph
"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
"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
"RefFreeEWAS" # requires isva
"PhViD" # requires LBE
"Actigraphy" # SDMTools.so: undefined symbol: X
"adaptsmoFMRI" # requires spatstat
"ads" # requires spatstat
"agridat" # requires pcaMethods
"aLFQ" # requires protiq
"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
"PerfMeas" # requires limma, graph, and RBGL
"rLindo" # requires LINDO API
"magma" # requires MAGMA
"HiPLARM" # requires MAGMA or PLASMA
"speaq" # requires MassSpecWavelet
"MAMA" # requires metaMA
"Rmosek" # requires mosek
"aoristic" # requires spatstat
"apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
"aroma_affymetrix" # requires aroma_core
"aroma_cn" # requires PSCBS
"aroma_core" # requires PSCBS
"ArrayBin" # requires SAGx
"babel" # requires edgeR
"BACA" # requires RDAVIDWebService
"bamboo" # depends on broken jvmr
"BcDiag" # requires fabia
"bdvis" # requres taxize
"beadarrayFilter" # requires beadarray
"beadarrayMSV" # requires rggobi
"bigGP" # requires MPI running. HELP WANTED!
"doMPI" # requires MPI running. HELP WANTED!
"metaMix" # 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
"Biograph" # requires mvna
"biotools" # requires rpanel
"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
"BLCOP" # depends on broken fPortfolio
"bmrm" # requires clpAPI
"branchLars" # requires Rgraphviz
"BRugs" # requires OpenBUGS
"x_ent" # requires opencpu
"calmate" # requires aroma_core
"CARrampsOcl" # depends on OpenCL
"CHAT" # requires DNAcopy
"ChemoSpec" # depends on broken speaq
"classGraph" # requires graph, and Rgraphviz
"clpAPI" # requires clp
"clusterfly" # requires rggobi
"compendiumdb" # requires Biobase
"CORM" # requires limma
"cplexAPI" # requires CPLEX
"cqrReg" # requires Rmosek
"crmn" # requires pcaMethods, and Biobase
"CrypticIBDcheck" # requires rJPSGCS
"cudaBayesreg" # requres Rmath
"curvHDR" # requires flowCore
"D2C" # requires gRbase
"DAAGbio" # requires limma
"dagbag" # requires Rlapack
"DBKGrad" # requires SDD
"dbmss" # requires spatstat
"DCGL" # requires limma
"dcGOR" # requires dnet
"demi" # requires affy, affxparser, and oligo
"DepthProc" # requires samr
"Digiroo2" # requires spatstat
"dixon" # requires spatstat
"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
"doMPI" # requires MPI running. HELP WANTED!
"dpcR" # requires spatstat
"DSpat" # requires spatstat
"ecespa" # requires spatstat
"ecoengine" # requires leafletR
"ecospat" # requires spatstat
"edgeRun" # requires edgeR
"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
"EMDomics" # requires BiocParallel
"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
"epoc" # requires graph, and Rgraphviz
"erpR" # requires rpanel
"ETAS" # requires spatstat
"eulerian" # requires graph
"evobiR" # requres taxiz
"evora" # requires qvalue
"ExomeDepth" # requires GenomicRanges, and Rsamtools
"FAMT" # requires impute
"fdrDiscreteNull" # requires edgeR
"FHtest" # requires interval
"flexCWM" # depends on broken mixture
"fPortfolio" # requires rneos
"FunctionalNetworks" # requires breastCancerVDX, and Biobase
"gamlss_demo" # requires rpanel
"GeneticTools" # requires snpStats
"GExMap" # requires Biobase and multtest
"gitter" # requires EBImage
"gmatrix" # depends on proprietary cudatoolkit
"GOGANPA" # requires WGCNA
"gputools" # depends on proprietary cudatoolkit
"gRain" # requires gRbase
"gRapHD" # requires graph
"gRbase" # requires RBGL, and graph
"gRc" # requires gRbase
"gridDebug" # requires gridGraphviz
"gridGraphviz" # requires graph, and Rgraphviz
"GriegSmith" # requires spatstat
"gRim" # requires gRbase
"GSAgm" # requires edgeR
"GUIDE" # requires rpanel
"h2o" # tries to download some h2o.jar during its build
"hasseDiagram" # requires Rgraphviz
"hddplot" # requires multtest
"HierO" # requires rneos
"HiPLARM" # requires MAGMA or PLASMA
"hpoPlot" # requires Rgraphviz
"HTSCluster" # requires edgeR
"iFes" # depends on proprietary cudatoolkit
"imputeLCMD" # requires pcaMethods, and impute
"intamapInteractive" # requires spatstat
"interval" # requires Icens
"ionflows" # requires Biostrings
"iRefR" # requires graph, and RBGL
"IsoGene" # requires Biobase, and affy
"isva" # requires qvalue
"jomo" # linking errors
"js" # requires broken V8
"jvmr" # tries to download files during its build
"KANT" # requires affy, and Biobase
"ktspair" # requires Biobase
"latticeDensity" # requires spatstat
"leapp" # requires sva
"lefse" # SDMTools.so: undefined symbol: X
"lgcp" # requires rpanel
"LinRegInteractive" # requires Rpanel
"LogisticDx" # requires gRbase
"LOST" # requires pcaMethods
"ltsk" # requires Rlapack and Rblas
"magma" # requires MAGMA
"MAMA" # requires metaMA
"MEET" # requires pcaMethods, and seqLogo
"metabolomics" # depends on broken crmn
"MetaDE" # requires impute, and Biobase
"MetaLandSim" # requires Biobase
"metaMA" # requires limma
"metaMix" # requires MPI running. HELP WANTED!
"mGSZ" # requires Biobase, and limma
"MigClim" # SDMTools.So: Undefined Symbol: X
"minimist" # requires broken V8
"miRtest" # requires globaltest, GlobalAncova, and limma
"mixture" # mixture.so: undefined symbol: dtrmm_
"moduleColor" # requires impute
"msarc" # requires AnnotationDbi
"MSeasy" # requires mzR, and xcms
"MSeasyTkGUI" # requires MSeasyTkGUI
"MSIseq" # requires IRanges
"msSurv" # requires graph
"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
"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
"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
"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
"RQuantLib" # requires QuantLib
"evora" # requires qvalue
"isva" # requires qvalue
"NBPSeq" # requires qvalue
"pi0" # requires qvalue
"RSNPset" # requires qvalue
"gRbase" # requires RBGL, and graph
"RSeed" # requires RBGL, and graph
"BACA" # requires RDAVIDWebService
"beadarrayMSV" # requires rggobi
"clusterfly" # requires rggobi
"PKgraph" # requires rggobi
"SeqGrapheR" # requires rggobi
"branchLars" # 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
"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
"pcaL1" # requires clp
"pcalg" # requires graph, and RBGL
"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
"snpEnrichment" # requires snpStats
"snpStatsWriter" # requires snpStats
"wgsea" # requires snpStats
"rysgran" # requires soiltexture
"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
"PCS" # requires multtest
"PepPrep" # requires biomaRt
"PerfMeas" # requires limma, graph, and RBGL
"permGPU" # requires Biobase
"PhViD" # requires LBE
"pi0" # requires qvalue
"PKgraph" # requires rggobi
"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
"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
"QuasiSeq" # requires edgeR
"RADami" # requires Biostrings
"raincpc" # SDMTools.so: undefined symbol: X
"rainfreq" # SDMTools.so: undefined symbol: X
"RAM" # requires Heatplus
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
"RbioRXN" # requires fmcsR, and KEGGREST
"Rcell" # requires EBImage
"RcmdrPlugin_seeg" # requires seeg
"Rcplex" # requires cplexAPI
"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
"rggobi" # requires GGobi
"RImageJROI" # requires spatstat
"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
"rsprng" # requres sprng
"Rsymphony" # FIXME: requires SYMPHONY
"RVideoPoker" # requires Rpanel
"rysgran" # requires soiltexture
"samr" # requires impute
"saps" # requires piano, and survcomp
"SDD" # requires rpanel
"seeg" # requires spatstat
"selectspm" # depends on broken ecespa
"semiArtificial" # requires RSNNS
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
"SeqGrapheR" # requires rggobi
"sequenza" # requires copynumber
"SGCS" # requires spatstat
"siar" # requires spatstat
"SimRAD" # requires Biostrings, and ShortRead
"SimSeq" # requires edgeR
"siplab" # requires spatstat
"smart" # requires PMA
"snpEnrichment" # requires snpStats
"snplist" # requires biomaRt
"snpStatsWriter" # requires snpStats
"SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
"SOD" # depends on proprietary cudatoolkit
"soilphysics" # requires rpanel
"sparr" # requires spatstat
"spatialsegregation" # requires spatstat
"SpatialVx" # requires spatstat
"speaq" # requires MassSpecWavelet
"spocc" # requires leafletR
"SQDA" # requires limma
"Statomica" # requires Biobase, multtest
"StochKit2R" # tarball is invalid on server
"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
"GOGANPA" # requires WGCNA
"nettools" # requires WGCNA
"rneos" # requires XMLRPC
"structSSI" # requires multtest
"strum" # requires Rgraphviz
"superbiclust" # requires fabia
"surveillance" # requires polyCub
"swamp" # requires impute
"sybilSBML" # requires libSBML
"taxize" # requres bold
"cudaBayesreg" # requres Rmath
"rsprng" # requres sprng
"evobiR" # requres taxiz
"bdvis" # requres taxize
"RNeXML" # requres taxize
"TcGSA" # requires multtest
"topologyGSA" # requires gRbase
"TR8" # requres taxize
"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
"jvmr" # tries to download files during its build
"h2o" # tries to download some h2o.jar during its build
"trip" # requires spatstat
"ttScreening" # requires sva, and limma
"V8" # compilation error
"vows" # requires rpanel
"WGCNA" # requires impute
"wgsea" # requires snpStats
"WideLM" # depends on proprietary cudatoolkit
"x_ent" # requires opencpu
"zoib" # tarball is invalid on server
];
otherOverrides = old: new: {