Package: transcriptR

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2019-12-12 07:35:16 -0500 (Thu, 12 Dec 2019)

EndedAt: 2019-12-12 07:45:29 -0500 (Thu, 12 Dec 2019)

EllapsedTime: 613.0 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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/transcriptR.Rcheck’
* using R Under development (unstable) (2019-11-03 r77362)
* 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 ‘1.15.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
breakTranscriptsByPeaks-methods 17.548  3.061  16.594
peaksToBed-methods               9.016  2.070   9.790
predictStrand-methods            9.810  1.012   9.937
predictTssOverlap-methods        6.103  2.376   2.721
plotROC-methods                  5.371  1.678   2.887
* 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/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)

R Under development (unstable) (2019-11-03 r77362) -- "Unsuffered Consequences"
Copyright (C) 2019 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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
103.114  11.175 104.781 

name	user	system	elapsed
addFeature-methods	0.220	0.043	0.263
annotateTranscripts-methods	4.019	0.220	4.240
breakTranscriptsByPeaks-methods	17.548	3.061	16.594
constructCDS	0.005	0.003	0.007
constructTDS	0.270	0.044	0.313
detectTranscripts-methods	2.002	0.202	2.202
estimateBackground-methods	0.470	0.083	0.553
estimateGapDistance-methods	1.532	0.107	1.639
exportCoverage-methods	0.350	0.055	0.403
getConfusionMatrix-methods	0.005	0.018	0.023
getGenomicAnnot-methods	0.006	0.014	0.020
getPeaks-methods	0.050	0.018	0.068
getPredictorSignificance-methods	0.005	0.019	0.023
getProbTreshold-methods	0.005	0.020	0.025
getQuadProb-methods	0.326	0.054	0.380
getTestedGapDistances-methods	0.307	0.039	0.346
getTranscripts-methods	0.301	0.043	0.344
peaksToBed-methods	9.016	2.070	9.790
plotErrorRate-methods	1.627	0.125	1.752
plotFeatures-methods	2.956	0.056	3.013
plotGenomicAnnot-methods	0.523	0.006	0.535
plotROC-methods	5.371	1.678	2.887
predictStrand-methods	9.810	1.012	9.937
predictTssOverlap-methods	6.103	2.376	2.721
show	0.317	0.055	0.372
transcriptsToBed-methods	1.918	0.223	2.141