forked from mirrors/nixpkgs
cran-packages: updated sources
This commit is contained in:
taku0
Peter Simons
parent
2532844fb5
commit
4647743ed7
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@ -3,9 +3,9 @@
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# sort -t '#' -k 2
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"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
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"Actigraphy" # SDMTools.so: undefined symbol: X
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"MigClim" # SDMTools.So: Undefined Symbol: X
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"PatternClass" # SDMTools.So: Undefined Symbol: X
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"Actigraphy" # SDMTools.so: undefined symbol: X
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"lefse" # SDMTools.so: undefined symbol: X
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"raincpc" # SDMTools.so: undefined symbol: X
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"rainfreq" # SDMTools.so: undefined symbol: X
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@ -39,7 +39,7 @@
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"slackr" # jsonlite.so: undefined symbol: XXX
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"webutils" # jsonlite.so: undefined symbol: XXX
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"msarc" # requires AnnotationDbi
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"ppiPre" # requires AnnotationDbi
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"MetaLandSim" # requires Biobase
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"RobLox" # requires Biobase
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"RobLoxBioC" # requires Biobase
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"compendiumdb" # requires Biobase
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@ -49,13 +49,17 @@
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"GExMap" # requires Biobase and multtest
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"IsoGene" # requires Biobase, and affy
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"mGSZ" # requires Biobase, and limma
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"netweavers" # requires BiocGenerics, Biobase, and limma
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"NCmisc" # requires BiocInstaller
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"EMDomics" # requires BiocParallel
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"RADami" # requires Biostrings
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"ionflows" # requires Biostrings
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"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
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"SimRAD" # requires Biostrings, and ShortRead
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"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
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"OpenCL" # requires CL/opencl.h
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"cplexAPI" # requires CPLEX
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"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
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"CHAT" # requires DNAcopy
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"PSCBS" # requires DNAcopy
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"ParDNAcopy" # requires DNAcopy
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@ -63,6 +67,7 @@
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"RockFab" # requires EBImage
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"gitter" # requires EBImage
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"rggobi" # requires GGobi
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"PANDA" # requires GO.db
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"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
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"PubMedWordcloud" # requires GOsummaries
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"ExomeDepth" # requires GenomicRanges, and Rsamtools
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@ -102,6 +107,7 @@
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"dagbag" # requires Rlapack
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"ltsk" # requires Rlapack and Rblas
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"REBayes" # requires Rmosek
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"cqrReg" # requires Rmosek
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"LinRegInteractive" # requires Rpanel
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"RVideoPoker" # requires Rpanel
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"ArrayBin" # requires SAGx
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@ -141,9 +147,9 @@
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"superbiclust" # requires fabia
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"curvHDR" # requires flowCore
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"RbioRXN" # requires fmcsR, and KEGGREST
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"D2C" # requires gRbase
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"LogisticDx" # requires gRbase
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"gRain" # requires gRbase
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"gRbase" # requires gRbase
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"gRc" # requires gRbase
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"gRim" # requires gRbase
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"topologyGSA" # requires gRbase
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@ -155,6 +161,7 @@
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"eulerian" # requires graph
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"gRapHD" # requires graph
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"msSurv" # requires graph
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"QuACN" # requires graph, RBGL
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"RnavGraph" # requires graph, and RBGL
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"iRefR" # requires graph, and RBGL
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"pcalg" # requires graph, and RBGL
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@ -164,7 +171,6 @@
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"gridGraphviz" # requires graph, and Rgraphviz
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"ddepn" # requires graph, and genefilter
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"gridDebug" # requires gridGraphviz
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"DRI" # requires impute
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"FAMT" # requires impute
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"PMA" # requires impute
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"WGCNA" # requires impute
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@ -203,6 +209,7 @@
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"pbdDMAT" # requires pbdMPI
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"pbdSLAP" # requires pbdMPI
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"LOST" # requires pcaMethods
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"agridat" # requires pcaMethods
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"multiDimBio" # requires pcaMethods
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"crmn" # requires pcaMethods, and Biobase
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"imputeLCMD" # requires pcaMethods, and impute
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@ -272,12 +279,13 @@
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"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
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"plsRcox" # requires survcomp
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"rsig" # requires survcomp
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"leapp" # requires sva
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"ttScreening" # requires sva, and limma
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"cudaBayesreg" # requres Rmath
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"taxize" # requres bold
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"rsprng" # requres sprng
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"evobiR" # requres taxiz
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"RNeXML" # requres taxize
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"TR8" # requres taxize
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"bdvis" # requres taxize
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"evobiR" # requres taxiz
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]
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@ -125,10 +125,6 @@ stdenv: pkgs: old: new: {
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patches = [ ./patches/BayesBridge.patch ];
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});
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dbarts = old.dbarts.overrideDerivation (attrs: {
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patches = [ ./patches/dbarts.patch ];
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});
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openssl = old.openssl.overrideDerivation (attrs: {
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patches = [ ./patches/openssl.patch ];
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OPENSSL_HOME = "${pkgs.openssl}";
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@ -3,11 +3,14 @@
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"AnnotLists"
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"AnthropMMD"
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"AtelieR"
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"BAT"
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"BCA"
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"BEQI2"
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"BHMSMAfMRI"
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"BioGeoBEARS"
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"BiodiversityR"
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"CCTpack"
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"CommunityCorrelogram"
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"ConvergenceConcepts"
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"DALY"
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"DSpat"
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@ -18,38 +21,49 @@
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"DeducerSpatial"
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"DeducerSurvival"
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"DeducerText"
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"Demerelate"
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"DescTools"
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"DivMelt"
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"ENiRG"
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"EcoVirtual"
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"EnQuireR"
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"FAiR"
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"FD"
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"FFD"
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"FeedbackTS"
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"FreeSortR"
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"GGEBiplotGUI"
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"GPCSIV"
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"GUniFrac"
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"Geneland"
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"GeoGenetix"
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"GeoXp"
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"GrammR"
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"GrapheR"
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"GroupSeq"
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"HH"
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"HiveR"
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"IsotopeR"
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"JGR"
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"KappaGUI"
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"LS2Wstat"
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"MAR1"
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"MTurkR"
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"MVPARTwrap"
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"MareyMap"
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"MergeGUI"
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"Meth27QC"
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"MicroStrategyR"
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"MissingDataGUI"
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"MplusAutomation"
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"OligoSpecificitySystem"
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"OpenRepGrid"
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"PBSadmb"
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"PBSmodelling"
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"PCPS"
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"PKmodelFinder"
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"PoMoS"
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"PopGenReport"
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"PredictABEL"
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"PrevMap"
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"ProbForecastGOP"
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@ -57,6 +71,7 @@
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"R2STATS"
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"RHRV"
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"RNCEP"
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"RQDA"
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"RSDA"
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"RSurvey"
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"RandomFields"
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@ -102,6 +117,8 @@
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"SPACECAP"
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"SRRS"
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"SSDforR"
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"STEPCAM"
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"SYNCSA"
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"Simile"
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"SimpleTable"
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"StatDA"
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@ -118,17 +135,26 @@
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"accrual"
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"ade4TkGUI"
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"adehabitat"
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"analogue"
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"analogueExtra"
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"aplpack"
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"aqfig"
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"arf3DS4"
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"asbio"
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"bayesDem"
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"betapart"
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"betaper"
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"bio_infer"
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"bipartite"
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"biplotbootGUI"
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"blender"
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"cairoDevice"
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"cncaGUI"
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"cocorresp"
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"confidence"
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"constrainedKriging"
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"cpa"
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"dave"
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"debug"
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"detrendeR"
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"dgmb"
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@ -144,33 +170,53 @@
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"fgui"
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"fisheyeR"
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"fit4NM"
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"forams"
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"forensim"
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"fscaret"
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"gWidgets2RGtk2"
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"gWidgets2tcltk"
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"gWidgetsRGtk2"
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"gWidgetstcltk"
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"gcmr"
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"geoR"
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"geoRglm"
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"geomorph"
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"georob"
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"gnm"
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"gsubfn"
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"iBUGS"
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"iDynoR"
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"ic50"
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"in2extRemes"
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"iplots"
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"isopam"
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"likeLTD"
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"loe"
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"logmult"
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"memgene"
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"metacom"
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"migui"
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"miniGUI"
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"mixsep"
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"mlDNA"
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"mpmcorrelogram"
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"mritc"
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"multgee"
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"multibiplotGUI"
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"nodiv"
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"onemap"
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"palaeoSig"
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"paleoMAS"
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"pbatR"
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"pez"
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"phylotools"
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"picante"
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"playwith"
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"plotSEMM"
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"plsRbeta"
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"plsRglm"
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"pmg"
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"poppr"
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"powerpkg"
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"prefmod"
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"qtbase"
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@ -178,27 +224,47 @@
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"qtutils"
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"r4ss"
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"rAverage"
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"rareNMtests"
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"recluster"
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"relax"
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"relimp"
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"reportRx"
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"reshapeGUI"
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"rgl"
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"rich"
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"ringscale"
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"rioja"
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"ripa"
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"rite"
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"rnbn"
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"rriskDistributions"
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"rsgcc"
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"sdcMicroGUI"
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"sharpshootR"
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"simba"
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"soundecology"
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"spacodiR"
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"spatsurv"
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"sqldf"
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"statcheck"
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"stosim"
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"strvalidator"
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"stylo"
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"svDialogstcltk"
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"svIDE"
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"svSocket"
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"svWidgets"
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"tcltk2"
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"titan"
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"tkrgl"
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"tkrplot"
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"tmap"
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"tspmeta"
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"twiddler"
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"vcdExtra"
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"vegan"
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"vegan3d"
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"vegclust"
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"x12GUI"
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"xergm"
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]
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@ -2,6 +2,7 @@ pkgs: {
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# sort -t '=' -k 2
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RAppArmor = [ pkgs.apparmor ];
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SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
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curl = [ pkgs.curl pkgs.openldap ];
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Rssa = [ pkgs.fftw ];
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fftw = [ pkgs.fftw ];
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fftwtools = [ pkgs.fftw ];
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@ -1,12 +0,0 @@
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diff -ru -x '*~' dbarts_orig/src/Makevars.in dbarts/src/Makevars.in
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--- dbarts_orig/src/Makevars.in 2014-07-01 02:30:57.000000000 +0900
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+++ dbarts/src/Makevars.in 2014-10-25 19:25:58.910704279 +0900
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@@ -6,7 +6,7 @@
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PKG_CPPFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
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PKG_CPPXXFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
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-PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) dbarts/libdbarts.a external/libexternal.a @PTHREAD_LIBS@
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+PKG_LIBS=dbarts/libdbarts.a external/libexternal.a $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @PTHREAD_LIBS@
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.PHONY: all dbarts/libdbarts.a external/libexternal.a clean
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@ -1,28 +1,30 @@
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diff -ru -x '*~' openssl_orig/configure openssl/configure
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--- openssl_orig/configure 2014-10-18 08:14:15.000000000 +0900
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+++ openssl/configure 2014-11-03 15:05:25.122906126 +0900
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@@ -1,23 +1 @@
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-# Check for include
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-if [ ! -e /usr/include/openssl/rand.h ]
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-then
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- echo "openssl/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
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--- openssl_orig/configure 2014-11-08 02:32:33.000000000 +0900
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+++ openssl/configure 2014-11-29 20:57:19.919495325 +0900
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@@ -4,14 +4,15 @@
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# if present, hence this script is not really required. On CRAN, we use
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# the $OPENSSL_INCLUDES variable; elsewhere we assume to the standard
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# linux location: /usr/include/openssl.
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-if [ -z "$OPENSSL_INCLUDES" ]; then
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- OPENSSL_INCLUDES="/usr/include"
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-else
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- echo "PKG_CPPFLAGS= -I$OPENSSL_INCLUDES" >> src/Makevars
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-fi
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+# if [ -z "$OPENSSL_INCLUDES" ]; then
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+# OPENSSL_INCLUDES="/usr/include"
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+# else
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+# echo "PKG_CPPFLAGS= -I$OPENSSL_INCLUDES" >> src/Makevars
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+# fi
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-# Verify that openssl RNG is present
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-if [ ! -e $OPENSSL_INCLUDES/openssl/rand.h ]; then
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- echo "File $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
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- exit 1
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-fi
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-
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-# Not linux. Probably OSX.
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-if [ ! -e /sbin/ldconfig ]
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-then
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- exit 0
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-fi
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-
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-# looks like unix
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-LIBFILE=$(/sbin/ldconfig -p | egrep -ohm1 " [-_a-zA-Z0-9/]*/libssl[0-9]*.so$")
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-
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-if [ -z "$LIBFILE" ]
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-then
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- echo "libssl.so not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
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- exit 1
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-fi
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-
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-echo "PKG_LIBS= -L"$(dirname $LIBFILE)" -lssl -lcrypto" > src/Makevars
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+# # Verify that openssl RNG is present
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+# if [ ! -e $OPENSSL_INCLUDES/openssl/rand.h ]; then
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+# echo "File $OPENSSL_INCLUDES/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
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+# exit 1
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+# fi
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+echo "PKG_LIBS= -L"${OPENSSL_HOME}/lib" -lssl -lcrypto" > src/Makevars
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\ No newline at end of file
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