BioC 3.5: CHECK report for transcriptR on veracruz2

Package: transcriptR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.4.0.tar.gz

StartedAt: 2017-10-18 09:49:01 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:55:57 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 415.4 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/transcriptR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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 12.052  0.398  12.784
peaksToBed-methods               7.314  0.314   7.930
predictStrand-methods            7.200  0.304   7.726
* 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	0.390	0.021	0.422
annotateTranscripts-methods	3.710	0.138	3.966
breakTranscriptsByPeaks-methods	12.052	0.398	12.784
constructCDS	0.003	0.001	0.003
constructTDS	0.226	0.018	0.249
detectTranscripts-methods	1.277	0.062	1.368
estimateBackground-methods	0.873	0.042	0.960
estimateGapDistance-methods	0.975	0.048	1.090
exportCoverage-methods	0.786	0.031	0.847
getConfusionMatrix-methods	0.003	0.009	0.012
getGenomicAnnot-methods	0.005	0.009	0.013
getPeaks-methods	0.038	0.010	0.049
getPredictorSignificance-methods	0.003	0.009	0.012
getProbTreshold-methods	0.003	0.009	0.012
getQuadProb-methods	0.232	0.023	0.260
getTestedGapDistances-methods	0.260	0.018	0.288
getTranscripts-methods	0.238	0.019	0.263
peaksToBed-methods	7.314	0.314	7.930
plotErrorRate-methods	1.517	0.045	1.604
plotFeatures-methods	4.789	0.033	4.938
plotGenomicAnnot-methods	1.664	0.009	1.715
plotROC-methods	1.710	0.019	1.767
predictStrand-methods	7.200	0.304	7.726
predictTssOverlap-methods	1.625	0.023	1.685
show	0.225	0.016	0.249
transcriptsToBed-methods	1.207	0.067	1.305