BioC 3.1: CHECK report for GSEABase on morelia

Package: GSEABase

Version: 1.30.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GSEABase_1.30.2.tar.gz

StartedAt: 2015-10-09 02:50:13 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:52:41 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 148.4 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_1.30.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/GSEABase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.30.2’
* 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 ... [11s/11s] 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 : .local: no visible binding for
  global variable ‘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 ... [15s/15s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
GeneSetCollection-methods 6.343  0.379   6.745
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unitTests.R’ [38s/38s]
 [38s/38s] 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-3.1-bioc/meat/GSEABase.Rcheck/00check.log’
for details.

* installing *source* package ‘GSEABase’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GSEABase)

name	user	system	elapsed
CollectionType-class	0.566	0.131	0.734
CollectionType-constructors	0.219	0.025	0.244
GSEABase-package	0.295	0.063	0.358
GeneColorSet-class	0.168	0.067	0.235
GeneIdentifierType-class	0.107	0.008	0.115
GeneIdentifierType-constructors	0.297	0.014	0.406
GeneSet-class	0.243	0.013	0.256
GeneSet-methods	0.133	0.009	0.142
GeneSetCollection-class	0.012	0.000	0.013
GeneSetCollection-methods	6.343	0.379	6.745
OBOCollection-class	0.130	0.003	0.133
getOBOCollection	0.103	0.001	0.104
getObjects	0.038	0.001	0.039
goSlim-methods	0.659	0.040	0.726
incidence-methods	0.038	0.001	0.039