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CHECK report for transcriptR on merida2

This page was generated on 2019-04-09 13:32:29 -0400 (Tue, 09 Apr 2019).

Package 1630/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.11.1
Armen R. Karapetyan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/transcriptR
Branch: master
Last Commit: ff68fa4
Last Changed Date: 2019-01-04 13:52:49 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: transcriptR
Version: 1.11.1
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_1.11.1.tar.gz
StartedAt: 2019-04-09 04:11:09 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:18:33 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 443.5 seconds
RetCode: 0
Status:  OK 
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.11.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/transcriptR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
breakTranscriptsByPeaks-methods 13.894  5.017  11.606
predictStrand-methods            9.700  5.053   6.405
peaksToBed-methods              10.223  3.861   6.729
predictTssOverlap-methods        5.755  5.096   2.187
plotROC-methods                  5.985  4.764   2.274
* 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


Installation output

transcriptR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL transcriptR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘transcriptR’ ...
** 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
* DONE (transcriptR)

Tests output

transcriptR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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(transcriptR)
> 
> test_check("transcriptR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 87 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 78.981  12.720  82.248 

Example timings

transcriptR.Rcheck/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.1150.0040.120
annotateTranscripts-methods3.2950.1043.421
breakTranscriptsByPeaks-methods13.894 5.01711.606
constructCDS0.0050.0020.010
constructTDS0.3650.0310.689
detectTranscripts-methods1.5600.0971.675
estimateBackground-methods0.4900.0580.556
estimateGapDistance-methods1.3630.0561.432
exportCoverage-methods0.3180.0230.347
getConfusionMatrix-methods0.0040.0070.012
getGenomicAnnot-methods0.0060.0080.014
getPeaks-methods0.0320.0080.041
getPredictorSignificance-methods0.0040.0080.012
getProbTreshold-methods0.0040.0090.014
getQuadProb-methods0.2940.0220.319
getTestedGapDistances-methods0.3230.0140.341
getTranscripts-methods0.3010.0110.318
peaksToBed-methods10.223 3.861 6.729
plotErrorRate-methods1.0950.0661.173
plotFeatures-methods2.5310.0132.573
plotGenomicAnnot-methods0.5560.0050.564
plotROC-methods5.9854.7642.274
predictStrand-methods9.7005.0536.405
predictTssOverlap-methods5.7555.0962.187
show0.2930.0250.319
transcriptsToBed-methods1.3480.0631.430