r-modules: update list of broken packages

1 files changed, 174 insertions, 134 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
-    "OpenCL" # requires CL/opencl.h
-    "cplexAPI" # requires CPLEX
-    "empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
-    "CHAT" # requires DNAcopy
-    "PSCBS" # requires DNAcopy
-    "ParDNAcopy" # requires DNAcopy
-    "Rcell" # requires EBImage
-    "RockFab" # requires EBImage
-    "gitter" # requires EBImage
-    "rggobi" # requires GGobi
-    "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
-    "RAM" # requires Heatplus
-    "RcppRedis" # requires Hiredis
-    "MSIseq" # requires IRanges
-    "SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
-    "interval" # requires Icens
-    "PhViD" # requires LBE
-    "rLindo" # requires LINDO API
-    "magma" # requires MAGMA
-    "HiPLARM" # requires MAGMA or PLASMA
-    "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
-    "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
+    "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
+    "ParDNAcopy" # requires DNAcopy
+    "PSCBS" # requires DNAcopy
     "dcGOR" # requires dnet
     "bcool" # requires doMPI
+    "gitter" # requires EBImage
+    "Rcell" # requires EBImage
+    "RockFab" # requires EBImage
+    "babel" # requires edgeR
+    "edgeRun" # requires edgeR
     "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
+    "ExomeDepth" # requires GenomicRanges, and Rsamtools
+    "rggobi" # requires GGobi
     "miRtest" # requires globaltest, GlobalAncova, and limma
-    "PairViz" # requires graph
+    "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
-    "QuACN" # requires graph, RBGL
-    "RnavGraph" # requires graph, and RBGL
+    "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
-    "ddepn" # requires graph, and genefilter
+    "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
-    "PMA" # requires impute
-    "WGCNA" # 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
     "AntWeb" # requires leafletR
     "ecoengine" # requires leafletR
     "spocc" # requires leafletR
-    "sybilSBML" # requires libSBML
     "RDieHarder" # requires libdieharder
+    "sybilSBML" # requires libSBML
     "CORM" # requires limma
     "DAAGbio" # requires limma
     "DCGL" # requires limma
-    "SQDA" # 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
-    "PCS" # requires multtest
-    "TcGSA" # requires multtest
+    "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
     "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: {