BioC 3.5: CHECK report for transcriptR on toluca2

Package: transcriptR

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.3.0.tar.gz

StartedAt: 2017-04-23 10:51:58 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 10:59:10 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 432.3 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/transcriptR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.3.0’
* 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 13.032  0.399  13.505
peaksToBed-methods               8.544  0.363   8.959
predictStrand-methods            7.218  0.394   7.651
plotFeatures-methods             5.734  0.022   5.891
* 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	0.361	0.007	0.368
annotateTranscripts-methods	4.271	0.144	4.430
breakTranscriptsByPeaks-methods	13.032	0.399	13.505
constructCDS	0.004	0.003	0.008
constructTDS	0.274	0.021	0.299
detectTranscripts-methods	1.462	0.087	1.603
estimateBackground-methods	0.914	0.053	0.972
estimateGapDistance-methods	1.069	0.075	1.149
exportCoverage-methods	0.266	0.023	0.294
getConfusionMatrix-methods	0.004	0.008	0.012
getGenomicAnnot-methods	0.006	0.008	0.014
getPeaks-methods	0.037	0.009	0.045
getPredictorSignificance-methods	0.003	0.007	0.011
getProbTreshold-methods	0.003	0.007	0.009
getQuadProb-methods	0.258	0.024	0.284
getTestedGapDistances-methods	0.268	0.017	0.286
getTranscripts-methods	0.254	0.015	0.270
peaksToBed-methods	8.544	0.363	8.959
plotErrorRate-methods	1.221	0.054	1.280
plotFeatures-methods	5.734	0.022	5.891
plotGenomicAnnot-methods	2.067	0.008	2.087
plotROC-methods	2.191	0.038	2.240
predictStrand-methods	7.218	0.394	7.651
predictTssOverlap-methods	1.632	0.034	1.671
show	0.260	0.020	0.279
transcriptsToBed-methods	1.445	0.074	1.524