BioC 3.3: CHECK report for transcriptR on zin2

Package: transcriptR

Version: 1.0.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.0.2.tar.gz

StartedAt: 2016-10-13 07:32:07 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:37:14 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 306.6 seconds

RetCode: 0

Status:  OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings transcriptR_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.0.2’
* 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 11.170  0.108  11.306
predictStrand-methods            7.562  0.012   7.615
peaksToBed-methods               7.058  0.044   7.110
* 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	0.101	0.000	0.100
annotateTranscripts-methods	2.672	0.028	2.703
breakTranscriptsByPeaks-methods	11.170	0.108	11.306
constructCDS	0.004	0.000	0.004
constructTDS	0.247	0.000	0.250
detectTranscripts-methods	1.313	0.000	1.314
estimateBackground-methods	0.502	0.004	0.506
estimateGapDistance-methods	1.384	0.004	1.388
exportCoverage-methods	0.231	0.000	0.231
getConfusionMatrix-methods	0.003	0.000	0.003
getGenomicAnnot-methods	0.000	0.004	0.004
getPeaks-methods	0.029	0.000	0.028
getPredictorSignificance-methods	0.003	0.000	0.003
getProbTreshold-methods	0.004	0.000	0.004
getQuadProb-methods	0.236	0.008	0.246
getTestedGapDistances-methods	0.256	0.008	0.263
getTranscripts-methods	0.264	0.000	0.265
peaksToBed-methods	7.058	0.044	7.110
plotErrorRate-methods	1.123	0.004	1.141
plotFeatures-methods	2.120	0.004	2.124
plotGenomicAnnot-methods	0.345	0.000	0.357
plotROC-methods	1.523	0.004	1.539
predictStrand-methods	7.562	0.012	7.615
predictTssOverlap-methods	1.470	0.008	1.476
show	0.235	0.008	0.243
transcriptsToBed-methods	1.327	0.008	1.335