BioC 3.2: CHECK report for GeneBreak on oaxaca

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: 2015-10-27 03:53:27 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:57:33 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 245.7 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 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [13s/13s] 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 ... [103s/103s] OK
Examples with CPU or elapsed time > 5s
                                                  user system elapsed
CopyNumberBreakPointGenes-class                 11.318  0.943  12.280
bpPlot-CopyNumberBreakPoints-method              9.484  0.963  10.467
bpStats-CopyNumberBreakPoints-method             9.435  0.926  10.378
recurrentGenes-CopyNumberBreakPointGenes-method  9.223  1.108  10.340
* 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	11.318	0.943	12.280
CopyNumberBreakPoints-class	2.561	0.252	2.817
accessOptions-CopyNumberBreakPoints-method	1.507	0.119	1.627
addGeneAnnotation-CopyNumberBreakPoints-method	3.963	0.233	4.204
bpFilter-CopyNumberBreakPoints-method	2.378	0.249	2.631
bpGenes-CopyNumberBreakPointGenes-method	3.976	0.247	4.230
bpPlot-CopyNumberBreakPoints-method	9.484	0.963	10.467
bpStats-CopyNumberBreakPoints-method	9.435	0.926	10.378
breakpointData-CopyNumberBreakPoints-method	1.810	0.424	2.235
breakpointsPerGene-CopyNumberBreakPointGenes-method	4.424	0.503	4.939
callData-CopyNumberBreakPoints-method	2.017	0.429	2.450
featureChromosomes-CopyNumberBreakPoints-method	1.728	0.129	1.861
featureInfo-CopyNumberBreakPoints-method	4.196	0.281	4.485
featuresPerGene-CopyNumberBreakPointGenes-method	3.881	0.210	4.094
geneChromosomes-CopyNumberBreakPointGenes-method	3.949	0.267	4.220
geneInfo-CopyNumberBreakPointGenes-method	3.756	0.265	4.028
getBreakpoints	3.084	0.208	3.296
namesFeatures-CopyNumberBreakPoints-method	1.553	0.156	1.711
recurrentGenes-CopyNumberBreakPointGenes-method	9.223	1.108	10.340
sampleNames-CopyNumberBreakPoints-method	1.615	0.145	1.760
segmentData-CopyNumberBreakPoints-method	1.851	0.417	2.272