BioC 3.3: CHECK report for transcriptR on morelia

Package: transcriptR

Version: 0.99.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_0.99.6.tar.gz

StartedAt: 2016-04-21 08:15:32 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 08:22:06 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 394.3 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_0.99.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/transcriptR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.6’
* 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 ... [26s/26s] 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 ... [59s/59s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
breakTranscriptsByPeaks-methods 11.990  0.506  12.536
peaksToBed-methods               8.780  0.403   9.195
predictStrand-methods            8.295  0.357   8.660
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [71s/79s]
 [71s/79s] 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	0.127	0.005	0.131
annotateTranscripts-methods	3.435	0.111	3.551
breakTranscriptsByPeaks-methods	11.990	0.506	12.536
constructCDS	0.004	0.007	0.011
constructTDS	0.278	0.031	0.311
detectTranscripts-methods	1.530	0.074	1.606
estimateBackground-methods	0.837	0.066	0.905
estimateGapDistance-methods	1.122	0.070	1.193
exportCoverage-methods	0.288	0.023	0.312
getConfusionMatrix-methods	0.003	0.007	0.011
getGenomicAnnot-methods	0.004	0.008	0.012
getPeaks-methods	0.041	0.008	0.050
getPredictorSignificance-methods	0.004	0.009	0.012
getProbTreshold-methods	0.004	0.009	0.013
getQuadProb-methods	0.284	0.025	0.308
getTestedGapDistances-methods	0.261	0.016	0.277
getTranscripts-methods	0.263	0.016	0.280
peaksToBed-methods	8.780	0.403	9.195
plotErrorRate-methods	1.072	0.067	1.142
plotFeatures-methods	2.512	0.018	2.537
plotGenomicAnnot-methods	0.446	0.004	0.452
plotROC-methods	1.681	0.033	1.717
predictStrand-methods	8.295	0.357	8.660
predictTssOverlap-methods	1.671	0.025	1.697
show	0.279	0.022	0.302
transcriptsToBed-methods	1.429	0.070	1.499