BioC 3.4: CHECK report for transcriptR on morelia

Package: transcriptR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.2.0.tar.gz

StartedAt: 2017-04-15 08:58:30 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 09:04:43 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 373.3 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/transcriptR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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 11.117  0.429  11.601
predictStrand-methods            7.579  0.387   7.971
peaksToBed-methods               6.547  0.355   6.902
* 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	0.107	0.017	0.124
annotateTranscripts-methods	2.866	0.094	2.963
breakTranscriptsByPeaks-methods	11.117	0.429	11.601
constructCDS	0.002	0.008	0.011
constructTDS	0.249	0.028	0.276
detectTranscripts-methods	1.163	0.068	1.231
estimateBackground-methods	0.677	0.039	0.716
estimateGapDistance-methods	0.778	0.049	0.827
exportCoverage-methods	0.209	0.016	0.225
getConfusionMatrix-methods	0.003	0.007	0.010
getGenomicAnnot-methods	0.004	0.007	0.011
getPeaks-methods	0.025	0.007	0.033
getPredictorSignificance-methods	0.003	0.008	0.011
getProbTreshold-methods	0.003	0.008	0.010
getQuadProb-methods	0.213	0.018	0.231
getTestedGapDistances-methods	0.214	0.011	0.226
getTranscripts-methods	0.219	0.008	0.227
peaksToBed-methods	6.547	0.355	6.902
plotErrorRate-methods	1.533	0.087	1.621
plotFeatures-methods	2.999	0.016	3.020
plotGenomicAnnot-methods	0.464	0.010	0.475
plotROC-methods	1.741	0.023	1.766
predictStrand-methods	7.579	0.387	7.971
predictTssOverlap-methods	1.733	0.027	1.762
show	0.239	0.019	0.257
transcriptsToBed-methods	1.402	0.076	1.479