Package: transcriptR

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.6.0.tar.gz

StartedAt: 2018-04-12 03:24:24 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:30:20 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 355.3 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/transcriptR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
breakTranscriptsByPeaks-methods 12.252  0.104  12.643
predictStrand-methods            7.104  0.008   7.640
peaksToBed-methods               6.872  0.036   6.911
* 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

* installing *source* package ‘transcriptR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (transcriptR)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 65.776   0.420  68.461 

name	user	system	elapsed
addFeature-methods	0.312	0.000	0.314
annotateTranscripts-methods	3.776	0.036	3.814
breakTranscriptsByPeaks-methods	12.252	0.104	12.643
constructCDS	0.004	0.000	0.003
constructTDS	0.236	0.008	0.243
detectTranscripts-methods	1.240	0.004	1.246
estimateBackground-methods	0.432	0.008	0.439
estimateGapDistance-methods	1.500	0.008	1.509
exportCoverage-methods	0.224	0.004	0.232
getConfusionMatrix-methods	0.004	0.000	0.004
getGenomicAnnot-methods	0.004	0.000	0.004
getPeaks-methods	0.028	0.000	0.029
getPredictorSignificance-methods	0.004	0.000	0.003
getProbTreshold-methods	0.004	0.000	0.003
getQuadProb-methods	0.216	0.012	0.229
getTestedGapDistances-methods	0.232	0.016	0.248
getTranscripts-methods	0.236	0.000	0.234
peaksToBed-methods	6.872	0.036	6.911
plotErrorRate-methods	0.916	0.016	0.932
plotFeatures-methods	3.804	0.000	3.805
plotGenomicAnnot-methods	1.232	0.000	1.233
plotROC-methods	2.132	0.000	2.636
predictStrand-methods	7.104	0.008	7.640
predictTssOverlap-methods	1.952	0.000	1.985
show	0.228	0.008	0.235
transcriptsToBed-methods	1.272	0.000	1.272