BioC 3.2: CHECK report for GeneBreak on linux1.bioconductor.org

Package: GeneBreak

Version: 1.0.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.0.0.tar.gz

StartedAt: 2015-10-27 03:47:37 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:50:40 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 182.2 seconds

RetCode: 0

Status:  OK

CheckDir: GeneBreak.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings GeneBreak_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/GeneBreak.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [72s/72s] OK
Examples with CPU or elapsed time > 5s
                                                 user system elapsed
CopyNumberBreakPointGenes-class                 9.798  0.076   9.889
bpPlot-CopyNumberBreakPoints-method             7.356  0.052   7.420
bpStats-CopyNumberBreakPoints-method            6.959  0.024   6.994
recurrentGenes-CopyNumberBreakPointGenes-method 6.584  0.020   6.604
* 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	9.798	0.076	9.889
CopyNumberBreakPoints-class	1.824	0.020	1.846
accessOptions-CopyNumberBreakPoints-method	0.965	0.008	0.974
addGeneAnnotation-CopyNumberBreakPoints-method	3.031	0.044	3.079
bpFilter-CopyNumberBreakPoints-method	1.752	0.020	1.774
bpGenes-CopyNumberBreakPointGenes-method	3.047	0.016	3.075
bpPlot-CopyNumberBreakPoints-method	7.356	0.052	7.420
bpStats-CopyNumberBreakPoints-method	6.959	0.024	6.994
breakpointData-CopyNumberBreakPoints-method	1.158	0.172	1.333
breakpointsPerGene-CopyNumberBreakPointGenes-method	3.355	0.155	3.525
callData-CopyNumberBreakPoints-method	1.528	0.144	1.679
featureChromosomes-CopyNumberBreakPoints-method	0.935	0.012	0.947
featureInfo-CopyNumberBreakPoints-method	3.048	0.080	3.128
featuresPerGene-CopyNumberBreakPointGenes-method	2.645	0.008	2.655
geneChromosomes-CopyNumberBreakPointGenes-method	2.783	0.008	2.793
geneInfo-CopyNumberBreakPointGenes-method	2.483	0.020	2.502
getBreakpoints	2.039	0.008	2.048
namesFeatures-CopyNumberBreakPoints-method	0.889	0.032	0.921
recurrentGenes-CopyNumberBreakPointGenes-method	6.584	0.020	6.604
sampleNames-CopyNumberBreakPoints-method	1.158	0.008	1.166
segmentData-CopyNumberBreakPoints-method	1.461	0.172	1.633