BioC 3.3: CHECK report for GeneBreak on morelia

Package: GeneBreak

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneBreak_1.1.0.tar.gz

StartedAt: 2015-10-22 06:17:58 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 06:20:56 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 178.0 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GeneBreak.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.1.0’
* 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 ... [9s/9s] 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 ... [75s/75s] OK
Examples with CPU or elapsed time > 5s
                                                 user system elapsed
CopyNumberBreakPointGenes-class                 8.132  0.895   9.033
bpPlot-CopyNumberBreakPoints-method             7.117  0.812   7.962
bpStats-CopyNumberBreakPoints-method            6.962  0.843   7.820
recurrentGenes-CopyNumberBreakPointGenes-method 6.915  0.843   7.804
* 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	8.132	0.895	9.033
CopyNumberBreakPoints-class	1.769	0.179	1.950
accessOptions-CopyNumberBreakPoints-method	1.555	0.144	1.702
addGeneAnnotation-CopyNumberBreakPoints-method	2.949	0.198	3.149
bpFilter-CopyNumberBreakPoints-method	1.543	0.176	1.718
bpGenes-CopyNumberBreakPointGenes-method	3.314	0.215	3.531
bpPlot-CopyNumberBreakPoints-method	7.117	0.812	7.962
bpStats-CopyNumberBreakPoints-method	6.962	0.843	7.820
breakpointData-CopyNumberBreakPoints-method	1.320	0.344	1.665
breakpointsPerGene-CopyNumberBreakPointGenes-method	2.986	0.447	3.434
callData-CopyNumberBreakPoints-method	1.454	0.380	1.834
featureChromosomes-CopyNumberBreakPoints-method	1.335	0.116	1.452
featureInfo-CopyNumberBreakPoints-method	2.692	0.223	2.915
featuresPerGene-CopyNumberBreakPointGenes-method	2.606	0.210	2.816
geneChromosomes-CopyNumberBreakPointGenes-method	2.697	0.221	2.920
geneInfo-CopyNumberBreakPointGenes-method	2.437	0.227	2.669
getBreakpoints	2.196	0.182	2.380
namesFeatures-CopyNumberBreakPoints-method	1.121	0.107	1.228
recurrentGenes-CopyNumberBreakPointGenes-method	6.915	0.843	7.804
sampleNames-CopyNumberBreakPoints-method	1.182	0.138	1.320
segmentData-CopyNumberBreakPoints-method	1.439	0.348	1.791