Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:56:52 -0400 (Wed, 17 Oct 2018).
Package 1193/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
RCAS 1.6.0 Bora Uyar
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: RCAS |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCAS_1.6.0.tar.gz |
StartedAt: 2018-10-16 23:32:53 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 23:47:42 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 888.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RCAS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RCAS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RCAS_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RCAS.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RCAS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RCAS’ version ‘1.6.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RCAS’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘DBI’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed runMotifRG 49.939 11.235 38.801 getMotifSummaryTable 47.883 11.142 34.757 getFeatureBoundaryCoverageMulti 30.102 1.572 32.267 calculateCoverageProfileList 23.310 1.226 24.823 calculateCoverageProfile 21.395 0.918 22.549 calculateCoverageProfileListFromTxdb 20.767 1.095 22.104 summarizeQueryRegionsMulti 20.862 0.843 37.967 getTxdbFeatures 18.815 0.708 19.663 summarizeQueryRegions 18.107 0.705 19.050 getTargetedGenesTable 17.131 0.729 18.032 calculateCoverageProfileFromTxdb 14.311 0.580 15.064 getTxdbFeaturesFromGRanges 13.754 0.596 14.411 getFeatureBoundaryCoverage 13.673 0.576 14.553 plotFeatureBoundaryCoverage 13.754 0.460 14.349 getFeatureBoundaryCoverageBin 13.225 0.454 13.926 createDB 4.005 0.059 20.250 createOrthologousGeneSetList 0.486 0.032 14.740 retrieveOrthologs 0.324 0.050 11.199 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.7-bioc/meat/RCAS.Rcheck/00check.log’ for details.
RCAS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RCAS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘RCAS’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. * DONE (RCAS)
RCAS.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(RCAS) Loading required package: plotly Loading required package: ggplot2 Attaching package: 'plotly' The following object is masked from 'package:ggplot2': last_plot The following object is masked from 'package:stats': filter The following object is masked from 'package:graphics': layout Loading required package: DT Loading required package: data.table Loading required package: topGO Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: graph Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:data.table': first, second The following object is masked from 'package:plotly': rename The following object is masked from 'package:base': expand.grid Attaching package: 'IRanges' The following object is masked from 'package:data.table': shift The following object is masked from 'package:plotly': slice Attaching package: 'AnnotationDbi' The following object is masked from 'package:plotly': select Loading required package: SparseM Attaching package: 'SparseM' The following object is masked from 'package:base': backsolve groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. Attaching package: 'topGO' The following object is masked from 'package:IRanges': members Loading required package: motifRG Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:graph': complement The following object is masked from 'package:base': strsplit Loading required package: seqLogo Loading required package: grid Attaching package: 'grid' The following object is masked from 'package:topGO': depth Loading required package: BSgenome Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:plotly': export Loading required package: BSgenome.Hsapiens.UCSC.hg19 > > test_check("RCAS") GAAGAA 1.554582e-06 Refine GAAGAA 11.75173 : 12.09648 11.52659 11.44651 12.5975 12.79872 TRUE 623 231 566 212 New motif: GAAGAA ══ testthat results ═══════════════════════════════════════════════════════════ OK: 102 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 126.162 13.445 140.975
RCAS.Rcheck/RCAS-Ex.timings
name | user | system | elapsed | |
calculateCoverageProfile | 21.395 | 0.918 | 22.549 | |
calculateCoverageProfileFromTxdb | 14.311 | 0.580 | 15.064 | |
calculateCoverageProfileList | 23.310 | 1.226 | 24.823 | |
calculateCoverageProfileListFromTxdb | 20.767 | 1.095 | 22.104 | |
createControlRegions | 0.408 | 0.005 | 0.426 | |
createDB | 4.005 | 0.059 | 20.250 | |
createOrthologousGeneSetList | 0.486 | 0.032 | 14.740 | |
discoverFeatureSpecificMotifs | 0.002 | 0.000 | 0.002 | |
extractSequences | 1.503 | 0.092 | 1.670 | |
getFeatureBoundaryCoverage | 13.673 | 0.576 | 14.553 | |
getFeatureBoundaryCoverageBin | 13.225 | 0.454 | 13.926 | |
getFeatureBoundaryCoverageMulti | 30.102 | 1.572 | 32.267 | |
getIntervalOverlapMatrix | 1.359 | 0.110 | 1.856 | |
getMotifSummaryTable | 47.883 | 11.142 | 34.757 | |
getTargetedGenesTable | 17.131 | 0.729 | 18.032 | |
getTxdbFeatures | 18.815 | 0.708 | 19.663 | |
getTxdbFeaturesFromGRanges | 13.754 | 0.596 | 14.411 | |
importBed | 0.294 | 0.010 | 0.309 | |
importBedFiles | 1.166 | 0.050 | 1.225 | |
importGtf | 0.002 | 0.000 | 0.003 | |
parseMsigdb | 0.004 | 0.000 | 0.004 | |
plotFeatureBoundaryCoverage | 13.754 | 0.460 | 14.349 | |
printMsigdbDataset | 0.062 | 0.004 | 0.066 | |
queryGff | 0.663 | 0.082 | 0.755 | |
retrieveOrthologs | 0.324 | 0.050 | 11.199 | |
runGSEA | 1.501 | 0.084 | 1.610 | |
runMotifRG | 49.939 | 11.235 | 38.801 | |
runReport | 0.003 | 0.000 | 0.004 | |
runReportMetaAnalysis | 1.499 | 0.195 | 1.770 | |
runTopGO | 0.002 | 0.000 | 0.002 | |
summarizeQueryRegions | 18.107 | 0.705 | 19.050 | |
summarizeQueryRegionsMulti | 20.862 | 0.843 | 37.967 | |