BioC 3.2: CHECK report for GeneBreak on zin1

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: 2016-04-23 00:54:49 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:57:57 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 187.9 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 3.2.4 Revised (2016-03-16 r70336)
* 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 ... [10s/10s] 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 ... [83s/84s] OK
Examples with CPU or elapsed time > 5s
                                                      user system elapsed
bpStats-CopyNumberBreakPoints-method                10.708  0.032  10.800
CopyNumberBreakPointGenes-class                      9.450  0.079   9.560
bpPlot-CopyNumberBreakPoints-method                  8.300  0.016   8.382
recurrentGenes-CopyNumberBreakPointGenes-method      8.238  0.012   8.264
breakpointsPerGene-CopyNumberBreakPointGenes-method  5.113  0.268   5.403
* 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	9.450	0.079	9.560
CopyNumberBreakPoints-class	1.906	0.028	1.936
accessOptions-CopyNumberBreakPoints-method	1.021	0.004	1.025
addGeneAnnotation-CopyNumberBreakPoints-method	3.040	0.012	3.056
bpFilter-CopyNumberBreakPoints-method	1.709	0.016	1.727
bpGenes-CopyNumberBreakPointGenes-method	3.000	0.024	3.028
bpPlot-CopyNumberBreakPoints-method	8.300	0.016	8.382
bpStats-CopyNumberBreakPoints-method	10.708	0.032	10.800
breakpointData-CopyNumberBreakPoints-method	1.845	0.336	2.204
breakpointsPerGene-CopyNumberBreakPointGenes-method	5.113	0.268	5.403
callData-CopyNumberBreakPoints-method	1.917	0.296	2.230
featureChromosomes-CopyNumberBreakPoints-method	1.486	0.028	1.526
featureInfo-CopyNumberBreakPoints-method	3.736	0.088	3.821
featuresPerGene-CopyNumberBreakPointGenes-method	3.114	0.048	3.168
geneChromosomes-CopyNumberBreakPointGenes-method	3.419	0.016	3.443
geneInfo-CopyNumberBreakPointGenes-method	3.092	0.019	3.139
getBreakpoints	2.314	0.013	2.326
namesFeatures-CopyNumberBreakPoints-method	0.966	0.016	0.980
recurrentGenes-CopyNumberBreakPointGenes-method	8.238	0.012	8.264
sampleNames-CopyNumberBreakPoints-method	1.091	0.011	1.112
segmentData-CopyNumberBreakPoints-method	1.433	0.216	1.659