BioC 3.3: CHECK report for transcriptR on oaxaca

Package: transcriptR

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.0.2.tar.gz

StartedAt: 2016-10-13 06:57:53 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:04:22 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 388.6 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_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/transcriptR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.0.2’
* 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 13.049  0.488  13.580
predictStrand-methods            8.931  0.363   9.303
peaksToBed-methods               8.589  0.398   8.995
* 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	0.158	0.010	0.168
annotateTranscripts-methods	2.937	0.100	3.041
breakTranscriptsByPeaks-methods	13.049	0.488	13.580
constructCDS	0.003	0.003	0.006
constructTDS	0.269	0.022	0.292
detectTranscripts-methods	1.931	0.107	2.040
estimateBackground-methods	0.440	0.057	0.497
estimateGapDistance-methods	1.221	0.064	1.288
exportCoverage-methods	0.282	0.024	0.307
getConfusionMatrix-methods	0.004	0.012	0.015
getGenomicAnnot-methods	0.006	0.012	0.018
getPeaks-methods	0.039	0.013	0.052
getPredictorSignificance-methods	0.004	0.011	0.016
getProbTreshold-methods	0.004	0.012	0.016
getQuadProb-methods	0.293	0.030	0.327
getTestedGapDistances-methods	0.281	0.019	0.302
getTranscripts-methods	0.287	0.020	0.308
peaksToBed-methods	8.589	0.398	8.995
plotErrorRate-methods	1.207	0.050	1.264
plotFeatures-methods	2.841	0.018	2.872
plotGenomicAnnot-methods	0.418	0.009	0.429
plotROC-methods	1.762	0.036	1.801
predictStrand-methods	8.931	0.363	9.303
predictTssOverlap-methods	1.683	0.053	1.737
show	0.287	0.019	0.307
transcriptsToBed-methods	1.598	0.077	1.682