BioC 3.5: CHECK report for transcriptR on malbec2

Package: transcriptR

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.4.0.tar.gz

StartedAt: 2017-08-16 02:43:32 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:48:57 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 325.4 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.4.0’
* 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 10.664  0.044  10.741
peaksToBed-methods               7.332  0.008   7.345
predictStrand-methods            5.820  0.040   5.866
* 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	0.251
annotateTranscripts-methods	3.552	0.028	3.582
breakTranscriptsByPeaks-methods	10.664	0.044	10.741
constructCDS	0.000	0.000	0.003
constructTDS	0.224	0.008	0.234
detectTranscripts-methods	1.736	0.008	1.744
estimateBackground-methods	0.432	0.000	0.430
estimateGapDistance-methods	0.912	0.004	0.919
exportCoverage-methods	0.228	0.000	0.231
getConfusionMatrix-methods	0.000	0.000	0.003
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	0.004
getQuadProb-methods	0.224	0.004	0.227
getTestedGapDistances-methods	0.216	0.004	0.222
getTranscripts-methods	0.228	0.004	0.232
peaksToBed-methods	7.332	0.008	7.345
plotErrorRate-methods	2.156	0.008	2.442
plotFeatures-methods	3.936	0.000	3.939
plotGenomicAnnot-methods	1.204	0.000	1.205
plotROC-methods	1.312	0.004	1.318
predictStrand-methods	5.820	0.040	5.866
predictTssOverlap-methods	1.340	0.000	1.342
show	0.224	0.000	0.223
transcriptsToBed-methods	1.096	0.004	1.098