Package: transcriptR

Version: 1.12.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings transcriptR_1.12.0.tar.gz

StartedAt: 2019-10-16 05:30:53 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:37:37 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 404.1 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings transcriptR_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/transcriptR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 or elapsed time > 5s
                                  user system elapsed
breakTranscriptsByPeaks-methods 14.331  0.265  11.815
predictStrand-methods            9.646  0.047   6.882
peaksToBed-methods               9.459  0.050   6.767
predictTssOverlap-methods        5.412  0.028   2.693
plotROC-methods                  5.365  0.031   2.368
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL transcriptR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 73.689   0.964  71.396 

name	user	system	elapsed
addFeature-methods	0.128	0.000	0.128
annotateTranscripts-methods	3.682	0.064	3.748
breakTranscriptsByPeaks-methods	14.331	0.265	11.815
constructCDS	0.000	0.004	0.004
constructTDS	0.258	0.007	0.265
detectTranscripts-methods	1.354	0.028	1.382
estimateBackground-methods	0.565	0.020	0.585
estimateGapDistance-methods	0.968	0.008	0.977
exportCoverage-methods	0.283	0.022	0.305
getConfusionMatrix-methods	0.004	0.000	0.004
getGenomicAnnot-methods	0.006	0.000	0.007
getPeaks-methods	0.022	0.000	0.023
getPredictorSignificance-methods	0.000	0.003	0.003
getProbTreshold-methods	0.003	0.000	0.003
getQuadProb-methods	0.223	0.003	0.228
getTestedGapDistances-methods	0.338	0.015	0.354
getTranscripts-methods	0.331	0.008	0.339
peaksToBed-methods	9.459	0.050	6.767
plotErrorRate-methods	0.770	0.012	0.782
plotFeatures-methods	1.600	0.012	1.612
plotGenomicAnnot-methods	0.339	0.000	0.339
plotROC-methods	5.365	0.031	2.368
predictStrand-methods	9.646	0.047	6.882
predictTssOverlap-methods	5.412	0.028	2.693
show	0.298	0.004	0.306
transcriptsToBed-methods	1.524	0.008	1.532