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pkgs/development/r-modules: fix evaluation errors

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This commit is contained in:
Peter Simons 2015-02-20 14:29:47 +01:00
parent 3391728c63
commit 7afe039842
1 changed files with 25 additions and 12 deletions
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37
pkgs/development/r-modules/default.nix
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@ -648,16 +648,35 @@ let
# Packages which cannot be installed due to lack of dependencies or other reasons. # Packages which cannot be installed due to lack of dependencies or other reasons.
brokenPackages = [ # sort -t '#' -k 2 brokenPackages = [ # sort -t '#' -k 2
"V8" # compilation error
"metabolomics" # depends on broken crmn "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 "retistruct" # depends on broken RImageJROI
"ROI_plugin_symphony" # depends on broken Rsymphony
"ChemoSpec" # depends on broken speaq
"CARrampsOcl" # depends on OpenCL "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! "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 "demi" # requires affy, affxparser, and oligo
"KANT" # requires affy, and Biobase "KANT" # requires affy, and Biobase
"pathClass" # requires affy, and Biobase "pathClass" # requires affy, and Biobase
"msarc" # requires AnnotationDbi "msarc" # requires AnnotationDbi
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
"ACNE" # requires aroma_affymetrix "ACNE" # requires aroma_affymetrix
"Statomica" # requires Biobase, multtest
"aroma_affymetrix" # requires aroma_core "aroma_affymetrix" # requires aroma_core
"calmate" # requires aroma_core "calmate" # requires aroma_core
"NSA" # requires aroma_core "NSA" # requires aroma_core
@ -672,6 +691,7 @@ let
"IsoGene" # requires Biobase, and affy "IsoGene" # requires Biobase, and affy
"mGSZ" # requires Biobase, and limma "mGSZ" # requires Biobase, and limma
"GExMap" # requires Biobase and multtest "GExMap" # requires Biobase and multtest
"Statomica" # requires Biobase, multtest
"netweavers" # requires BiocGenerics, Biobase, and limma "netweavers" # requires BiocGenerics, Biobase, and limma
"NCmisc" # requires BiocInstaller "NCmisc" # requires BiocInstaller
"EMDomics" # requires BiocParallel "EMDomics" # requires BiocParallel
@ -683,12 +703,9 @@ let
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools "SeqFeatR" # requires Biostrings, qvalue, and widgetTools
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
"FunctionalNetworks" # requires breastCancerVDX, and Biobase "FunctionalNetworks" # requires breastCancerVDX, and Biobase
"rJPSGCS" # requires chopsticks
"OpenCL" # FIXME: requires CL/opencl.h
"Rsymphony" # FIXME: requires SYMPHONY
"V8" # compilation error
"js" # requires broken V8 "js" # requires broken V8
"minimist" # requires broken V8 "minimist" # requires broken V8
"rJPSGCS" # requires chopsticks
"clpAPI" # requires clp "clpAPI" # requires clp
"pcaL1" # requires clp "pcaL1" # requires clp
"bmrm" # requires clpAPI "bmrm" # requires clpAPI
@ -701,17 +718,16 @@ let
"PSCBS" # requires DNAcopy "PSCBS" # requires DNAcopy
"dcGOR" # requires dnet "dcGOR" # requires dnet
"gitter" # requires EBImage "gitter" # requires EBImage
"speaq" # requires MassSpecWavelet
"Rcell" # requires EBImage "Rcell" # requires EBImage
"RockFab" # requires EBImage "RockFab" # requires EBImage
"babel" # requires edgeR "babel" # requires edgeR
"edgeRun" # requires edgeR "edgeRun" # requires edgeR
"fdrDiscreteNull" # requires edgeR
"GSAgm" # requires edgeR "GSAgm" # requires edgeR
"HTSCluster" # requires edgeR "HTSCluster" # requires edgeR
"QuasiSeq" # requires edgeR "QuasiSeq" # requires edgeR
"SimSeq" # requires edgeR "SimSeq" # requires edgeR
"BcDiag" # requires fabia "BcDiag" # requires fabia
"BACA" # requires RDAVIDWebService
"superbiclust" # requires fabia "superbiclust" # requires fabia
"curvHDR" # requires flowCore "curvHDR" # requires flowCore
"RbioRXN" # requires fmcsR, and KEGGREST "RbioRXN" # requires fmcsR, and KEGGREST
@ -747,7 +763,6 @@ let
"RcppRedis" # requires Hiredis "RcppRedis" # requires Hiredis
"interval" # requires Icens "interval" # requires Icens
"FAMT" # requires impute "FAMT" # requires impute
"fdrDiscreteNull" # requires edgeR
"moduleColor" # requires impute "moduleColor" # requires impute
"PMA" # requires impute "PMA" # requires impute
"samr" # requires impute "samr" # requires impute
@ -771,10 +786,10 @@ let
"plmDE" # requires limma "plmDE" # requires limma
"SQDA" # requires limma "SQDA" # requires limma
"PerfMeas" # requires limma, graph, and RBGL "PerfMeas" # requires limma, graph, and RBGL
"ppiPre" # requires AnnotationDbi, GOSemSim, GO.db
"rLindo" # requires LINDO API "rLindo" # requires LINDO API
"magma" # requires MAGMA "magma" # requires MAGMA
"HiPLARM" # requires MAGMA or PLASMA "HiPLARM" # requires MAGMA or PLASMA
"speaq" # requires MassSpecWavelet
"MAMA" # requires metaMA "MAMA" # requires metaMA
"Rmosek" # requires mosek "Rmosek" # requires mosek
"bigGP" # requires MPI running. HELP WANTED! "bigGP" # requires MPI running. HELP WANTED!
@ -821,6 +836,7 @@ let
"RSNPset" # requires qvalue "RSNPset" # requires qvalue
"gRbase" # requires RBGL, and graph "gRbase" # requires RBGL, and graph
"RSeed" # requires RBGL, and graph "RSeed" # requires RBGL, and graph
"BACA" # requires RDAVIDWebService
"beadarrayMSV" # requires rggobi "beadarrayMSV" # requires rggobi
"clusterfly" # requires rggobi "clusterfly" # requires rggobi
"PKgraph" # requires rggobi "PKgraph" # requires rggobi
@ -899,9 +915,6 @@ let
"taxize" # requres bold "taxize" # requres bold
"cudaBayesreg" # requres Rmath "cudaBayesreg" # requres Rmath
"rsprng" # requres sprng "rsprng" # requres sprng
"rDEA" # no such file or directory
"jomo" # linking errors
"mixture" # mixture.so: undefined symbol: dtrmm_
"evobiR" # requres taxiz "evobiR" # requres taxiz
"bdvis" # requres taxize "bdvis" # requres taxize
"RNeXML" # requres taxize "RNeXML" # requres taxize