From aaa9f837a94ebac7347cd911f5476fc9b1343c3b Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Wed, 13 May 2015 11:21:09 +0200 Subject: [PATCH] r-modules: fix Hydra evaluation errors --- pkgs/development/r-modules/default.nix | 45 ++++++++++++++------------ 1 file changed, 24 insertions(+), 21 deletions(-) diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index ecc8abf64608..e0b19f465c98 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -665,9 +665,9 @@ let "babel" # requires edgeR "BACA" # requires RDAVIDWebService "BcDiag" # requires fabia - "beadarrayMSV" # requires Biobase, geneplotter, andlimma "bdvis" # requres taxize "beadarrayFilter" # requires beadarray + "beadarrayMSV" # requires Biobase, geneplotter, andlimma "bigGP" # requires MPI running. HELP WANTED! "bigpca" # requires NCmisc "Biograph" # requires mvna @@ -681,13 +681,13 @@ let "CARrampsOcl" # depends on OpenCL "CHAT" # requires DNAcopy "ChemoSpec" # depends on broken speaq - "Crossover" # fails self-test "classGraph" # requires graph, and Rgraphviz "clpAPI" # requires clp "compendiumdb" # requires Biobase "CORM" # requires limma "cplexAPI" # requires CPLEX "crmn" # requires pcaMethods, and Biobase + "Crossover" # fails self-test "CrypticIBDcheck" # requires rJPSGCS "cudaBayesreg" # requres Rmath "curvHDR" # requires flowCore @@ -702,6 +702,7 @@ let "demi" # requires affy, affxparser, and oligo "DepthProc" # requires samr "DiagrammeR" # requires V8 to build + "DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest' "Digiroo2" # requires spatstat "dixon" # requires spatstat "dnet" # requires supraHex, graph, Rgraphviz, and Biobase @@ -729,13 +730,14 @@ let "FunctionalNetworks" # requires breastCancerVDX, and Biobase "gamlss_demo" # requires rpanel "GeneticTools" # requires snpStats + "geojsonio" # requires V8 to build "GExMap" # requires Biobase and multtest "gitter" # requires EBImage "glmgraph" # test suite says: "undefined symbol: dgemv_" "gmatrix" # depends on proprietary cudatoolkit + "gMCP" # fails self-test "GOGANPA" # requires WGCNA "gputools" # depends on proprietary cudatoolkit - "gMCP" # fails self-test "gRain" # requires gRbase "gRapHD" # requires graph "gRbase" # requires RBGL, and graph @@ -752,6 +754,7 @@ let "HierO" # requires rneos "HiPLARM" # requires MAGMA or PLASMA "hpoPlot" # requires Rgraphviz + "hsdar" # fails to build "HTSCluster" # requires edgeR "iFes" # depends on proprietary cudatoolkit "imputeLCMD" # requires pcaMethods, and impute @@ -768,6 +771,7 @@ let "latticeDensity" # requires spatstat "leapp" # requires sva "lefse" # SDMTools.so: undefined symbol: X + "lfe" # fails to compile "lgcp" # requires rpanel "LinRegInteractive" # requires Rpanel "LogisticDx" # requires gRbase @@ -785,13 +789,16 @@ let "MigClim" # SDMTools.So: Undefined Symbol: X "minimist" # requires broken V8 "miRtest" # requires globaltest, GlobalAncova, and limma + "MixGHD" # requires mixture to build "mixture" # mixture.so: undefined symbol: dtrmm_ "moduleColor" # requires impute + "mongolite" # doesn't find OpenSSL "msarc" # requires AnnotationDbi "MSeasy" # requires mzR, and xcms "MSeasyTkGUI" # requires MSeasyTkGUI "MSIseq" # requires IRanges "msSurv" # requires graph + "muir" # requires DiagrammeR to build "multiDimBio" # requires pcaMethods "mutossGUI" # requires mutoss "mutoss" # requires multtest @@ -800,17 +807,14 @@ let "NCmisc" # requires BiocInstaller "netClass" # requires samr "nettools" # requires WGCNA - "NORRRM" # can't load SDMTools properly "netweavers" # requires BiocGenerics, Biobase, and limma "NLPutils" # requires qdap + "NORRRM" # can't load SDMTools properly "NSA" # requires aroma_core "OpenCL" # FIXME: requires CL/opencl.h "optBiomarker" # requires rpanel "ora" # requires ROracle "orQA" # requires genefilter - "pRF" # requires multtest - "PBSmapping" # fails its test suite for unclear reasons - "PBSddesolve" # fails its test suite for unclear reasons "PairViz" # requires graph "PANDA" # requires GO.db "ParDNAcopy" # requires DNAcopy @@ -820,6 +824,8 @@ let "pbdDEMO" # requires pbdMPI "pbdDMAT" # requires pbdMPI "pbdSLAP" # requires pbdMPI + "PBSddesolve" # fails its test suite for unclear reasons + "PBSmapping" # fails its test suite for unclear reasons "pcaL1" # requires clp "pcalg" # requires graph, and RBGL "PCGSE" # requires safe @@ -836,6 +842,7 @@ let "pmclust" # requires MPI running. HELP WANTED! "polyCub" # requires spatstat "ppiPre" # requires AnnotationDbi, GOSemSim, GO.db + "pRF" # requires multtest "propOverlap" # requires Biobase "protiq" # requires graph, and RBGL "PSCBS" # requires DNAcopy @@ -845,17 +852,18 @@ let "qtlnet" # requires pcalg "qtpaint" # can't find QtCore libraries "QuACN" # requires graph, RBGL + "quanteda" # fails to build "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 "RapidPolygonLookup" # depends on broken PBSmapping + "RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges "RbioRXN" # requires fmcsR, and KEGGREST - "RcppAPT" # configure script depends on /bin/sh "RcmdrPlugin_seeg" # requires seeg "Rcplex" # requires cplexAPI + "RcppAPT" # configure script depends on /bin/sh "RcppRedis" # requires Hiredis "rDEA" # no such file or directory "RDieHarder" # requires libdieharder @@ -863,6 +871,8 @@ let "REBayes" # requires Rmosek "RefFreeEWAS" # requires isva "retistruct" # depends on broken RImageJROI + "rgp" # fails self-test + "rgpui" # depends on broken rgp "RImageJROI" # requires spatstat "rjade" # requires V8 to build "rJPSGCS" # requires chopsticks @@ -879,8 +889,6 @@ let "rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED! "RQuantLib" # requires QuantLib "RSAP" # requires SAPNWRFCSDK - "rgp" # fails self-test - "rgpui" # depends on broken rgp "RSeed" # requires RBGL, and graph "rsig" # requires survcomp "RSNPset" # requires qvalue @@ -893,6 +901,7 @@ let "selectspm" # depends on broken ecespa "semiArtificial" # requires RSNNS "SeqFeatR" # requires Biostrings, qvalue, and widgetTools + "SeqGrapheR" # depends on Biostrings "sequenza" # requires copynumber "SGCS" # requires spatstat "siar" # requires spatstat @@ -913,9 +922,9 @@ let "speaq" # requires MassSpecWavelet "spocc" # requires leafletR "SQDA" # requires limma - "Statomica" # requires Biobase, multtest "stagePop" # depends on broken PBSddesolve - "SeqGrapheR" # depends on Biostrings + "statar" # depends on broken lfe + "Statomica" # requires Biobase, multtest "stpp" # requires spatstat "structSSI" # requires multtest "strum" # requires Rgraphviz @@ -928,22 +937,16 @@ let "topologyGSA" # requires gRbase "TR8" # requres taxize "trip" # requires spatstat + "TROM" # misses undeclared dependencies topGO', 'AnnotationDbi', 'GO.db' "ttScreening" # requires sva, and limma "V8" # compilation error - "vows" # requires rpanel "vmsbase" # depends on broken PBSmapping + "vows" # requires rpanel "WGCNA" # requires impute "wgsea" # requires snpStats "WideLM" # depends on proprietary cudatoolkit "x_ent" # requires opencpu "zoib" # tarball is invalid on server - "DiffCorr" # misses undeclared dependencies 'pcaMethods', 'multtest' - "TROM" # misses undeclared dependencies topGO', 'AnnotationDbi', 'GO.db' - "lfe" # fails to compile - "mongolite" # doesn't find OpenSSL - "quanteda" # fails to build - "statar" # depends on broken lfe - "hsdar" # fails to build ]; otherOverrides = old: new: {