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

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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

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### Running command:
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###   /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)

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 

name	user	system	elapsed
addFeature-methods	0.115	0.004	0.120
annotateTranscripts-methods	3.295	0.104	3.421
breakTranscriptsByPeaks-methods	13.894	5.017	11.606
constructCDS	0.005	0.002	0.010
constructTDS	0.365	0.031	0.689
detectTranscripts-methods	1.560	0.097	1.675
estimateBackground-methods	0.490	0.058	0.556
estimateGapDistance-methods	1.363	0.056	1.432
exportCoverage-methods	0.318	0.023	0.347
getConfusionMatrix-methods	0.004	0.007	0.012
getGenomicAnnot-methods	0.006	0.008	0.014
getPeaks-methods	0.032	0.008	0.041
getPredictorSignificance-methods	0.004	0.008	0.012
getProbTreshold-methods	0.004	0.009	0.014
getQuadProb-methods	0.294	0.022	0.319
getTestedGapDistances-methods	0.323	0.014	0.341
getTranscripts-methods	0.301	0.011	0.318
peaksToBed-methods	10.223	3.861	6.729
plotErrorRate-methods	1.095	0.066	1.173
plotFeatures-methods	2.531	0.013	2.573
plotGenomicAnnot-methods	0.556	0.005	0.564
plotROC-methods	5.985	4.764	2.274
predictStrand-methods	9.700	5.053	6.405
predictTssOverlap-methods	5.755	5.096	2.187
show	0.293	0.025	0.319
transcriptsToBed-methods	1.348	0.063	1.430