Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:59:48 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE transcriptR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1823/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
transcriptR 1.16.0 Armen R. Karapetyan
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: transcriptR |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transcriptR_1.16.0.tar.gz |
StartedAt: 2020-10-17 06:00:44 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 06:11:19 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 634.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: transcriptR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transcriptR_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/transcriptR.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘transcriptR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘transcriptR’ version ‘1.16.0’ * 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 ‘transcriptR’ 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 ... OK * 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 (user + system) or elapsed time > 5s user system elapsed breakTranscriptsByPeaks-methods 12.329 0.381 12.721 predictStrand-methods 7.572 0.205 7.786 peaksToBed-methods 7.181 0.166 7.351 * 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: OK
transcriptR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL transcriptR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘transcriptR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (transcriptR)
transcriptR.Rcheck/tests/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(transcriptR) > > test_check("transcriptR") ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 87 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 89.283 2.241 94.334
transcriptR.Rcheck/transcriptR-Ex.timings
name | user | system | elapsed | |
addFeature-methods | 0.164 | 0.006 | 0.170 | |
annotateTranscripts-methods | 3.479 | 0.073 | 3.555 | |
breakTranscriptsByPeaks-methods | 12.329 | 0.381 | 12.721 | |
constructCDS | 0.005 | 0.002 | 0.007 | |
constructTDS | 0.322 | 0.007 | 0.329 | |
detectTranscripts-methods | 1.772 | 0.071 | 1.844 | |
estimateBackground-methods | 0.413 | 0.030 | 0.443 | |
estimateGapDistance-methods | 1.472 | 0.041 | 1.517 | |
exportCoverage-methods | 0.324 | 0.004 | 0.329 | |
getConfusionMatrix-methods | 0.004 | 0.002 | 0.006 | |
getGenomicAnnot-methods | 0.006 | 0.001 | 0.008 | |
getPeaks-methods | 0.041 | 0.003 | 0.045 | |
getPredictorSignificance-methods | 0.004 | 0.001 | 0.005 | |
getProbTreshold-methods | 0.004 | 0.002 | 0.005 | |
getQuadProb-methods | 0.350 | 0.005 | 0.356 | |
getTestedGapDistances-methods | 0.348 | 0.004 | 0.353 | |
getTranscripts-methods | 0.345 | 0.008 | 0.354 | |
peaksToBed-methods | 7.181 | 0.166 | 7.351 | |
plotErrorRate-methods | 1.583 | 0.030 | 1.615 | |
plotFeatures-methods | 2.665 | 0.043 | 2.743 | |
plotGenomicAnnot-methods | 0.523 | 0.004 | 0.528 | |
plotROC-methods | 2.551 | 0.071 | 2.624 | |
predictStrand-methods | 7.572 | 0.205 | 7.786 | |
predictTssOverlap-methods | 2.486 | 0.059 | 2.549 | |
show | 0.339 | 0.004 | 0.343 | |
transcriptsToBed-methods | 1.692 | 0.058 | 1.751 | |