BioC 3.6: CHECK report for transcriptR on malbec1

Package: transcriptR

Version: 1.5.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.5.0.tar.gz

StartedAt: 2017-08-16 02:51:30 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:56:53 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 323.9 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_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/transcriptR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.0’
* 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 10.576  0.032  10.968
peaksToBed-methods               7.248  0.020   7.276
predictStrand-methods            7.156  0.004   7.584
* 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)

name	user	system	elapsed
addFeature-methods	0.252	0.000	0.252
annotateTranscripts-methods	4.216	0.036	4.307
breakTranscriptsByPeaks-methods	10.576	0.032	10.968
constructCDS	0.000	0.004	0.004
constructTDS	0.224	0.000	0.223
detectTranscripts-methods	1.132	0.004	1.138
estimateBackground-methods	0.464	0.004	0.467
estimateGapDistance-methods	0.840	0.004	0.845
exportCoverage-methods	0.220	0.000	0.219
getConfusionMatrix-methods	0.004	0.000	0.003
getGenomicAnnot-methods	0.004	0.000	0.004
getPeaks-methods	0.024	0.000	0.026
getPredictorSignificance-methods	0.004	0.000	0.003
getProbTreshold-methods	0.004	0.000	0.002
getQuadProb-methods	0.224	0.000	0.222
getTestedGapDistances-methods	0.228	0.000	0.230
getTranscripts-methods	0.224	0.000	0.223
peaksToBed-methods	7.248	0.020	7.276
plotErrorRate-methods	1.428	0.008	1.438
plotFeatures-methods	4.040	0.008	4.222
plotGenomicAnnot-methods	1.784	0.004	2.195
plotROC-methods	1.560	0.000	1.563
predictStrand-methods	7.156	0.004	7.584
predictTssOverlap-methods	1.288	0.004	1.293
show	0.224	0.000	0.222
transcriptsToBed-methods	1.120	0.012	1.131