BioC 2.14: CHECK report for GSEABase on petty

Package: GSEABase

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.26.0.tar.gz

StartedAt: 2014-10-07 22:23:26 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:29:23 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 356.8 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.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 --no-multiarch GSEABase_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GSEABase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEABase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABase’ version ‘1.26.0’
* 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 ‘GSEABase’ can be installed ... [22s/22s] 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
GeneSetCollection-methods 18.181  0.305  18.611
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘unitTests.R’ [79s/80s]
 [80s/81s] OK
* 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

* installing *source* package ‘GSEABase’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GSEABase)

name	user	system	elapsed
CollectionType-class	1.639	0.080	1.741
CollectionType-constructors	0.741	0.017	0.763
GSEABase-package	0.382	0.021	0.402
GeneColorSet-class	0.406	0.017	0.427
GeneIdentifierType-class	0.325	0.015	0.343
GeneIdentifierType-constructors	0.645	0.019	0.670
GeneSet-class	0.892	0.025	0.926
GeneSet-methods	0.323	0.015	0.367
GeneSetCollection-class	0.057	0.001	0.060
GeneSetCollection-methods	18.181	0.305	18.611
OBOCollection-class	0.286	0.006	0.292
getOBOCollection	0.204	0.003	0.208
getObjects	0.138	0.009	0.151
goSlim-methods	2.008	0.090	2.101
incidence-methods	0.079	0.003	0.082