BioC 3.3: CHECK report for GSEABase on morelia

Package: GSEABase

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSEABase_1.33.0.tar.gz

StartedAt: 2015-10-22 06:58:40 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 07:00:40 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 120.8 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 GSEABase_1.33.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GSEABase.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 ‘GSEABase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABase’ version ‘1.33.0’
* 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 ... [8s/8s] 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 ... NOTE
goSlim,ExpressionSet-GOCollection: no visible binding for global
  variable ‘sample.ExpressionSet’
Undefined global functions or variables:
  sample.ExpressionSet
* 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 ... [11s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unitTests.R’ [29s/30s]
 [29s/30s] 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
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/GSEABase.Rcheck/00check.log’
for details.

* 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	0.535	0.027	0.744
CollectionType-constructors	0.227	0.007	0.233
GSEABase-package	0.135	0.006	0.141
GeneColorSet-class	0.148	0.006	0.154
GeneIdentifierType-class	0.106	0.005	0.111
GeneIdentifierType-constructors	0.304	0.009	0.314
GeneSet-class	0.288	0.010	0.299
GeneSet-methods	0.078	0.009	0.087
GeneSetCollection-class	0.012	0.000	0.012
GeneSetCollection-methods	4.580	0.120	4.721
OBOCollection-class	0.087	0.002	0.089
getOBOCollection	0.062	0.001	0.063
getObjects	0.034	0.002	0.068
goSlim-methods	0.427	0.026	0.598
incidence-methods	0.018	0.000	0.018