From 7afe039842d83d21b3f2f6ad7b318934cd2243f4 Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Fri, 20 Feb 2015 14:29:47 +0100 Subject: [PATCH] pkgs/development/r-modules: fix evaluation errors --- pkgs/development/r-modules/default.nix | 37 +++++++++++++++++--------- 1 file changed, 25 insertions(+), 12 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index d901c8b6d63..0998668beae 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -648,16 +648,35 @@ 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 "ACNE" # requires aroma_affymetrix - "Statomica" # requires Biobase, multtest "aroma_affymetrix" # requires aroma_core "calmate" # requires aroma_core "NSA" # requires aroma_core @@ -672,6 +691,7 @@ let "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 @@ -683,12 +703,9 @@ let "SeqFeatR" # requires Biostrings, qvalue, and widgetTools "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges "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 "minimist" # requires broken V8 + "rJPSGCS" # requires chopsticks "clpAPI" # requires clp "pcaL1" # requires clp "bmrm" # requires clpAPI @@ -701,17 +718,16 @@ let "PSCBS" # requires DNAcopy "dcGOR" # requires dnet "gitter" # requires EBImage - "speaq" # requires MassSpecWavelet "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 - "BACA" # requires RDAVIDWebService "superbiclust" # requires fabia "curvHDR" # requires flowCore "RbioRXN" # requires fmcsR, and KEGGREST @@ -747,7 +763,6 @@ let "RcppRedis" # requires Hiredis "interval" # requires Icens "FAMT" # requires impute - "fdrDiscreteNull" # requires edgeR "moduleColor" # requires impute "PMA" # requires impute "samr" # requires impute @@ -771,10 +786,10 @@ let "plmDE" # requires limma "SQDA" # requires limma "PerfMeas" # requires limma, graph, and RBGL - "ppiPre" # requires AnnotationDbi, GOSemSim, GO.db "rLindo" # requires LINDO API "magma" # requires MAGMA "HiPLARM" # requires MAGMA or PLASMA + "speaq" # requires MassSpecWavelet "MAMA" # requires metaMA "Rmosek" # requires mosek "bigGP" # requires MPI running. HELP WANTED! @@ -821,6 +836,7 @@ let "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 @@ -899,9 +915,6 @@ let "taxize" # requres bold "cudaBayesreg" # requres Rmath "rsprng" # requres sprng - "rDEA" # no such file or directory - "jomo" # linking errors - "mixture" # mixture.so: undefined symbol: dtrmm_ "evobiR" # requres taxiz "bdvis" # requres taxize "RNeXML" # requres taxize