Package: transcriptR

Version: 1.11.1

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_1.11.1.tar.gz

StartedAt: 2019-04-09 04:06:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:13:41 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 406.0 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/transcriptR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.11.1’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
breakTranscriptsByPeaks-methods 13.248  0.112  10.492
peaksToBed-methods               8.065  0.017   5.086
predictStrand-methods            7.939  0.040   4.961
plotROC-methods                  5.758  0.024   4.139
predictTssOverlap-methods        5.228  0.020   2.409
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL transcriptR
###
##############################################################################
##############################################################################


* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 76.503   0.875  74.972 

name	user	system	elapsed
addFeature-methods	0.092	0.000	0.091
annotateTranscripts-methods	2.642	0.024	2.666
breakTranscriptsByPeaks-methods	13.248	0.112	10.492
constructCDS	0.003	0.000	0.003
constructTDS	0.301	0.020	0.322
detectTranscripts-methods	1.394	0.020	1.414
estimateBackground-methods	0.385	0.008	0.393
estimateGapDistance-methods	1.149	0.012	1.164
exportCoverage-methods	0.312	0.016	0.328
getConfusionMatrix-methods	0.003	0.000	0.003
getGenomicAnnot-methods	0.003	0.000	0.004
getPeaks-methods	0.015	0.004	0.020
getPredictorSignificance-methods	0.000	0.003	0.003
getProbTreshold-methods	0.001	0.001	0.003
getQuadProb-methods	0.261	0.008	0.270
getTestedGapDistances-methods	0.264	0.012	0.277
getTranscripts-methods	0.247	0.012	0.259
peaksToBed-methods	8.065	0.017	5.086
plotErrorRate-methods	0.822	0.012	0.834
plotFeatures-methods	1.829	0.000	1.828
plotGenomicAnnot-methods	0.426	0.000	0.426
plotROC-methods	5.758	0.024	4.139
predictStrand-methods	7.939	0.040	4.961
predictTssOverlap-methods	5.228	0.020	2.409
show	0.235	0.004	0.239
transcriptsToBed-methods	1.596	0.004	1.599