BioC 3.4: CHECK report for transcriptR on zin1

Package: transcriptR

Version: 1.1.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.1.2.tar.gz

StartedAt: 2016-09-20 13:28:42 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:33:36 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 294.2 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/transcriptR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.2’
* 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 10.444  1.288  11.730
predictStrand-methods            6.408  1.656   8.073
peaksToBed-methods               5.484  1.360   6.844
* 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	0.092	0.004	0.100
annotateTranscripts-methods	2.880	0.072	2.955
breakTranscriptsByPeaks-methods	10.444	1.288	11.730
constructCDS	0.000	0.000	0.004
constructTDS	0.240	0.128	0.368
detectTranscripts-methods	1.256	0.004	1.259
estimateBackground-methods	0.764	0.108	0.872
estimateGapDistance-methods	0.900	0.396	1.298
exportCoverage-methods	0.216	0.424	0.638
getConfusionMatrix-methods	0.004	0.000	0.003
getGenomicAnnot-methods	0.004	0.000	0.004
getPeaks-methods	0.028	0.000	0.027
getPredictorSignificance-methods	0.004	0.000	0.003
getProbTreshold-methods	0.004	0.000	0.002
getQuadProb-methods	0.220	0.448	0.668
getTestedGapDistances-methods	0.228	0.372	0.599
getTranscripts-methods	0.200	0.468	0.668
peaksToBed-methods	5.484	1.360	6.844
plotErrorRate-methods	1.276	0.452	1.727
plotFeatures-methods	1.908	0.000	1.909
plotGenomicAnnot-methods	0.288	0.000	0.287
plotROC-methods	1.360	0.000	1.364
predictStrand-methods	6.408	1.656	8.073
predictTssOverlap-methods	1.400	0.000	1.399
show	0.220	0.564	0.782
transcriptsToBed-methods	1.264	0.420	1.685