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: 2016-04-23 00:24:00 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:28:10 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 249.9 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 3.2.4 (2016-03-10)
* 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 ... [14s/16s] 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 ... [105s/105s] OK
Examples with CPU or elapsed time > 5s
                                                  user system elapsed
CopyNumberBreakPointGenes-class                 11.384  0.986  12.388
bpStats-CopyNumberBreakPoints-method             9.854  0.826  10.697
bpPlot-CopyNumberBreakPoints-method              9.597  0.924  10.540
recurrentGenes-CopyNumberBreakPointGenes-method  9.345  1.099  10.457
* 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	11.384	0.986	12.388
CopyNumberBreakPoints-class	2.572	0.245	2.820
accessOptions-CopyNumberBreakPoints-method	1.503	0.113	1.618
addGeneAnnotation-CopyNumberBreakPoints-method	3.994	0.244	4.244
bpFilter-CopyNumberBreakPoints-method	2.423	0.228	2.654
bpGenes-CopyNumberBreakPointGenes-method	4.239	0.221	4.466
bpPlot-CopyNumberBreakPoints-method	9.597	0.924	10.540
bpStats-CopyNumberBreakPoints-method	9.854	0.826	10.697
breakpointData-CopyNumberBreakPoints-method	1.919	0.461	2.430
breakpointsPerGene-CopyNumberBreakPointGenes-method	4.053	0.492	4.550
callData-CopyNumberBreakPoints-method	2.067	0.416	2.527
featureChromosomes-CopyNumberBreakPoints-method	1.397	0.125	1.523
featureInfo-CopyNumberBreakPoints-method	4.384	0.323	4.783
featuresPerGene-CopyNumberBreakPointGenes-method	4.257	0.252	4.531
geneChromosomes-CopyNumberBreakPointGenes-method	4.226	0.273	4.505
geneInfo-CopyNumberBreakPointGenes-method	4.053	0.276	4.337
getBreakpoints	3.199	0.219	3.428
namesFeatures-CopyNumberBreakPoints-method	1.543	0.154	1.698
recurrentGenes-CopyNumberBreakPointGenes-method	9.345	1.099	10.457
sampleNames-CopyNumberBreakPoints-method	1.695	0.167	1.870
segmentData-CopyNumberBreakPoints-method	2.012	0.449	2.463