BioC 3.2: CHECK report for GeneBreak on perceval

Package: GeneBreak

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneBreak_1.0.0.tar.gz

StartedAt: 2015-11-10 05:05:24 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 05:09:51 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 267.0 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.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 GeneBreak_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GeneBreak.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneBreak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneBreak’ version ‘1.0.0’
* 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 ‘GeneBreak’ can be installed ... [15s/15s] 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 ... [114s/114s] OK
Examples with CPU or elapsed time > 5s
                                                  user system elapsed
CopyNumberBreakPointGenes-class                 12.517  0.679  13.199
bpStats-CopyNumberBreakPoints-method            11.099  0.803  11.902
bpPlot-CopyNumberBreakPoints-method             10.976  0.921  11.899
recurrentGenes-CopyNumberBreakPointGenes-method 10.793  1.006  11.800
* 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 ‘GeneBreak’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘segmentData’ in package ‘GeneBreak’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneBreak)

name	user	system	elapsed
CopyNumberBreakPointGenes-class	12.517	0.679	13.199
CopyNumberBreakPoints-class	2.801	0.329	3.131
accessOptions-CopyNumberBreakPoints-method	1.651	0.197	1.849
addGeneAnnotation-CopyNumberBreakPoints-method	3.852	0.328	4.180
bpFilter-CopyNumberBreakPoints-method	2.731	0.279	3.012
bpGenes-CopyNumberBreakPointGenes-method	4.347	0.256	4.604
bpPlot-CopyNumberBreakPoints-method	10.976	0.921	11.899
bpStats-CopyNumberBreakPoints-method	11.099	0.803	11.902
breakpointData-CopyNumberBreakPoints-method	2.209	0.512	2.721
breakpointsPerGene-CopyNumberBreakPointGenes-method	4.312	0.587	4.898
callData-CopyNumberBreakPoints-method	2.232	0.497	2.730
featureChromosomes-CopyNumberBreakPoints-method	1.631	0.141	1.772
featureInfo-CopyNumberBreakPoints-method	4.613	0.338	4.950
featuresPerGene-CopyNumberBreakPointGenes-method	4.257	0.273	4.530
geneChromosomes-CopyNumberBreakPointGenes-method	4.316	0.269	4.586
geneInfo-CopyNumberBreakPointGenes-method	4.225	0.313	4.538
getBreakpoints	3.406	0.258	3.665
namesFeatures-CopyNumberBreakPoints-method	1.696	0.171	1.867
recurrentGenes-CopyNumberBreakPointGenes-method	10.793	1.006	11.800
sampleNames-CopyNumberBreakPoints-method	1.731	0.212	1.944
segmentData-CopyNumberBreakPoints-method	2.293	0.485	2.779