cran-packages: restructured

This commit is contained in:
taku0 2014-11-21 22:23:36 +09:00 committed by Peter Simons
parent e125997df6
commit 2a1d9ddbf2
28 changed files with 7317 additions and 6034 deletions

File diff suppressed because it is too large Load diff

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overrideDerivation: pkgs: old: new: {
RcppArmadillo = overrideDerivation old.RcppArmadillo (attrs: {
patchPhase = "patchShebangs configure";
});
rpf = overrideDerivation old.rpf (attrs: {
patchPhase = "patchShebangs configure";
});
BayesXsrc = overrideDerivation old.BayesXsrc (attrs: {
patches = [ ./patches/BayesXsrc.patch ];
});
rJava = overrideDerivation old.rJava (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
JavaGD = overrideDerivation old.JavaGD (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
Mposterior = overrideDerivation old.Mposterior (attrs: {
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
});
qtbase = overrideDerivation old.qtbase (attrs: {
patches = [ ./patches/qtbase.patch ];
});
Rmpi = overrideDerivation old.Rmpi (attrs: {
configureFlags = [
"--with-Rmpi-type=OPENMPI"
];
});
npRmpi = overrideDerivation old.npRmpi (attrs: {
configureFlags = [
"--with-Rmpi-type=OPENMPI"
];
});
Rmpfr = overrideDerivation old.Rmpfr (attrs: {
configureFlags = [
"--with-mpfr-include=${pkgs.mpfr}/include"
];
});
RVowpalWabbit = overrideDerivation old.RVowpalWabbit (attrs: {
configureFlags = [
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
];
});
RAppArmor = overrideDerivation old.RAppArmor (attrs: {
patches = [ ./patches/RAppArmor.patch ];
LIBAPPARMOR_HOME = "${pkgs.apparmor}";
});
RMySQL = overrideDerivation old.RMySQL (attrs: {
configureFlags = [
"--with-mysql-dir=${pkgs.mysql}"
];
});
slfm = overrideDerivation old.slfm (attrs: {
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
});
SamplerCompare = overrideDerivation old.SamplerCompare (attrs: {
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
});
gputools = overrideDerivation old.gputools (attrs: {
patches = [ ./patches/gputools.patch ];
CUDA_HOME = "${pkgs.cudatoolkit}";
});
CARramps = overrideDerivation old.CARramps (attrs: {
patches = [ ./patches/CARramps.patch ];
configureFlags = [
"--with-cuda-home=${pkgs.cudatoolkit}"
];
});
gmatrix = overrideDerivation old.gmatrix (attrs: {
patches = [ ./patches/gmatrix.patch ];
CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
R_INC_PATH = "${pkgs.R}/lib/R/include";
CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include";
});
rpud = overrideDerivation old.rpud (attrs: {
patches = [ ./patches/rpud.patch ];
CUDA_HOME = "${pkgs.cudatoolkit}";
});
WideLM = overrideDerivation old.WideLM (attrs: {
patches = [ ./patches/WideLM.patch ];
configureFlags = [
"--with-cuda-home=${pkgs.cudatoolkit}"
];
});
EMCluster = overrideDerivation old.EMCluster (attrs: {
patches = [ ./patches/EMCluster.patch ];
});
spMC = overrideDerivation old.spMC (attrs: {
patches = [ ./patches/spMC.patch ];
});
BayesLogit = overrideDerivation old.BayesLogit (attrs: {
patches = [ ./patches/BayesLogit.patch ];
});
BayesBridge = overrideDerivation old.BayesBridge (attrs: {
patches = [ ./patches/BayesBridge.patch ];
});
dbarts = overrideDerivation old.dbarts (attrs: {
patches = [ ./patches/dbarts.patch ];
});
openssl = overrideDerivation old.openssl (attrs: {
patches = [ ./patches/openssl.patch ];
OPENSSL_HOME = "${pkgs.openssl}";
});
Rserve = overrideDerivation old.Rserve (attrs: {
patches = [ ./patches/Rserve.patch ];
configureFlags = [
"--with-server" "--with-client"
];
});
nloptr = overrideDerivation old.nloptr (attrs: {
configureFlags = [
"--with-nlopt-cflags=-I${pkgs.nlopt}/include"
"--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
];
});
}

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library(data.table)
library(parallel)
cl <- makeCluster(10)
options(repos=structure(c(CRAN="http://cran.rstudio.com/")))
nixPrefetch <- function(name, version) {
system(paste0("nix-prefetch-url --type sha256 http://cran.rstudio.com/src/contrib/", name, "_", version, ".tar.gz"), intern=TRUE)
# system(paste0("nix-hash --flat --base32 --type sha256 /nix/store/*", name, "_", version, ".tar.gz", "| head -n 1"), intern=TRUE)
}
formatPackage <- function(name, version, sha256, depends, imports, linkingTo, knownPackages) {
attr <- gsub(".", "_", name, fixed=TRUE)
if (is.na(depends)) depends <- "";
depends <- unlist(strsplit(depends, split="[ \t\n]*,[ \t\n]*", fixed=FALSE))
depends <- c(depends, unlist(strsplit(imports, split="[ \t\n]*,[ \t\n]*", fixed=FALSE)))
depends <- c(depends, unlist(strsplit(linkingTo, split="[ \t\n]*,[ \t\n]*", fixed=FALSE)))
depends <- sapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1")
depends <- depends[depends %in% knownPackages]
depends <- sapply(depends, gsub, pattern=".", replacement="_", fixed=TRUE)
depends <- paste(depends, collapse=" ")
paste0(attr, " = derive { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
}
clusterExport(cl, c("nixPrefetch"))
pkgs <- as.data.table(available.packages(filters=c("R_version", "OS_type", "CRAN", "duplicates")))
pkgs <- subset(pkgs, Repository=="http://cran.rstudio.com/src/contrib")
pkgs <- pkgs[order(Package)]
pkgs$sha256 <- parApply(cl, pkgs, 1, function(p) nixPrefetch(p[1], p[2]))
knownPackages <- unique(pkgs$Package)
nix <- apply(pkgs, 1, function(p) formatPackage(p[1], p[2], p[18], p[4], p[5], p[6], knownPackages))
cat("# This file is generated from generate_sources.R. DO NOT EDIT.\n")
cat("# Execute the following command to update the file.\n")
cat("#\n")
cat("# Rscript generate_sources.R > sources.nix\n")
cat("\n")
cat("{ self, derive }: with self; {\n")
cat(paste(nix, collapse="\n"), "\n")
cat("}\n")
stopCluster(cl)

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@ -1,9 +1,9 @@
R:
{ R, xvfb_run, utillinux }:
{ name, buildInputs ? [], ... } @ attrs:
R.stdenv.mkDerivation ({
buildInputs = buildInputs ++ [R];
buildInputs = buildInputs ++ [R xvfb_run utillinux];
configurePhase = ''
runHook preConfigure
@ -16,10 +16,22 @@ R.stdenv.mkDerivation ({
runHook postBuild
'';
installOptions = if attrs.skipTest or false then
"--no-test-load "
else
"";
rCommand = if attrs.requireX or false then
# Unfortunately, xvfb-run has a race condition even with -a option, so that
# we acquire a lock explicitly.
"flock ${xvfb_run} xvfb-run -a -e xvfb-error R"
else
"R";
installPhase = ''
runHook preInstall
mkdir -p $out/library
R CMD INSTALL -l $out/library .
$rCommand CMD INSTALL $installOptions --configure-args="$configureFlags" -l $out/library .
runHook postInstall
'';

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# Packages which cannot be installed due to lack of dependencies or other reasons.
[
# sort -t '#' -k 2
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
"Actigraphy" # SDMTools.so: undefined symbol: X
"MigClim" # SDMTools.So: Undefined Symbol: X
"PatternClass" # SDMTools.So: Undefined Symbol: X
"lefse" # SDMTools.so: undefined symbol: X
"raincpc" # SDMTools.so: undefined symbol: X
"rainfreq" # SDMTools.so: undefined symbol: X
"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
"alm" # jsonlite.so: undefined symbol: XXX
"archivist" # jsonlite.so: undefined symbol: XXX
"bold" # jsonlite.so: undefined symbol: XXX
"enigma" # jsonlite.so: undefined symbol: XXX
"exCon" # jsonlite.so: undefined symbol: XXX
"gender" # jsonlite.so: undefined symbol: XXX
"jSonarR" # jsonlite.so: undefined symbol: XXX
"leafletR" # jsonlite.so: undefined symbol: XXX
"opencpu" # jsonlite.so: undefined symbol: XXX
"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
"rinat" # jsonlite.so: undefined symbol: XXX
"rjstat" # jsonlite.so: undefined symbol: XXX
"rmongodb" # jsonlite.so: undefined symbol: XXX
"rnoaa" # jsonlite.so: undefined symbol: XXX
"rsunlight" # jsonlite.so: undefined symbol: XXX
"slackr" # jsonlite.so: undefined symbol: XXX
"webutils" # jsonlite.so: undefined symbol: XXX
"HPO" # requires AnnotationDbi
"HPO.db" # requires AnnotationDbi
"HPO_db" # requires AnnotationDbi
"msarc" # requires AnnotationDbi
"ppiPre" # requires AnnotationDbi
"RobLox" # requires Biobase
"RobLoxBioC" # requires Biobase
"compendiumdb" # requires Biobase
"ktspair" # requires Biobase
"permGPU" # requires Biobase
"propOverlap" # requires Biobase
"GExMap" # requires Biobase and multtest
"IsoGene" # requires Biobase, and affy
"mGSZ" # requires Biobase, and limma
"NCmisc" # requires BiocInstaller
"RADami" # requires Biostrings
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
"SimRAD" # requires Biostrings, and ShortRead
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
"OpenCL" # requires CL/opencl.h
"cplexAPI" # requires CPLEX
"CHAT" # requires DNAcopy
"PSCBS" # requires DNAcopy
"ParDNAcopy" # requires DNAcopy
"Rcell" # requires EBImage
"RockFab" # requires EBImage
"gitter" # requires EBImage
"rggobi" # requires GGobi
"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
"PubMedWordcloud" # requires GOsummaries
"ExomeDepth" # requires GenomicRanges, and Rsamtools
"HPOSim" # requires HPO_db
"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
"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
"oposSOM" # requires biomaRt
"snplist" # requires biomaRt
"FunctionalNetworks" # requires breastCancerVDX, and Biobase
"rJPSGCS" # requires chopsticks
"clpAPI" # requires clp
"pcaL1" # requires clp
"bmrm" # requires clpAPI
"sequenza" # requires copynumber
"Rcplex" # requires cplexAPI
"dcGOR" # requires dnet
"bcool" # requires doMPI
"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
"LogisticDx" # requires gRbase
"gRain" # requires gRbase
"gRbase" # 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
"miRtest" # requires globaltest, GlobalAncova, and limma
"PairViz" # requires graph
"eulerian" # requires graph
"gRapHD" # requires graph
"msSurv" # requires graph
"RnavGraph" # requires graph, and RBGL
"iRefR" # requires graph, and RBGL
"pcalg" # requires graph, and RBGL
"protiq" # requires graph, and RBGL
"classGraph" # requires graph, and Rgraphviz
"epoc" # requires graph, and Rgraphviz
"gridGraphviz" # requires graph, and Rgraphviz
"ddepn" # requires graph, and genefilter
"gridDebug" # requires gridGraphviz
"DRI" # requires impute
"FAMT" # requires impute
"PMA" # requires impute
"WGCNA" # requires impute
"moduleColor" # requires impute
"samr" # requires impute
"swamp" # requires impute
"MetaDE" # requires impute, and Biobase
"FHtest" # requires interval
"RefFreeEWAS" # requires isva
"AntWeb" # requires leafletR
"ecoengine" # requires leafletR
"spocc" # requires leafletR
"sybilSBML" # requires libSBML
"RDieHarder" # requires libdieharder
"CORM" # requires limma
"DAAGbio" # requires limma
"DCGL" # requires limma
"GOsummaries" # requires limma
"SQDA" # requires limma
"metaMA" # requires limma
"plmDE" # requires limma
"RPPanalyzer" # requires limma, and Biobase
"PerfMeas" # requires limma, graph, and RBGL
"MAMA" # requires metaMA
"Rmosek" # requires mosek
"PCS" # requires multtest
"TcGSA" # requires multtest
"hddplot" # requires multtest
"mutoss" # requires multtest
"structSSI" # requires multtest
"mutossGUI" # requires mutoss
"Biograph" # requires mvna
"MSeasy" # requires mzR, and xcms
"x_ent" # requires opencpu
"pbdBASE" # requires pbdMPI
"pbdDEMO" # requires pbdMPI
"pbdDMAT" # requires pbdMPI
"pbdSLAP" # requires pbdMPI
"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
"sgof" # requires plot2D
"surveillance" # requires polyCub
"aLFQ" # requires protiq
"NLPutils" # requires qdap
"NBPSeq" # requires qvalue
"RSNPset" # requires qvalue
"evora" # requires qvalue
"isva" # requires qvalue
"pi0" # requires qvalue
"CrypticIBDcheck" # requires rJPSGCS
"PKgraph" # requires rggobi
"SeqGrapheR" # requires rggobi
"beadarrayMSV" # requires rggobi
"clusterfly" # requires rggobi
"HierO" # requires rneos
"fPortfolio" # requires rneos
"GUIDE" # requires rpanel
"SDD" # requires rpanel
"biotools" # requires rpanel
"erpR" # requires rpanel
"gamlss_demo" # requires rpanel
"lgcp" # requires rpanel
"optBiomarker" # requires rpanel
"soilphysics" # requires rpanel
"vows" # requires rpanel
"PCGSE" # requires safe
"DepthProc" # requires samr
"netClass" # requires samr
"RcmdrPlugin_seeg" # requires seeg
"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
"GeneticTools" # requires snpStats
"snpEnrichment" # requires snpStats
"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
"dixon" # requires spatstat
"dpcR" # requires spatstat
"ecespa" # requires spatstat
"ecospat" # requires spatstat
"intamapInteractive" # requires spatstat
"latticeDensity" # requires spatstat
"polyCub" # requires spatstat
"seeg" # requires spatstat
"siar" # requires spatstat
"siplab" # requires spatstat
"sparr" # requires spatstat
"spatialsegregation" # requires spatstat
"stpp" # requires spatstat
"trip" # requires spatstat
"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
"plsRcox" # requires survcomp
"rsig" # requires survcomp
"ttScreening" # requires sva, and limma
"cudaBayesreg" # requres Rmath
"taxize" # requres bold
"rsprng" # requres sprng
"RNeXML" # requres taxize
"TR8" # requres taxize
"bdvis" # requres taxize
"evobiR" # requres taxiz
]

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[
"AnalyzeFMRI"
"AnnotLists"
"AnthropMMD"
"AtelieR"
"BCA"
"BEQI2"
"BHMSMAfMRI"
"BiodiversityR"
"CCTpack"
"ConvergenceConcepts"
"DALY"
"DSpat"
"Deducer"
"DeducerExtras"
"DeducerPlugInExample"
"DeducerPlugInScaling"
"DeducerSpatial"
"DeducerSurvival"
"DeducerText"
"DescTools"
"DivMelt"
"ENiRG"
"EcoVirtual"
"EnQuireR"
"FFD"
"FeedbackTS"
"GGEBiplotGUI"
"GPCSIV"
"Geneland"
"GeoGenetix"
"GeoXp"
"GrapheR"
"GroupSeq"
"HH"
"HiveR"
"JGR"
"KappaGUI"
"LS2Wstat"
"MAR1"
"MTurkR"
"MareyMap"
"MergeGUI"
"Meth27QC"
"MissingDataGUI"
"MplusAutomation"
"OligoSpecificitySystem"
"OpenRepGrid"
"PBSadmb"
"PBSmodelling"
"PKmodelFinder"
"PoMoS"
"PredictABEL"
"PrevMap"
"ProbForecastGOP"
"QCAGUI"
"R2STATS"
"RHRV"
"RNCEP"
"RSDA"
"RSurvey"
"RandomFields"
"Rcmdr"
"RcmdrPlugin_BCA"
"RcmdrPlugin_DoE"
"RcmdrPlugin_EACSPIR"
"RcmdrPlugin_EBM"
"RcmdrPlugin_EZR"
"RcmdrPlugin_EcoVirtual"
"RcmdrPlugin_FactoMineR"
"RcmdrPlugin_HH"
"RcmdrPlugin_IPSUR"
"RcmdrPlugin_KMggplot2"
"RcmdrPlugin_MA"
"RcmdrPlugin_MPAStats"
"RcmdrPlugin_NMBU"
"RcmdrPlugin_ROC"
"RcmdrPlugin_SCDA"
"RcmdrPlugin_SLC"
"RcmdrPlugin_SM"
"RcmdrPlugin_StatisticalURV"
"RcmdrPlugin_TeachingDemos"
"RcmdrPlugin_UCA"
"RcmdrPlugin_coin"
"RcmdrPlugin_depthTools"
"RcmdrPlugin_doex"
"RcmdrPlugin_epack"
"RcmdrPlugin_lfstat"
"RcmdrPlugin_mosaic"
"RcmdrPlugin_orloca"
"RcmdrPlugin_plotByGroup"
"RcmdrPlugin_pointG"
"RcmdrPlugin_qual"
"RcmdrPlugin_sampling"
"RcmdrPlugin_sos"
"RcmdrPlugin_steepness"
"RcmdrPlugin_survival"
"RcmdrPlugin_temis"
"RenextGUI"
"RunuranGUI"
"SOLOMON"
"SPACECAP"
"SRRS"
"SSDforR"
"Simile"
"SimpleTable"
"StatDA"
"SyNet"
"TDMR"
"TED"
"TIMP"
"TTAinterfaceTrendAnalysis"
"TestScorer"
"VIMGUI"
"VecStatGraphs3D"
"VisuClust"
"WMCapacity"
"accrual"
"ade4TkGUI"
"adehabitat"
"aplpack"
"aqfig"
"arf3DS4"
"asbio"
"bio_infer"
"biplotbootGUI"
"cairoDevice"
"cncaGUI"
"confidence"
"constrainedKriging"
"cpa"
"debug"
"detrendeR"
"dgmb"
"dpa"
"dynBiplotGUI"
"dynamicGraph"
"eVenn"
"exactLoglinTest"
"fSRM"
"fat2Lpoly"
"fbati"
"feature"
"fgui"
"fisheyeR"
"fit4NM"
"forensim"
"fscaret"
"gWidgets2RGtk2"
"gWidgets2tcltk"
"gWidgetstcltk"
"gcmr"
"geoR"
"geoRglm"
"georob"
"gnm"
"gsubfn"
"ic50"
"in2extRemes"
"iplots"
"likeLTD"
"logmult"
"migui"
"miniGUI"
"mixsep"
"mlDNA"
"mritc"
"multgee"
"multibiplotGUI"
"onemap"
"pbatR"
"playwith"
"plotSEMM"
"powerpkg"
"prefmod"
"qtbase"
"qtpaint"
"qtutils"
"r4ss"
"rAverage"
"relax"
"relimp"
"reportRx"
"ringscale"
"ripa"
"rite"
"rnbn"
"rriskDistributions"
"rsgcc"
"sdcMicroGUI"
"spatsurv"
"sqldf"
"stosim"
"stylo"
"svDialogstcltk"
"svIDE"
"svSocket"
"svWidgets"
"titan"
"tkrgl"
"twiddler"
"vcdExtra"
"x12GUI"
]

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@ -0,0 +1,6 @@
[
"Rmpi" # tries to run MPI processes
"gmatrix" # requires CUDA runtime
"npRmpi" # tries to run MPI processes
"sprint" # tries to run MPI processes
]

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pkgs: {
# sort -t '=' -k 2
qtpaint = [ pkgs.cmake ];
qtbase = [ pkgs.cmake pkgs.perl ];
gmatrix = [ pkgs.cudatoolkit ];
WideLM = [ pkgs.cudatoolkit ];
RCurl = [ pkgs.curl ];
Rgnuplot = [ pkgs.gnuplot ];
R2SWF = [ pkgs.pkgconfig ];
RGtk2 = [ pkgs.pkgconfig ];
RProtoBuf = [ pkgs.pkgconfig ];
Rpoppler = [ pkgs.pkgconfig ];
VBmix = [ pkgs.pkgconfig ];
XML = [ pkgs.pkgconfig ];
cairoDevice = [ pkgs.pkgconfig ];
chebpol = [ pkgs.pkgconfig ];
fftw = [ pkgs.pkgconfig ];
geoCount = [ pkgs.pkgconfig ];
kza = [ pkgs.pkgconfig ];
mwaved = [ pkgs.pkgconfig ];
showtext = [ pkgs.pkgconfig ];
spate = [ pkgs.pkgconfig ];
stringi = [ pkgs.pkgconfig ];
sysfonts = [ pkgs.pkgconfig ];
Cairo = [ pkgs.pkgconfig ];
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
qtutils = [ pkgs.qt4 ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
tikzDevice = [ pkgs.texLive ];
rPython = [ pkgs.which ];
CARramps = [ pkgs.which pkgs.cudatoolkit ];
gputools = [ pkgs.which pkgs.cudatoolkit ];
rpud = [ pkgs.which pkgs.cudatoolkit ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
}

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@ -0,0 +1,117 @@
pkgs: {
# sort -t '=' -k 2
RAppArmor = [ pkgs.apparmor ];
SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
Rssa = [ pkgs.fftw ];
fftw = [ pkgs.fftw ];
fftwtools = [ pkgs.fftw ];
kza = [ pkgs.fftw ];
mwaved = [ pkgs.fftw ];
spate = [ pkgs.fftw ];
chebpol = [ pkgs.fftw ];
seewave = [ pkgs.fftw pkgs.libsndfile ];
rgeos = [ pkgs.geos ];
Rglpk = [ pkgs.glpk ];
RCA = [ pkgs.gmp ];
gmp = [ pkgs.gmp ];
rcdd = [ pkgs.gmp ];
igraph = [ pkgs.gmp ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
sdcTable = [ pkgs.gmp pkgs.glpk ];
Rmpfr = [ pkgs.gmp pkgs.mpfr ];
BNSP = [ pkgs.gsl ];
BayesSAE = [ pkgs.gsl ];
BayesVarSel = [ pkgs.gsl ];
HiCseg = [ pkgs.gsl ];
KFKSDS = [ pkgs.gsl ];
R2GUESS = [ pkgs.gsl ];
RcppZiggurat = [ pkgs.gsl ];
SemiCompRisks = [ pkgs.gsl ];
VBLPCM = [ pkgs.gsl ];
abn = [ pkgs.gsl ];
cit = [ pkgs.gsl ];
libamtrack = [ pkgs.gsl ];
mixcat = [ pkgs.gsl ];
outbreaker = [ pkgs.gsl ];
pcaPA = [ pkgs.gsl ];
ridge = [ pkgs.gsl ];
simplexreg = [ pkgs.gsl ];
stsm = [ pkgs.gsl ];
survSNP = [ pkgs.gsl ];
topicmodels = [ pkgs.gsl ];
RcppGSL = [ pkgs.gsl ];
bnpmr = [ pkgs.gsl ];
geoCount = [ pkgs.gsl ];
gsl = [ pkgs.gsl ];
mvabund = [ pkgs.gsl ];
diversitree = [ pkgs.gsl pkgs.fftw ];
VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
RGtk2 = [ pkgs.gtk2 ];
cairoDevice = [ pkgs.gtk2 ];
adimpro = [ pkgs.imagemagick ];
rjags = [ pkgs.jags ];
runjags = [ pkgs.jags ];
JavaGD = [ pkgs.jdk ];
RODBC = [ pkgs.libiodbc ];
RODBCext = [ pkgs.libiodbc ];
jpeg = [ pkgs.libjpeg ];
EMCluster = [ pkgs.liblapack ];
png = [ pkgs.libpng ];
rtiff = [ pkgs.libtiff ];
tiff = [ pkgs.libtiff ];
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
rpud = [ pkgs.linuxPackages.nvidia_x11 ];
CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
rgl = [ pkgs.mesa pkgs.x11 ];
ncdf = [ pkgs.netcdf ];
ncdf4 = [ pkgs.netcdf ];
pbdNCDF4 = [ pkgs.netcdf ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
nloptr = [ pkgs.nlopt ];
npRmpi = [ pkgs.openmpi ];
pbdPROF = [ pkgs.openmpi ];
sprint = [ pkgs.openmpi ];
Rmpi = [ pkgs.openmpi ];
openssl = [ pkgs.openssl ];
PKI = [ pkgs.openssl ];
RSclient = [ pkgs.openssl ];
Rserve = [ pkgs.openssl ];
Rpoppler = [ pkgs.poppler ];
audio = [ pkgs.portaudio ];
rpg = [ pkgs.postgresql ];
RPostgreSQL = [ pkgs.postgresql ];
ssanv = [ pkgs.proj ];
proj4 = [ pkgs.proj ];
rgdal = [ pkgs.proj pkgs.gdal ];
RProtoBuf = [ pkgs.protobuf ];
rPython = [ pkgs.python ];
qtpaint = [ pkgs.qt4 ];
qtbase = [ pkgs.qt4 ];
BayesXsrc = [ pkgs.readline pkgs.ncurses ];
udunits2 = [ pkgs.udunits pkgs.expat ];
tkrplot = [ pkgs.xlibs.libX11 ];
rzmq = [ pkgs.zeromq2 ];
PopGenome = [ pkgs.zlib ];
RJaCGH = [ pkgs.zlib ];
RcppCNPy = [ pkgs.zlib ];
Rniftilib = [ pkgs.zlib ];
WhopGenome = [ pkgs.zlib ];
devEMF = [ pkgs.zlib ];
gdsfmt = [ pkgs.zlib ];
rbamtools = [ pkgs.zlib ];
rmatio = [ pkgs.zlib ];
RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
seqminer = [ pkgs.zlib pkgs.bzip2 ];
rphast = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
rtfbs = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
XBRL = [ pkgs.zlib pkgs.libxml2 ];
RMySQL = [ pkgs.zlib pkgs.mysql ];
}

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@ -0,0 +1,9 @@
diff -ru -x '*~' BayesBridge_orig/src/Makevars BayesBridge/src/Makevars
--- BayesBridge_orig/src/Makevars 2014-07-19 05:08:55.000000000 +0900
+++ BayesBridge/src/Makevars 2014-10-25 18:35:01.398539305 +0900
@@ -9,4 +9,4 @@
# PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -I../inst/include/ -DDISABLE_SINGLE -DNTHROW
PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -DDISABLE_SINGLE -DNTHROW
# PKG_CPPFLAGS = -DUSE_R -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wshadow -ansi -Wsequence-point
-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS)
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

View file

@ -0,0 +1,9 @@
diff -ru -x '*~' BayesBridge_orig/src/Makevars BayesBridge/src/Makevars
--- BayesBridge_orig/src/Makevars 2014-07-19 05:08:55.000000000 +0900
+++ BayesBridge/src/Makevars 2014-10-25 14:44:23.422592445 +0900
@@ -9,4 +9,4 @@
# PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -I../inst/include/ -DDISABLE_SINGLE -DNTHROW
PKG_CPPFLAGS = -DUSE_R -DDISABLE_FIO -DDISABLE_SINGLE -DNTHROW
# PKG_CPPFLAGS = -DUSE_R -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wshadow -ansi -Wsequence-point
-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS)
+PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -lcblas

View file

@ -0,0 +1,12 @@
diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
--- BayesLogit_orig/src/Makevars 2014-04-24 23:31:13.000000000 +0900
+++ BayesLogit/src/Makevars 2014-10-25 18:33:32.398572641 +0900
@@ -6,7 +6,7 @@
## W/OUT Dynamic Stuff
OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS)
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
# PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW

View file

@ -0,0 +1,12 @@
diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
--- BayesLogit_orig/src/Makevars 2014-04-24 23:31:13.000000000 +0900
+++ BayesLogit/src/Makevars 2014-10-21 21:00:15.570699136 +0900
@@ -6,7 +6,7 @@
## W/OUT Dynamic Stuff
OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
-PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS)
+PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -llapack -lf77blas -lcblas -latlas -lgfortran
# PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW

View file

@ -0,0 +1,55 @@
diff -ru -x '*~' BayesXsrc_org/MD5 BayesXsrc/MD5
--- BayesXsrc_org/MD5 2013-11-22 21:59:01.000000000 +0900
+++ BayesXsrc/MD5 2014-10-14 22:50:46.040754675 +0900
@@ -4,7 +4,7 @@
cba21fc7e2d39608d0241d8cedc4fd43 *R/run.bayesx.R
112cb3aff0f8f0cd60bb146b14df1fcf *inst/CITATION
cf04425475f03ee67c06efcebbd8d476 *man/run.bayesx.Rd
-1f73de4dba1228cdaa8d5435d1c1656b *src/Makefile
+658152ec0b336198a2654385bb27666d *src/Makefile
2971212d003d1d647110264fb471e63b *src/Makefile.win
e0fd1515e0d2f8553d4034c3f7544fc5 *src/bayesxsrc/adaptiv/fullcond_adaptiv.cpp
08cd954d541c3c0d635bbbd61cd05d15 *src/bayesxsrc/adaptiv/fullcond_adaptiv.h
@@ -320,7 +320,7 @@
465ac930657299f89a0a164232dc15d2 *src/dev-Makefile
d9aafe726622cd8c46bab760fef0d813 *src/dev-Makefile.win
50413e579bc999d49037293a612190c0 *src/install.libs.R
-1f73de4dba1228cdaa8d5435d1c1656b *src/rel-Makefile
+658152ec0b336198a2654385bb27666d *src/rel-Makefile
2971212d003d1d647110264fb471e63b *src/rel-Makefile.win
4d675785837670b6a9b2b3405812a910 *tests/data.raw
1d3777462fcefa39559aa645305a65f2 *tests/mcmc.R
diff -ru -x '*~' BayesXsrc_org/src/Makefile BayesXsrc/src/Makefile
--- BayesXsrc_org/src/Makefile 2013-11-22 21:49:16.000000000 +0900
+++ BayesXsrc/src/Makefile 2014-10-14 22:47:15.458766001 +0900
@@ -137,11 +137,11 @@
${PSPLINES_OBJS}\
${STRUCTADD_OBJS}\
bayesxsrc/main.o\
- bayesxsrc/samson/multgaussian.o\
+ bayesxsrc/samson/multgaussian.o\
bayesxsrc/adaptiv/fullcond_adaptiv.o\
bayesxsrc/alex/mixture.o
-LDFLAGS += -L${R_HOME}/lib -lreadline -lcurses
+LDFLAGS += -L${R_HOME}/lib -lreadline -lncurses
CPPFLAGS += -Ibayesxsrc/. -I"bayesxsrc/bib" -I"bayesxsrc/alex" -I"bayesxsrc/adaptiv" -I"bayesxsrc/andrea" -I"bayesxsrc/dag" -I"bayesxsrc/graph" -I"bayesxsrc/mcmc" -I"bayesxsrc/psplines" -I"bayesxsrc/samson" -I"bayesxsrc/leyre" -I"bayesxsrc/structadd"
CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
# CXXFLAGS += -O3 -ansi
diff -ru -x '*~' BayesXsrc_org/src/rel-Makefile BayesXsrc/src/rel-Makefile
--- BayesXsrc_org/src/rel-Makefile 2013-10-08 21:28:09.000000000 +0900
+++ BayesXsrc/src/rel-Makefile 2014-10-14 22:47:04.601766431 +0900
@@ -137,11 +137,11 @@
${PSPLINES_OBJS}\
${STRUCTADD_OBJS}\
bayesxsrc/main.o\
- bayesxsrc/samson/multgaussian.o\
+ bayesxsrc/samson/multgaussian.o\
bayesxsrc/adaptiv/fullcond_adaptiv.o\
bayesxsrc/alex/mixture.o
-LDFLAGS += -L${R_HOME}/lib -lreadline -lcurses
+LDFLAGS += -L${R_HOME}/lib -lreadline -lncurses
CPPFLAGS += -Ibayesxsrc/. -I"bayesxsrc/bib" -I"bayesxsrc/alex" -I"bayesxsrc/adaptiv" -I"bayesxsrc/andrea" -I"bayesxsrc/dag" -I"bayesxsrc/graph" -I"bayesxsrc/mcmc" -I"bayesxsrc/psplines" -I"bayesxsrc/samson" -I"bayesxsrc/leyre" -I"bayesxsrc/structadd"
CPPFLAGS += -D__BUILDING_GNU -D__BUILDING_LINUX -DTEMPL_INCL_DEF -D_MSC_VER2 -DNO_TEMPLATE_FRIENDS -DINCLUDE_REML -DINCLUDE_MCMC
# CXXFLAGS += -O3 -ansi

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@ -0,0 +1,24 @@
diff -ru -x '*~' CARramps_orig/configure CARramps/configure
--- CARramps_orig/configure 2011-12-01 22:27:06.000000000 +0900
+++ CARramps/configure 2014-10-25 14:56:04.599337748 +0900
@@ -2395,7 +2395,7 @@
NCFLAGS="-arch=sm_13 -O2"
-CUDA_INC=${CUDA_HOME}/include
+CUDA_INC=${CUDA_HOME}/usr_include
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for CUDA headers" >&5
$as_echo_n "checking for CUDA headers... " >&6; }
as_ac_File=`$as_echo "ac_cv_file_${CUDA_INC}/cublas.h" | $as_tr_sh`
diff -ru -x '*~' CARramps_orig/src/combo1colForR1Q_d.cu CARramps/src/combo1colForR1Q_d.cu
--- CARramps_orig/src/combo1colForR1Q_d.cu 2011-12-01 22:27:06.000000000 +0900
+++ CARramps/src/combo1colForR1Q_d.cu 2014-10-25 14:59:06.869299163 +0900
@@ -4,7 +4,7 @@
#include <cuda.h>
#include <R.h>
#include <Rmath.h>
-#include <combo1colForR1Q_d.h>
+#include "combo1colForR1Q_d.h"
#define BLOCKSIZE 256

View file

@ -0,0 +1,6 @@
diff -ru -x '*~' EMCluster_orig/src/Makevars EMCluster/src/Makevars
--- EMCluster_orig/src/Makevars 2013-07-05 02:43:25.000000000 +0900
+++ EMCluster/src/Makevars 2014-10-25 18:10:19.190992120 +0900
@@ -1 +1 @@
-PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS)
+PKG_LIBS = $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS)

View file

@ -0,0 +1,20 @@
diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure
--- RAppArmor_orig/configure 2013-12-17 11:23:00.000000000 +0900
+++ RAppArmor/configure 2014-10-18 22:22:39.641341244 +0900
@@ -1,15 +1,2 @@
-if [ ! -e /usr/include/sys/apparmor.h ]
-then
- echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed."
- exit 1
-fi
-
-LIBFILE=$(/sbin/ldconfig -p | egrep -oh " [-_a-zA-Z0-9/]*/libapparmor.so(.1)?$")
-
-if [ -z "$LIBFILE" ]
-then
- echo "libapparmor.so not found. Make sure libapparmor-dev is installed."
- exit 1
-fi
-
+LIBFILE="$LIBAPPARMOR_HOME/lib/libapparmor.so.1"
echo "PKG_LIBS="$LIBFILE > src/Makevars

View file

@ -0,0 +1,15 @@
diff -ru -x '*~' Rserve_orig/src/Makevars.in Rserve/src/Makevars.in
--- Rserve_orig/src/Makevars.in 2013-08-22 06:09:33.000000000 +0900
+++ Rserve/src/Makevars.in 2014-11-09 21:36:31.184590320 +0900
@@ -12,8 +12,9 @@
$(CC) -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(PKG_CPPFLAGS) $(PKG_CFLAGS) -o Rserve.dbg $(SERVER_SRC) $(ALL_LIBS) $(PKG_LIBS)
# merging to bin/Rserve works only if installed from sources, won't work for binary
- -./mergefat Rserve "$(R_HOME)/bin/Rserve"
- -./mergefat Rserve.dbg "$(R_HOME)/bin/Rserve.dbg"
+ mkdir $(out)/bin
+ -./mergefat Rserve "$(out)/bin/Rserve"
+ -./mergefat Rserve.dbg "$(out)/bin/Rserve.dbg"
client: config.h
cp config.h client/cxx/

View file

@ -0,0 +1,19 @@
diff -ru -x '*~' WideLM_orig/src/Makefile.in WideLM/src/Makefile.in
--- WideLM_orig/src/Makefile.in 2012-02-17 04:28:05.000000000 +0900
+++ WideLM/src/Makefile.in 2014-10-25 18:54:49.110011921 +0900
@@ -12,12 +12,12 @@
#compiler/preprocessor options
R_INCS := @R_INCL@ @RCPP_INCL@
CC_ARGS := @CU_PARAMS@ -Xcompiler @R_CPIC@
-CU_INCS := -I@CUDA_HOME@/include
+CU_INCS := -I@CUDA_HOME@/usr_include
CU_ARCH := -gencode arch=compute_20,code=sm_20
#linker options
-LD_PARAMS := -Xlinker "@RCPP_LDFLAGS@"
-RCU_LIBS := @R_LIB@ -L@CU_LIBDIR@ -lcublas
+LD_PARAMS := -Xlinker "--export-dynamic -fopenmp -L${R_HOME}/lib -lR"
+RCU_LIBS := -Xlinker "-L@CU_LIBDIR@ -lcublas"
all : WideLM.so

View file

@ -0,0 +1,12 @@
diff -ru -x '*~' dbarts_orig/src/Makevars.in dbarts/src/Makevars.in
--- dbarts_orig/src/Makevars.in 2014-07-01 02:30:57.000000000 +0900
+++ dbarts/src/Makevars.in 2014-10-25 19:25:58.910704279 +0900
@@ -6,7 +6,7 @@
PKG_CPPFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
PKG_CPPXXFLAGS=-I$(INST_DIR)/include -Iinclude @PTHREAD_CFLAGS@ $(THREAD_SAFE_UNLOAD)
-PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) dbarts/libdbarts.a external/libexternal.a @PTHREAD_LIBS@
+PKG_LIBS=dbarts/libdbarts.a external/libexternal.a $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) @PTHREAD_LIBS@
.PHONY: all dbarts/libdbarts.a external/libexternal.a clean

View file

@ -0,0 +1,48 @@
diff -ru -x '*~' gmatrix_orig/src/Makefile gmatrix/src/Makefile
--- gmatrix_orig/src/Makefile 2014-08-27 02:42:04.000000000 +0900
+++ gmatrix/src/Makefile 2014-10-25 15:35:29.797202981 +0900
@@ -21,6 +21,7 @@
# to the manual on the gmatrix install instructions)
CUDA_LIB_PATH ?= /usr/local/cuda/lib64
R_INC_PATH ?= /usr/include/R
+CUDA_INC_PATH ?= /usr/local/cuda/include
# Nvidia CUDA Compiler
@@ -49,25 +50,25 @@
# Build rules
build: $(OUT_OBJ)
$(R_CC) $(OUT_OBJ) -o $(OUT_SO) $(LIBS) -L$(CUDA_LIB_PATH)
-
+
conversions.o:
- $(NVCC) -c conversions.cu -o conversions.o $(NVCC_FLAGS) -I$(R_INC_PATH)
-
+ $(NVCC) -c conversions.cu -o conversions.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
manipulation.o:
- $(NVCC) -c manipulation.cu -o manipulation.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+ $(NVCC) -c manipulation.cu -o manipulation.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
general.o:
- $(NVCC) -c general.cu -o general.o $(NVCC_FLAGS) -I$(R_INC_PATH)
+ $(NVCC) -c general.cu -o general.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
matrix.o:
- $(NVCC) -c matrix.cu -o matrix.o $(NVCC_FLAGS) -I$(R_INC_PATH)
-
+ $(NVCC) -c matrix.cu -o matrix.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
ops.o:
- $(NVCC) -c ops.cu -o ops.o $(NVCC_FLAGS) -I$(R_INC_PATH)
-
+ $(NVCC) -c ops.cu -o ops.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
dist.o:
- $(NVCC) -c dist.cu -o dist.o $(NVCC_FLAGS) -I$(R_INC_PATH)
-
+ $(NVCC) -c dist.cu -o dist.o $(NVCC_FLAGS) -I$(R_INC_PATH) -I${CUDA_INC_PATH}
+
clean:
-rm -f *.o core

View file

@ -0,0 +1,13 @@
diff -ru -x '*~' gputools_orig/src/Makefile gputools/src/Makefile
--- gputools_orig/src/Makefile 2013-05-09 01:43:32.000000000 +0900
+++ gputools/src/Makefile 2014-10-21 21:41:23.067148490 +0900
@@ -6,6 +6,9 @@
R_HOME := $(shell R RHOME)
+CUDA_INC := $(CUDA_HOME)/usr_include
+CUDA_LIB := $(CUDA_HOME)/lib
+
#compiler/preprocessor options
INCS := -I. -I"$(CUDA_INC)" -I"$(R_INC)"
PARAMS := $(DEVICEOPTS) -Xcompiler $(CPICFLAGS)

View file

@ -0,0 +1,12 @@
diff -ru -x '*~' magma_orig/configure magma/configure
--- magma_orig/configure 2013-04-03 11:07:42.000000000 +0900
+++ magma/configure 2014-10-18 21:58:48.745890187 +0900
@@ -2377,7 +2377,7 @@
NCFLAGS="-arch=sm_13 -O2 -DADD_"
-CUDA_INC=${CUDA_HOME}/include
+CUDA_INC=${CUDA_HOME}/usr_include
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for CUDA headers" >&5
$as_echo_n "checking for CUDA headers... " >&6; }
as_ac_File=`$as_echo "ac_cv_file_${CUDA_INC}/cublas.h" | $as_tr_sh`

View file

@ -0,0 +1,28 @@
diff -ru -x '*~' openssl_orig/configure openssl/configure
--- openssl_orig/configure 2014-10-18 08:14:15.000000000 +0900
+++ openssl/configure 2014-11-03 15:05:25.122906126 +0900
@@ -1,23 +1 @@
-# Check for include
-if [ ! -e /usr/include/openssl/rand.h ]
-then
- echo "openssl/rand.h not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
- exit 1
-fi
-
-# Not linux. Probably OSX.
-if [ ! -e /sbin/ldconfig ]
-then
- exit 0
-fi
-
-# looks like unix
-LIBFILE=$(/sbin/ldconfig -p | egrep -ohm1 " [-_a-zA-Z0-9/]*/libssl[0-9]*.so$")
-
-if [ -z "$LIBFILE" ]
-then
- echo "libssl.so not found. Make sure libssl-dev (deb) or openssl-devel (rpm) is installed."
- exit 1
-fi
-
-echo "PKG_LIBS= -L"$(dirname $LIBFILE)" -lssl -lcrypto" > src/Makevars
+echo "PKG_LIBS= -L"${OPENSSL_HOME}/lib" -lssl -lcrypto" > src/Makevars

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@ -0,0 +1,13 @@
diff -ru -x '*~' qtbase_orig/src/Makefile qtbase/src/Makefile
--- qtbase_orig/src/Makefile 2012-03-03 03:57:47.000000000 +0900
+++ qtbase/src/Makefile 2014-11-01 23:06:51.383876323 +0900
@@ -10,6 +10,9 @@
-DR_INCLUDES=${R_INCLUDE_DIR} \
-DCMAKE_INSTALL_PREFIX=../src; \
make install
+# I could not control RPATH via CMake. HELP WANTED!
+ patchelf --set-rpath ${CMAKE_LIBRARY_PATH} qtbase.so
+ find ../inst/local/ -executable -type f -print0 | xargs -0 patchelf --set-rpath ${CMAKE_LIBRARY_PATH}
clean:
rm -rf ../kdebindings-build

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@ -0,0 +1,29 @@
diff -ru -x '*~' rpud_orig/configure rpud/configure
--- rpud_orig/configure 2010-09-08 02:14:55.000000000 +0900
+++ rpud/configure 2014-10-25 16:46:39.479098648 +0900
@@ -1794,7 +1794,7 @@
fi
LIBS="-L${CUDA_HOME}${CUDA_LIB_DIR} -lcublas -lcuda"
-RPATHFLAG="-Wl,-rpath,${CUDA_HOME}${CUDA_LIB_DIR}"
+RPATHFLAG="-Xlinker -rpath=${CUDA_HOME}${CUDA_LIB_DIR}"
diff -ru -x '*~' rpud_orig/src/Makefile.in rpud/src/Makefile.in
--- rpud_orig/src/Makefile.in 2010-08-31 01:53:50.000000000 +0900
+++ rpud/src/Makefile.in 2014-10-25 16:45:30.248109883 +0900
@@ -3,11 +3,11 @@
OBJS := rpud.o rpudist.o
#compiler/preprocessor options
-INCS := -I@CUDA_HOME@/include
+INCS := -I@CUDA_HOME@/usr_include
PARAMS := -Xcompiler "@R_INCLUDE@ @CPICFLAGS@"
#linker options
-LD_PARAMS := -Xlinker "@R_LIB@ @RPATHFLAG@"
+LD_PARAMS := -Xlinker "--export-dynamic -fopenmp -L${R_HOME}/lib -lR @RPATHFLAG@"
LIBS := @LIBS@
TARGETS := rpud.so

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@ -0,0 +1,8 @@
Only in spMC_orig: spMC
diff -ru -x '*~' spMC_orig/src/Makevars spMC/src/Makevars
--- spMC_orig/src/Makevars 2014-09-19 21:23:30.000000000 +0900
+++ spMC/src/Makevars 2014-10-25 18:14:48.366954769 +0900
@@ -1,2 +1,2 @@
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS)
-PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(BLAS_LIBS) $(LAPACK_LIBS) $(FLIBS)
+PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

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