diff --git a/pkgs/development/r-modules/cran-packages.nix b/pkgs/development/r-modules/cran-packages.nix index fa8d40d71fc9..2418192e5fbf 100644 --- a/pkgs/development/r-modules/cran-packages.nix +++ b/pkgs/development/r-modules/cran-packages.nix @@ -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]; }; } diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 0998668beae7..c1100c79fac7 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -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: {