BioC 3.4: CHECK report for transcriptR on morelia

Package: transcriptR

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings transcriptR_1.1.2.tar.gz

StartedAt: 2016-09-20 14:00:24 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 14:05:14 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 290.6 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_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.1.2’
* 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 9.383  0.351   9.773
predictStrand-methods           6.347  0.358   6.707
peaksToBed-methods              5.803  0.264   6.067
plotFeatures-methods            1.899  0.013   5.985
* 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	0.096	0.006	0.102
annotateTranscripts-methods	2.960	0.090	3.052
breakTranscriptsByPeaks-methods	9.383	0.351	9.773
constructCDS	0.003	0.007	0.010
constructTDS	0.248	0.018	0.265
detectTranscripts-methods	1.485	0.091	1.576
estimateBackground-methods	0.336	0.034	0.370
estimateGapDistance-methods	1.258	0.048	1.306
exportCoverage-methods	0.287	0.020	0.308
getConfusionMatrix-methods	0.004	0.008	0.012
getGenomicAnnot-methods	0.006	0.008	0.014
getPeaks-methods	0.036	0.008	0.044
getPredictorSignificance-methods	0.003	0.008	0.011
getProbTreshold-methods	0.004	0.007	0.011
getQuadProb-methods	0.252	0.020	0.273
getTestedGapDistances-methods	0.215	0.011	0.225
getTranscripts-methods	0.218	0.010	0.228
peaksToBed-methods	5.803	0.264	6.067
plotErrorRate-methods	0.716	0.032	0.777
plotFeatures-methods	1.899	0.013	5.985
plotGenomicAnnot-methods	0.266	0.004	0.269
plotROC-methods	1.349	0.024	1.375
predictStrand-methods	6.347	0.358	6.707
predictTssOverlap-methods	1.220	0.037	1.257
show	0.219	0.020	0.238
transcriptsToBed-methods	1.173	0.070	1.244