From noreply at r-forge.r-project.org Mon Jan 6 18:44:47 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 6 Jan 2014 18:44:47 +0100 (CET) Subject: [Rcpp-commits] r4602 - scripts Message-ID: <20140106174447.F38FC1867BA@r-forge.r-project.org> Author: edd Date: 2014-01-06 18:44:47 +0100 (Mon, 06 Jan 2014) New Revision: 4602 Modified: scripts/runRcppDepends.r Log: committing uncommitted changes from previous release Modified: scripts/runRcppDepends.r =================================================================== --- scripts/runRcppDepends.r 2013-12-16 01:03:19 UTC (rev 4601) +++ scripts/runRcppDepends.r 2014-01-06 17:44:47 UTC (rev 4602) @@ -1,8 +1,11 @@ #!/usr/bin/r cat("Started at ", format(Sys.time()), "\n") -library(parallel) +#library(parallel) +## for the borked src/Makevars of ExactNumCI +Sys.setenv("BOOSTLIB"="/usr/include") + setwd("/tmp/RcppDepends") AP <- available.packages(contrib.url("http://cran.r-project.org"),filter=list()) # available package at CRAN @@ -12,9 +15,9 @@ if (grep("transnet", rcppset)) { ## not really an Rcpp user rcppset <- rcppset[ ! grepl("transnet", rcppset) ] } -#if (grep("BioGeoBears", rcppset)) { ## indirect match, no need to test -# rcppset <- rcppset[ ! grepl("BioGeoBears", rcppset) ] -#} +if (grep("BioGeoBEARS", rcppset)) { ## indirect match, no need to test + rcppset <- rcppset[ ! grepl("BioGeoBEARS", rcppset) ] +} if (grep("quadrupen", rcppset)) { ## takes hours, skipping rcppset <- rcppset[ ! grepl("quadrupen", rcppset) ] } @@ -25,7 +28,6 @@ #for (pi in 1:nrow(res)) { #lres <- mclapply(1:nrow(res), mc.cores = 4, FUN=function(pi) { lres <- lapply(1:nrow(res), FUN=function(pi) { - p <- rcppset[pi] i <- which(AP[,"Package"]==p) pkg <- paste(AP[i,"Package"], "_", AP[i,"Version"], ".tar.gz", sep="") From noreply at r-forge.r-project.org Tue Jan 14 04:09:54 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 14 Jan 2014 04:09:54 +0100 (CET) Subject: [Rcpp-commits] r4603 - testlogs Message-ID: <20140114030954.D8FE9181368@r-forge.r-project.org> Author: edd Date: 2014-01-14 04:09:51 +0100 (Tue, 14 Jan 2014) New Revision: 4603 Added: testlogs/result-20140112-230103.RData Log: result log for yesterday's run Added: testlogs/result-20140112-230103.RData =================================================================== (Binary files differ) Property changes on: testlogs/result-20140112-230103.RData ___________________________________________________________________ Added: svn:mime-type + application/octet-stream From noreply at r-forge.r-project.org Tue Jan 14 04:11:06 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 14 Jan 2014 04:11:06 +0100 (CET) Subject: [Rcpp-commits] r4604 - testlogs Message-ID: <20140114031106.873D4184B6B@r-forge.r-project.org> Author: edd Date: 2014-01-14 04:11:04 +0100 (Tue, 14 Jan 2014) New Revision: 4604 Added: testlogs/Rcpp-Summary-20140112.R testlogs/Rcpp-check-20140112-2139.txt testlogs/result-20140112-230103.txt Log: result log for yesterday's run Added: testlogs/Rcpp-Summary-20140112.R =================================================================== --- testlogs/Rcpp-Summary-20140112.R (rev 0) +++ testlogs/Rcpp-Summary-20140112.R 2014-01-14 03:11:04 UTC (rev 4604) @@ -0,0 +1,141 @@ + +## started with Rcpp (current on GitHub, as well as RcppArmadillo and RcppEigen) + +## loads 'res' +load("~/svn/rcpp/testlogs/result-20140112-230103.RData") + +## g +## good <- as.character(subset(res, res==0)[,1]) +## dput(good) +goodPkg <- c("accelerometry", "acer", "AdaptiveSparsity", "ALKr", "BayesComm", + "bcp", "bcpa", "bfa", "bfp", "bifactorial", "bilan", "ccaPP", + "cda", "cladoRcpp", "clogitL1", "clusteval", "ClustVarLV", "ConConPiWiFun", + "coneproj", "Delaporte", "ecp", "EpiContactTrace", "fastGHQuad", + "FastPCS", "FastRCS", "FBFsearch", "forecast", "geoCount", "growcurves", + "GSE", "GxM", "hawkes", "jaatha", "Kmisc", "minqa", "MPTinR", + "msgl", "MVB", "NetSim", "oem", "PedCNV", "phylobase", "planar", + "PReMiuM", "prospectr", "psgp", "Rankcluster", "Rclusterpp", + "RcppArmadillo", "RcppBDT", "rcppbugs", "RcppClassicExamples", + "RcppCNPy", "RcppDE", "RcppExamples", "RcppGSL", "RcppOctave", + "RcppProgress", "RcppRoll", "RcppSMC", "RcppXts", "rexpokit", + "rforensicbatwing", "RInside", "Rmalschains", "RMessenger", "robustgam", + "robustHD", "rococo", "RSNNS", "RSofia", "RVowpalWabbit", "sdcMicro", + "sequences", "simFrame", "sparseHessianFD", "sparseLTSEigen", + "stochvol", "survSNP", "termstrc", "trustOptim", "tvm", "unmarked", + "VIM", "waffect", "XBRL", "zic") + + +## bad <- as.character(subset(res, res==1)[,1]) +## dput(bad) +badPkg <- c("ALDqr", "Amelia", "apcluster", "CARBayes", "CDM", "classify", + "climdex.pcic", "dils", "disclapmix", "diversitree", "fdaMixed", + "fugeR", "geiger", "GeneticTools", "gMWT", "GOsummaries", "gRbase", + "gRim", "HLMdiag", "hsphase", "httpuv", "hypervolume", "inarmix", + "IsingSampler", "KernSmoothIRT", "kmc", "LaF", "lm.br", "lme4", + "marked", "maxent", "mets", "mirt", "miscF", "mvabund", "ndl", + "ngspatial", "openair", "orQA", "pROC", "protViz", "RcppClassic", + "RcppEigen", "RcppZiggurat", "rgam", "rmgarch", "Rmixmod", "rotations", + "RProtoBuf", "RQuantLib", "Ruchardet", "rugarch", "SBSA", "sdcTable", + "sglOptim", "sirt", "snplist", "spacodiR", "SpatialTools", "strum", + "surveillance", "TAM", "tbart", "VideoComparison", "WideLM", + "wordcloud", "wsrf") + +bad4missing <- c("ALDqr", # 'HyperbolicDist? + "CARBayes", # ?deldir? ?maptools? ?shapefiles? ?spdep? + "CDM", # ?psych? ?polycor? + "classify", # ?R2WinBUGS? ?R2jags? + "climdex.pcic", # 'PCIct' + "disclapmix", # disclap + "diversitree", # ?deSolve? ?subplex? + "fugeR", # snowfall + "geiger", # ?msm? ?subplex? ?deSolve? ?coda? ?ncbit? + "GeneticTools", # ?gMWT? ?snpStats? + "gMWT", # ?clinfun? + "GOsummaries", # ?gProfileR? ?limma? + "hsphase", # snowfall + "hypervolume", # raster, maps + "kmc", # ?rootSolve? ?emplik? + "LaF", # 'yaml' + "marked", # ?R2admb? + "mets", # ?lava? ?timereg? + "mirt", # ?GPArotation? + "miscF", # ?MCMCpack? + "ngspatial", # ?batchmeans? + "openair", # ?latticeExtra? + "orQA", # ?genefilter? + "pROC", # 'logcondens' + "sdcTable", # ?lpSolveAPI? + "sirt", # ?gregmisc? ?sfsmisc? ?TAM? ?CDM? ?ic.infer? ?psych? ?pbivnorm? + "snplist", #" 'biomaRt' + "spacodiR", # ?picante? + "strum", # 'pedigree' + "surveillance", # ?polyCub? ?spatstat? + "TAM", # ?tensor? ?sfsmisc? ?GPArotation? ?psych? + "VideoComparison", # ?pracma? + + "VIMGUI") # VIM, survey + +## Failing at compile-time +## error: ?set_sexp? is not a member of +## ?Rcpp::Matrix<14>::VECTOR {aka Rcpp::Vector<14, Rcpp::PreserveStorage>}? +bad4set_sexp <- c("Amelia", "apcluster", "inarmix", "IsingSampler", "rotations") + +## Failing at compile time +bad4otherAPI <- c("httpuv", # (Rcpp/exceptions.h:33:56: error: ?stack_trace? was not declared in this scope + "RcppClassic", # redefinition of 'Rcpp::internal::getPosixClasses()? + "Rmixmod", # overloaded ?S4_Impl(Rcpp::SlotProxyPolicy >::SlotProxy)? is ambiguous + "tbart", # tb.cpp:13:24: error: ?stop? is not a member of ?Rcpp? + "wsrf") # error: call of overloaded ?Vector(Rcpp::Vector<19>::const_Proxy)? is ambiguous + +## Failing at run-time +## function 'dataptr' not provided by package 'Rcpp' +bad4dataptr <- c("fdaMixed", "gRbase", "gRim", "HLMdiag", "lme4", "SpatialTools") + +## Failing at run-time +## function 'enterRNGScope' not provided by package 'Rcpp' +bad4rngscore <- c("RcppZiggurat", "rgam", "Ruchardet", "SBSA") + + +bad4unclear <- c("maxent", # weird segfault + "ndl", # unclear compile error + "sglOptim", # unclear run-time error + "wordcloud") # unclear run-time error + +bad4maybeuser <- c("mvabund", # 'cannot find Rcpp.h' + "protvix", # 'cannot find Rcpp.h' + "RcppEigen", # object 'SHLIB.maker' not found -- fixed in repo + "rmgarch", # ?trunc? is not a member of ?std::ios_base? + "RProtoBuf", # configure: error: C++ comp. cannot create executables + "RQuantLib", # configure: error: cannot run C++ compiled programs. + "rugarch", # ?trunc? is not a member of ?std::ios_base? + "WideLm") # configure: error: cannot run C++ compiled programs. + +#bad4rcpp <- c() # Yay! + +## these fail initially but can all be run with some extra effort +bad4notrcpp <- c("KernSmoothIRT") # rgl failed, needs full x11 session + +good <- length(goodPkg) +bad <- (length(bad4missing) + length(bad4set_sexp) + + length(bad4otherAPI) + length(bad4dataptr) + + length(bad4rngscore) + length(bad4unclear) + + length(bad4maybeuser) + length(bad4notrcpp)) + +#stopifnot(all.equal(bad,length(badPkg))) ## account for GeoBIO + +cat("Good ", good, "\n") +cat("Bad ", bad, "\n") +#cat(" RcppErr ", length(bad4rcpp), "\n") +cat(" MissDep ", length(bad4missing), "\n") +cat(" SetSexp ", length(bad4set_sexp), "\n") +cat(" Other ", length(bad4otherAPI), "\n") +cat(" Dataptr ", length(bad4dataptr), "\n") +cat(" Rngscore ", length(bad4rngscore), "\n") +cat(" Unclear ", length(bad4unclear), "\n") +cat(" MaybeUser ", length(bad4maybeuser), "\n") +cat(" NotRcpp ", length(bad4notrcpp), "\n") +cat("Total ", good + bad, "\n") +cat("Error Pct ", (bad-length(bad4missing)) / (good + bad), "\n") + + + Added: testlogs/Rcpp-check-20140112-2139.txt =================================================================== --- testlogs/Rcpp-check-20140112-2139.txt (rev 0) +++ testlogs/Rcpp-check-20140112-2139.txt 2014-01-14 03:11:04 UTC (rev 4604) @@ -0,0 +1,363 @@ +Started at 2014-01-12 21:39:19 + [1] "accelerometry" "acer" "AdaptiveSparsity" + [4] "ALDqr" "ALKr" "Amelia" + [7] "apcluster" "BayesComm" "bcp" + [10] "bcpa" "bfa" "bfp" + [13] "bifactorial" "bilan" "CARBayes" + [16] "ccaPP" "cda" "CDM" + [19] "cladoRcpp" "classify" "climdex.pcic" + [22] "clogitL1" "clusteval" "ClustVarLV" + [25] "ConConPiWiFun" "coneproj" "Delaporte" + [28] "dils" "disclapmix" "diversitree" + [31] "ecp" "EpiContactTrace" "fastGHQuad" + [34] "FastPCS" "FastRCS" "FBFsearch" + [37] "fdaMixed" "forecast" "fugeR" + [40] "geiger" "GeneticTools" "geoCount" + [43] "gMWT" "GOsummaries" "gRbase" + [46] "gRim" "growcurves" "GSE" + [49] "GxM" "hawkes" "HLMdiag" + [52] "hsphase" "httpuv" "hypervolume" + [55] "inarmix" "IsingSampler" "jaatha" + [58] "KernSmoothIRT" "kmc" "Kmisc" + [61] "LaF" "lm.br" "lme4" + [64] "marked" "maxent" "mets" + [67] "minqa" "mirt" "miscF" + [70] "MPTinR" "msgl" "mvabund" + [73] "MVB" "ndl" "NetSim" + [76] "ngspatial" "oem" "openair" + [79] "orQA" "PedCNV" "phylobase" + [82] "planar" "PReMiuM" "pROC" + [85] "prospectr" "protViz" "psgp" + [88] "Rankcluster" "Rclusterpp" "RcppArmadillo" + [91] "RcppBDT" "rcppbugs" "RcppClassic" + [94] "RcppClassicExamples" "RcppCNPy" "RcppDE" + [97] "RcppEigen" "RcppExamples" "RcppGSL" +[100] "RcppOctave" "RcppProgress" "RcppRoll" +[103] "RcppSMC" "RcppXts" "RcppZiggurat" +[106] "rexpokit" "rforensicbatwing" "rgam" +[109] "RInside" "Rmalschains" "RMessenger" +[112] "rmgarch" "Rmixmod" "robustgam" +[115] "robustHD" "rococo" "rotations" +[118] "RProtoBuf" "RQuantLib" "RSNNS" +[121] "RSofia" "Ruchardet" "rugarch" +[124] "RVowpalWabbit" "SBSA" "sdcMicro" +[127] "sdcTable" "sequences" "sglOptim" +[130] "simFrame" "sirt" "snplist" +[133] "spacodiR" "sparseHessianFD" "sparseLTSEigen" +[136] "SpatialTools" "stochvol" "strum" +[139] "surveillance" "survSNP" "TAM" +[142] "tbart" "termstrc" "trustOptim" +[145] "tvm" "unmarked" "VideoComparison" +[148] "VIM" "waffect" "WideLM" +[151] "wordcloud" "wsrf" "XBRL" +[154] "zic" +0 : accelerometry_2.0.tar.gz +0 : acer_0.1.2.tar.gz +0 : AdaptiveSparsity_1.4.tar.gz +1 : ALDqr_0.2.tar.gz +0 : ALKr_0.5.3.tar.gz +1 : Amelia_1.7.2.tar.gz +1 : apcluster_1.3.2.tar.gz +0 : BayesComm_0.1-0.tar.gz +0 : bcp_3.0.1.tar.gz +0 : bcpa_1.0.tar.gz +0 : bfa_0.3.tar.gz +0 : bfp_0.0-27.tar.gz +0 : bifactorial_1.4.7.tar.gz +0 : bilan_2013.12.tar.gz +1 : CARBayes_2.0.tar.gz +0 : ccaPP_0.3.0.tar.gz +0 : cda_1.5.tar.gz +1 : CDM_2.4-9.tar.gz +0 : cladoRcpp_0.14.2.tar.gz +1 : classify_1.1.tar.gz +1 : climdex.pcic_1.0-3.tar.gz +0 : clogitL1_1.1.tar.gz +0 : clusteval_0.1.tar.gz +0 : ClustVarLV_1.1.tar.gz +0 : ConConPiWiFun_0.4.2.tar.gz +0 : coneproj_1.2.tar.gz +0 : Delaporte_1.0-1.tar.gz +1 : dils_0.8.1.tar.gz +1 : disclapmix_1.2.tar.gz +1 : diversitree_0.9-6.tar.gz +0 : ecp_1.5.5.tar.gz +0 : EpiContactTrace_0.8.8.tar.gz +0 : fastGHQuad_0.1-1.tar.gz +0 : FastPCS_0.0.7.tar.gz +0 : FastRCS_0.0.1.tar.gz +0 : FBFsearch_1.0.tar.gz +1 : fdaMixed_0.3.tar.gz +0 : forecast_4.8.tar.gz +1 : fugeR_0.1.2.tar.gz +1 : geiger_1.99-3.1.tar.gz +1 : GeneticTools_0.2.1.tar.gz +0 : geoCount_1.131209.tar.gz +1 : gMWT_0.3.tar.gz +1 : GOsummaries_1.0.tar.gz +1 : gRbase_1.6-12.tar.gz +1 : gRim_0.1-17.tar.gz +0 : growcurves_0.2.3.7.tar.gz +0 : GSE_3.0.tar.gz +0 : GxM_1.0.tar.gz +0 : hawkes_0.0-1.tar.gz +1 : HLMdiag_0.2.3.tar.gz +1 : hsphase_1.2.4.tar.gz +1 : httpuv_1.2.1.tar.gz +1 : hypervolume_0.9.9.4.tar.gz +1 : inarmix_0.2.tar.gz +1 : IsingSampler_0.1.1.tar.gz +0 : jaatha_2.2.tar.gz +1 : KernSmoothIRT_6.0.tar.gz +1 : kmc_0.1-2.tar.gz +0 : Kmisc_0.5.0.tar.gz +1 : LaF_0.5.tar.gz +1 : lm.br_2.4.tar.gz +1 : lme4_1.0-5.tar.gz +1 : marked_1.1.3.tar.gz +1 : maxent_1.3.3.1.tar.gz +1 : mets_0.2.6.tar.gz +0 : minqa_1.2.2.tar.gz +1 : mirt_1.1.tar.gz +1 : miscF_0.1-2.tar.gz +0 : MPTinR_1.2.5.tar.gz +0 : msgl_0.1.6.tar.gz +1 : mvabund_3.8.4.tar.gz +0 : MVB_1.1.tar.gz +1 : ndl_0.2.14.tar.gz +0 : NetSim_0.9.tar.gz +1 : ngspatial_1.0-3.tar.gz +0 : oem_1.02.1.tar.gz +1 : openair_0.9-0.tar.gz +1 : orQA_0.2.1.tar.gz +0 : PedCNV_0.1.tar.gz +0 : phylobase_0.6.5.2.tar.gz +0 : planar_1.5.tar.gz +0 : PReMiuM_3.0.21.tar.gz +1 : pROC_1.6.0.1.tar.gz +0 : prospectr_0.1.1.tar.gz +1 : protViz_0.1.76.tar.gz +0 : psgp_0.3-4.tar.gz +0 : Rankcluster_0.91.6.tar.gz +0 : Rclusterpp_0.2.3.tar.gz +0 : RcppArmadillo_0.4.000.tar.gz +0 : RcppBDT_0.2.1.tar.gz +0 : rcppbugs_0.1.4.tar.gz +1 : RcppClassic_0.9.4.tar.gz +0 : RcppClassicExamples_0.1.1.tar.gz +0 : RcppCNPy_0.2.2.tar.gz +0 : RcppDE_0.1.2.tar.gz +1 : RcppEigen_0.3.2.0.1.tar.gz +0 : RcppExamples_0.1.6.tar.gz +0 : RcppGSL_0.2.0.tar.gz +0 : RcppOctave_0.11.3.tar.gz +0 : RcppProgress_0.1.tar.gz +0 : RcppRoll_0.1.0.tar.gz +0 : RcppSMC_0.1.1.tar.gz +0 : RcppXts_0.0.4.tar.gz +1 : RcppZiggurat_0.1.1.tar.gz +0 : rexpokit_0.24.1.tar.gz +0 : rforensicbatwing_1.1.tar.gz +1 : rgam_0.6.2.tar.gz +0 : RInside_0.2.10.tar.gz +0 : Rmalschains_0.2-1.tar.gz +0 : RMessenger_0.1.3.tar.gz +1 : rmgarch_1.2-0.tar.gz +1 : Rmixmod_2.0.1.tar.gz +0 : robustgam_0.1.7.tar.gz +0 : robustHD_0.4.0.tar.gz +0 : rococo_1.1.0.tar.gz +1 : rotations_0.2.tar.gz +1 : RProtoBuf_0.3.2.tar.gz +1 : RQuantLib_0.3.10.tar.gz +0 : RSNNS_0.4-4.tar.gz +0 : RSofia_1.1.tar.gz +1 : Ruchardet_0.0-2.tar.gz +1 : rugarch_1.2-9.tar.gz +0 : RVowpalWabbit_0.0.6.tar.gz +1 : SBSA_0.2.2.tar.gz +0 : sdcMicro_4.2.0.tar.gz +1 : sdcTable_0.10.3.tar.gz +0 : sequences_0.5.7.tar.gz +1 : sglOptim_0.0.80.tar.gz +0 : simFrame_0.5.1.tar.gz +1 : sirt_0.41-21.tar.gz +1 : snplist_0.12.tar.gz +1 : spacodiR_0.13.0115.tar.gz +0 : sparseHessianFD_0.1.1.tar.gz +0 : sparseLTSEigen_0.2.0.tar.gz +1 : SpatialTools_0.5.5.tar.gz +0 : stochvol_0.7-1.tar.gz +1 : strum_0.1.tar.gz +1 : surveillance_1.7-0.tar.gz +0 : survSNP_0.21-7.tar.gz +1 : TAM_1.0-0.tar.gz +1 : tbart_0.9.tar.gz +0 : termstrc_1.3.7.tar.gz +0 : trustOptim_0.8.3.tar.gz +0 : tvm_0.1.tar.gz +0 : unmarked_0.10-2.tar.gz +1 : VideoComparison_0.9-4.tar.gz +0 : VIM_4.0.0.tar.gz +0 : waffect_1.2.tar.gz +1 : WideLM_0.1-1.tar.gz +1 : wordcloud_2.4.tar.gz +1 : wsrf_1.2.523.tar.gz +0 : XBRL_0.99.10.tar.gz +0 : zic_0.8.1.tar.gz + pkg res +1 accelerometry 0 +2 acer 0 +3 AdaptiveSparsity 0 +4 ALDqr 1 +5 ALKr 0 +6 Amelia 1 +7 apcluster 1 +8 BayesComm 0 +9 bcp 0 +10 bcpa 0 +11 bfa 0 +12 bfp 0 +13 bifactorial 0 +14 bilan 0 +15 CARBayes 1 +16 ccaPP 0 +17 cda 0 +18 CDM 1 +19 cladoRcpp 0 +20 classify 1 +21 climdex.pcic 1 +22 clogitL1 0 +23 clusteval 0 +24 ClustVarLV 0 +25 ConConPiWiFun 0 +26 coneproj 0 +27 Delaporte 0 +28 dils 1 +29 disclapmix 1 +30 diversitree 1 +31 ecp 0 +32 EpiContactTrace 0 +33 fastGHQuad 0 +34 FastPCS 0 +35 FastRCS 0 +36 FBFsearch 0 +37 fdaMixed 1 +38 forecast 0 +39 fugeR 1 +40 geiger 1 +41 GeneticTools 1 +42 geoCount 0 +43 gMWT 1 +44 GOsummaries 1 +45 gRbase 1 +46 gRim 1 +47 growcurves 0 +48 GSE 0 +49 GxM 0 +50 hawkes 0 +51 HLMdiag 1 +52 hsphase 1 +53 httpuv 1 +54 hypervolume 1 +55 inarmix 1 +56 IsingSampler 1 +57 jaatha 0 +58 KernSmoothIRT 1 +59 kmc 1 +60 Kmisc 0 +61 LaF 1 +62 lm.br 1 +63 lme4 1 +64 marked 1 +65 maxent 1 +66 mets 1 +67 minqa 0 +68 mirt 1 +69 miscF 1 +70 MPTinR 0 +71 msgl 0 +72 mvabund 1 +73 MVB 0 +74 ndl 1 +75 NetSim 0 +76 ngspatial 1 +77 oem 0 +78 openair 1 +79 orQA 1 +80 PedCNV 0 +81 phylobase 0 +82 planar 0 +83 PReMiuM 0 +84 pROC 1 +85 prospectr 0 +86 protViz 1 +87 psgp 0 +88 Rankcluster 0 +89 Rclusterpp 0 +90 RcppArmadillo 0 +91 RcppBDT 0 +92 rcppbugs 0 +93 RcppClassic 1 +94 RcppClassicExamples 0 +95 RcppCNPy 0 +96 RcppDE 0 +97 RcppEigen 1 +98 RcppExamples 0 +99 RcppGSL 0 +100 RcppOctave 0 +101 RcppProgress 0 +102 RcppRoll 0 +103 RcppSMC 0 +104 RcppXts 0 +105 RcppZiggurat 1 +106 rexpokit 0 +107 rforensicbatwing 0 +108 rgam 1 +109 RInside 0 +110 Rmalschains 0 +111 RMessenger 0 +112 rmgarch 1 +113 Rmixmod 1 +114 robustgam 0 +115 robustHD 0 +116 rococo 0 +117 rotations 1 +118 RProtoBuf 1 +119 RQuantLib 1 +120 RSNNS 0 +121 RSofia 0 +122 Ruchardet 1 +123 rugarch 1 +124 RVowpalWabbit 0 +125 SBSA 1 +126 sdcMicro 0 +127 sdcTable 1 +128 sequences 0 +129 sglOptim 1 +130 simFrame 0 +131 sirt 1 +132 snplist 1 +133 spacodiR 1 +134 sparseHessianFD 0 +135 sparseLTSEigen 0 +136 SpatialTools 1 +137 stochvol 0 +138 strum 1 +139 surveillance 1 +140 survSNP 0 +141 TAM 1 +142 tbart 1 +143 termstrc 0 +144 trustOptim 0 +145 tvm 0 +146 unmarked 0 +147 VideoComparison 1 +148 VIM 0 +149 waffect 0 +150 WideLM 1 +151 wordcloud 1 +152 wsrf 1 +153 XBRL 0 +154 zic 0 +Ended at 2014-01-12 23:01:03 Added: testlogs/result-20140112-230103.txt =================================================================== --- testlogs/result-20140112-230103.txt (rev 0) +++ testlogs/result-20140112-230103.txt 2014-01-14 03:11:04 UTC (rev 4604) @@ -0,0 +1,155 @@ +"pkg","res" +"1","accelerometry",0 +"2","acer",0 +"3","AdaptiveSparsity",0 +"4","ALDqr",1 +"5","ALKr",0 +"6","Amelia",1 +"7","apcluster",1 +"8","BayesComm",0 +"9","bcp",0 +"10","bcpa",0 +"11","bfa",0 +"12","bfp",0 +"13","bifactorial",0 +"14","bilan",0 +"15","CARBayes",1 +"16","ccaPP",0 +"17","cda",0 +"18","CDM",1 +"19","cladoRcpp",0 +"20","classify",1 +"21","climdex.pcic",1 +"22","clogitL1",0 +"23","clusteval",0 +"24","ClustVarLV",0 +"25","ConConPiWiFun",0 +"26","coneproj",0 +"27","Delaporte",0 +"28","dils",1 +"29","disclapmix",1 +"30","diversitree",1 +"31","ecp",0 +"32","EpiContactTrace",0 +"33","fastGHQuad",0 +"34","FastPCS",0 +"35","FastRCS",0 +"36","FBFsearch",0 +"37","fdaMixed",1 +"38","forecast",0 +"39","fugeR",1 +"40","geiger",1 +"41","GeneticTools",1 +"42","geoCount",0 +"43","gMWT",1 +"44","GOsummaries",1 +"45","gRbase",1 +"46","gRim",1 +"47","growcurves",0 +"48","GSE",0 +"49","GxM",0 +"50","hawkes",0 +"51","HLMdiag",1 +"52","hsphase",1 +"53","httpuv",1 +"54","hypervolume",1 +"55","inarmix",1 +"56","IsingSampler",1 +"57","jaatha",0 +"58","KernSmoothIRT",1 +"59","kmc",1 +"60","Kmisc",0 +"61","LaF",1 +"62","lm.br",1 +"63","lme4",1 +"64","marked",1 +"65","maxent",1 +"66","mets",1 +"67","minqa",0 +"68","mirt",1 +"69","miscF",1 +"70","MPTinR",0 +"71","msgl",0 +"72","mvabund",1 +"73","MVB",0 +"74","ndl",1 +"75","NetSim",0 +"76","ngspatial",1 +"77","oem",0 +"78","openair",1 +"79","orQA",1 +"80","PedCNV",0 +"81","phylobase",0 +"82","planar",0 +"83","PReMiuM",0 +"84","pROC",1 +"85","prospectr",0 +"86","protViz",1 +"87","psgp",0 +"88","Rankcluster",0 +"89","Rclusterpp",0 +"90","RcppArmadillo",0 +"91","RcppBDT",0 +"92","rcppbugs",0 +"93","RcppClassic",1 +"94","RcppClassicExamples",0 +"95","RcppCNPy",0 +"96","RcppDE",0 +"97","RcppEigen",1 +"98","RcppExamples",0 +"99","RcppGSL",0 +"100","RcppOctave",0 +"101","RcppProgress",0 +"102","RcppRoll",0 +"103","RcppSMC",0 +"104","RcppXts",0 +"105","RcppZiggurat",1 +"106","rexpokit",0 +"107","rforensicbatwing",0 +"108","rgam",1 +"109","RInside",0 +"110","Rmalschains",0 +"111","RMessenger",0 +"112","rmgarch",1 +"113","Rmixmod",1 +"114","robustgam",0 +"115","robustHD",0 +"116","rococo",0 +"117","rotations",1 +"118","RProtoBuf",1 +"119","RQuantLib",1 +"120","RSNNS",0 +"121","RSofia",0 +"122","Ruchardet",1 +"123","rugarch",1 +"124","RVowpalWabbit",0 +"125","SBSA",1 +"126","sdcMicro",0 +"127","sdcTable",1 +"128","sequences",0 +"129","sglOptim",1 +"130","simFrame",0 +"131","sirt",1 +"132","snplist",1 +"133","spacodiR",1 +"134","sparseHessianFD",0 +"135","sparseLTSEigen",0 +"136","SpatialTools",1 +"137","stochvol",0 +"138","strum",1 +"139","surveillance",1 +"140","survSNP",0 +"141","TAM",1 +"142","tbart",1 +"143","termstrc",0 +"144","trustOptim",0 +"145","tvm",0 +"146","unmarked",0 +"147","VideoComparison",1 +"148","VIM",0 +"149","waffect",0 +"150","WideLM",1 +"151","wordcloud",1 +"152","wsrf",1 +"153","XBRL",0 +"154","zic",0 From noreply at r-forge.r-project.org Tue Jan 14 04:14:02 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 14 Jan 2014 04:14:02 +0100 (CET) Subject: [Rcpp-commits] r4605 - scripts Message-ID: <20140114031402.A81EA18653F@r-forge.r-project.org> Author: edd Date: 2014-01-14 04:14:00 +0100 (Tue, 14 Jan 2014) New Revision: 4605 Added: scripts/runRcppArmadilloDepends.r Modified: scripts/runRcppDepends.r Log: updated test script for Rcpp; added one for RcppArmadillo Added: scripts/runRcppArmadilloDepends.r =================================================================== --- scripts/runRcppArmadilloDepends.r (rev 0) +++ scripts/runRcppArmadilloDepends.r 2014-01-14 03:14:00 UTC (rev 4605) @@ -0,0 +1,35 @@ +#!/usr/bin/r + +cat("Started at ", format(Sys.time()), "\n") +pkg <- "RcppArmadillo" + +setwd("/tmp/RcppDepends") + +AP <- available.packages(contrib.url("http://cran.r-project.org"), filter=list()) # available package at CRAN +rcpparmaset <- sort(unname(AP[unique(c(grep(pkg, as.character(AP[,"Depends"])), + grep(pkg, as.character(AP[,"LinkingTo"])), + grep(pkg, as.character(AP[,"Imports"])))),"Package"])) +print( rcpparmaset ) + +res <- data.frame(pkg=rcpparmaset, res=NA) + +#for (pi in 1:nrow(res)) { +#lres <- mclapply(1:nrow(res), mc.cores = 4, FUN=function(pi) { +lres <- lapply(1:nrow(res), FUN=function(pi) { + p <- rcpparmaset[pi] + i <- which(AP[,"Package"]==p) + pkg <- paste(AP[i,"Package"], "_", AP[i,"Version"], ".tar.gz", sep="") + pathpkg <- paste(AP[i,"Repository"], "/", pkg, sep="") + #print(pathpkg) + if (!file.exists(pkg)) download.file(pathpkg, pkg, quiet=TRUE) + rc <- system(paste("R CMD check --no-manual --no-vignettes ", pkg, " > ", pkg, ".log", sep="")) + res[pi, "res"] <- rc + cat(rc, ":", pkg, "\n") + res[pi, ] +}) + +res <- do.call(rbind, lres) +print(res) +write.table(res, file=paste("result-", strftime(Sys.time(), "%Y%m%d-%H%M%S"), ".txt", sep=""), sep=",") +save(res, file=paste("result-", strftime(Sys.time(), "%Y%m%d-%H%M%S"), ".RData", sep="")) +cat("Ended at ", format(Sys.time()), "\n") Property changes on: scripts/runRcppArmadilloDepends.r ___________________________________________________________________ Added: svn:executable + * Modified: scripts/runRcppDepends.r =================================================================== --- scripts/runRcppDepends.r 2014-01-14 03:11:04 UTC (rev 4604) +++ scripts/runRcppDepends.r 2014-01-14 03:14:00 UTC (rev 4605) @@ -3,6 +3,10 @@ cat("Started at ", format(Sys.time()), "\n") #library(parallel) +## use a test-local directory, install Rcpp, RcppArmadillo, ... there +## this will work for sub-shells such as the ones started by system() below +Sys.setenv("R_LIBS_USER"="/tmp/RcppDepends/lib") + ## for the borked src/Makevars of ExactNumCI Sys.setenv("BOOSTLIB"="/usr/include") @@ -12,15 +16,19 @@ rcppset <- sort(unname(AP[unique(c(grep("Rcpp", as.character(AP[,"Depends"])), grep("Rcpp", as.character(AP[,"LinkingTo"])), grep("Rcpp", as.character(AP[,"Imports"])))),"Package"])) -if (grep("transnet", rcppset)) { ## not really an Rcpp user - rcppset <- rcppset[ ! grepl("transnet", rcppset) ] -} +#if (grep("transnet", rcppset)) { ## not really an Rcpp user +# rcppset <- rcppset[ ! grepl("transnet", rcppset) ] +#} if (grep("BioGeoBEARS", rcppset)) { ## indirect match, no need to test rcppset <- rcppset[ ! grepl("BioGeoBEARS", rcppset) ] } if (grep("quadrupen", rcppset)) { ## takes hours, skipping rcppset <- rcppset[ ! grepl("quadrupen", rcppset) ] } +if (grep("roxygen2", rcppset)) { ## seems to hang for reasons that are unclear + rcppset <- rcppset[ ! grepl("roxygen2", rcppset) ] +} + print( rcppset ) res <- data.frame(pkg=rcppset, res=NA) From noreply at r-forge.r-project.org Wed Jan 15 04:50:33 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 15 Jan 2014 04:50:33 +0100 (CET) Subject: [Rcpp-commits] r4606 - testlogs Message-ID: <20140115035033.AB130185F2C@r-forge.r-project.org> Author: edd Date: 2014-01-15 04:50:32 +0100 (Wed, 15 Jan 2014) New Revision: 4606 Modified: testlogs/Rcpp-Summary-20140112.R Log: update to quantlib Modified: testlogs/Rcpp-Summary-20140112.R =================================================================== --- testlogs/Rcpp-Summary-20140112.R 2014-01-14 03:14:00 UTC (rev 4605) +++ testlogs/Rcpp-Summary-20140112.R 2014-01-15 03:50:32 UTC (rev 4606) @@ -83,7 +83,8 @@ ## Failing at compile time bad4otherAPI <- c("httpuv", # (Rcpp/exceptions.h:33:56: error: ?stack_trace? was not declared in this scope "RcppClassic", # redefinition of 'Rcpp::internal::getPosixClasses()? - "Rmixmod", # overloaded ?S4_Impl(Rcpp::SlotProxyPolicy >::SlotProxy)? is ambiguous + "Rmixmod", # overloaded ?S4_Impl(Rcpp::SlotProxyPolicy >::SlotProxy)? is ambiguous + "RQuantLib", # 'QLtoJan1970Offset? is not a member of ?Rcpp::Date? "tbart", # tb.cpp:13:24: error: ?stop? is not a member of ?Rcpp? "wsrf") # error: call of overloaded ?Vector(Rcpp::Vector<19>::const_Proxy)? is ambiguous @@ -106,7 +107,6 @@ "RcppEigen", # object 'SHLIB.maker' not found -- fixed in repo "rmgarch", # ?trunc? is not a member of ?std::ios_base? "RProtoBuf", # configure: error: C++ comp. cannot create executables - "RQuantLib", # configure: error: cannot run C++ compiled programs. "rugarch", # ?trunc? is not a member of ?std::ios_base? "WideLm") # configure: error: cannot run C++ compiled programs. From noreply at r-forge.r-project.org Thu Jan 23 16:18:10 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 23 Jan 2014 16:18:10 +0100 (CET) Subject: [Rcpp-commits] r4607 - in pkg/RcppClassic: . src Message-ID: <20140123151810.3D3FF1865BF@r-forge.r-project.org> Author: edd Date: 2014-01-23 16:18:09 +0100 (Thu, 23 Jan 2014) New Revision: 4607 Modified: pkg/RcppClassic/ChangeLog pkg/RcppClassic/DESCRIPTION pkg/RcppClassic/NAMESPACE pkg/RcppClassic/src/RcppResultSet.cpp Log: Minor updates Add new #ifdef test to permit compilation under Rcpp versions later than 0.10.6 which changed once again Updated DESCRIPTION and NAMESPACE as well Modified: pkg/RcppClassic/ChangeLog =================================================================== --- pkg/RcppClassic/ChangeLog 2014-01-15 03:50:32 UTC (rev 4606) +++ pkg/RcppClassic/ChangeLog 2014-01-23 15:18:09 UTC (rev 4607) @@ -1,3 +1,8 @@ +2014-01-23 Dirk Eddelbuettel + + * src/RcppResultSet.cpp: Add new #ifdef test to permit compilation + under Rcpp versions later than 0.10.6 which changed once again + 2013-07-27 Dirk Eddelbuettel * DESCRIPTION: Release 0.9.4 Modified: pkg/RcppClassic/DESCRIPTION =================================================================== --- pkg/RcppClassic/DESCRIPTION 2014-01-15 03:50:32 UTC (rev 4606) +++ pkg/RcppClassic/DESCRIPTION 2014-01-23 15:18:09 UTC (rev 4607) @@ -1,6 +1,6 @@ Package: RcppClassic Title: Deprecated 'classic' Rcpp API -Version: 0.9.4 +Version: 0.9.4.1 Date: $Date$ Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss, and based on code written during 2005 and 2006 by Dominick Samperi @@ -9,7 +9,8 @@ facilitates the integration of R and C++. . New projects should use the new Rcpp API in the Rcpp package. -Depends: R (>= 2.12.0), Rcpp (>= 0.10.2), methods +Depends: R (>= 2.12.0), methods +Imports: Rcpp (>= 0.10.2) Suggests: RUnit, inline LinkingTo: Rcpp License: GPL (>= 2) Modified: pkg/RcppClassic/NAMESPACE =================================================================== --- pkg/RcppClassic/NAMESPACE 2014-01-15 03:50:32 UTC (rev 4606) +++ pkg/RcppClassic/NAMESPACE 2014-01-23 15:18:09 UTC (rev 4607) @@ -1,3 +1,3 @@ useDynLib(RcppClassic) -import( Rcpp ) +importFrom(Rcpp, evalCpp) Modified: pkg/RcppClassic/src/RcppResultSet.cpp =================================================================== --- pkg/RcppClassic/src/RcppResultSet.cpp 2014-01-15 03:50:32 UTC (rev 4606) +++ pkg/RcppClassic/src/RcppResultSet.cpp 2014-01-23 15:18:09 UTC (rev 4607) @@ -3,7 +3,7 @@ // RcppResultSet.cpp: RcppClassic R/C++ interface class library -- Results back to R // // Copyright (C) 2005 - 2006 Dominick Samperi -// Copyright (C) 2008 - 2009 Dirk Eddelbuettel +// Copyright (C) 2008 - 2014 Dirk Eddelbuettel // Copyright (C) 2010 - 2012 Dirk Eddelbuettel and Romain Francois // // This file is part of RcppClassic. @@ -28,7 +28,7 @@ namespace Rcpp { // these functions are no longer exported in Rcpp.h as of Rcpp 0.10.2 - #if defined(RCPP_VERSION) && RCPP_VERSION > Rcpp_Version(0,10,1) + #if defined(RCPP_VERSION) && RCPP_VERSION > Rcpp_Version(0,10,1) && RCPP_VERSION <= Rcpp_Version(0,10,6) namespace internal{ SEXP getPosixClasses(){ From noreply at r-forge.r-project.org Sat Jan 25 19:33:02 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 25 Jan 2014 19:33:02 +0100 (CET) Subject: [Rcpp-commits] r4608 - pkg/RcppClassicExamples Message-ID: <20140125183303.0B8DE186A28@r-forge.r-project.org> Author: edd Date: 2014-01-25 19:33:02 +0100 (Sat, 25 Jan 2014) New Revision: 4608 Modified: pkg/RcppClassicExamples/ChangeLog pkg/RcppClassicExamples/DESCRIPTION pkg/RcppClassicExamples/NAMESPACE Log: updated while testing new RcppClassic release Modified: pkg/RcppClassicExamples/ChangeLog =================================================================== --- pkg/RcppClassicExamples/ChangeLog 2014-01-23 15:18:09 UTC (rev 4607) +++ pkg/RcppClassicExamples/ChangeLog 2014-01-25 18:33:02 UTC (rev 4608) @@ -1,3 +1,10 @@ +2014-01-25 Dirk Eddelbuettel + + * DESCRIPTION: Version 0.1.2 + + * DESCRIPTION: Switch Depends: to Imports: for Rcpp, RcppClassic + * NAMESPACE: Add import() for Rcpp, RcppClassic + 2012-12-30 Dirk Eddelbuettel * DESCRIPTION: Version 0.1.1 Modified: pkg/RcppClassicExamples/DESCRIPTION =================================================================== --- pkg/RcppClassicExamples/DESCRIPTION 2014-01-23 15:18:09 UTC (rev 4607) +++ pkg/RcppClassicExamples/DESCRIPTION 2014-01-25 18:33:02 UTC (rev 4608) @@ -1,6 +1,6 @@ Package: RcppClassicExamples Title: Examples using RcppClassic to interface R and C++ -Version: 0.1.1 +Version: 0.1.2 Date: $Date$ Author: Dirk Eddelbuettel and Romain Francois, based on code written during 2005 and 2006 by Dominick Samperi @@ -13,7 +13,8 @@ the older, deprecated API. There is also a corresponding package RcppExamples package with examples for the newer, current API which we strongly recommend as the basis for all new development. -Depends: R (>= 2.15.2), Rcpp (>= 0.10.2), RcppClassic (>= 0.9.3) +Depends: R (>= 2.15.2) +Imports: Rcpp (>= 0.10.2), RcppClassic (>= 0.9.3) LinkingTo: Rcpp, RcppClassic Suggests: RUnit URL: http://dirk.eddelbuettel.com/code/rcpp.html, http://romainfrancois.blog.free.fr/index.php?category/R-package/Rcpp Modified: pkg/RcppClassicExamples/NAMESPACE =================================================================== --- pkg/RcppClassicExamples/NAMESPACE 2014-01-23 15:18:09 UTC (rev 4607) +++ pkg/RcppClassicExamples/NAMESPACE 2014-01-25 18:33:02 UTC (rev 4608) @@ -1,5 +1,8 @@ useDynLib(RcppClassicExamples) +import(Rcpp) +import(RcppClassic) + export(RcppExample, print.RcppExample, RcppDateExample,