BioC 2.13: CHECK report for GSEABase on perceval

Package: GSEABase

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEABase_1.24.0.tar.gz

StartedAt: 2014-04-05 01:52:57 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:57:48 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 291.2 seconds

RetCode: 0

Status:  OK

CheckDir: GSEABase.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GSEABase.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.24.0’
* 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 ... [17s/17s] 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.checkRequired’ ‘.constructors_Simple’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GSEABase.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [31s/32s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
GeneSetCollection-methods 15.316  0.398  16.394
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘unitTests.R’ [73s/73s]
 [73s/74s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	1.256	0.081	1.399
CollectionType-constructors	0.294	0.019	0.326
GSEABase-package	0.265	0.026	0.297
GeneColorSet-class	0.637	0.027	0.689
GeneIdentifierType-class	0.296	0.022	0.320
GeneIdentifierType-constructors	0.422	0.023	0.447
GeneSet-class	0.676	0.027	0.706
GeneSet-methods	0.319	0.021	0.345
GeneSetCollection-class	0.085	0.010	0.100
GeneSetCollection-methods	15.316	0.398	16.394
OBOCollection-class	0.175	0.019	0.214
getOBOCollection	0.122	0.014	0.165
getObjects	0.107	0.023	0.156
goSlim-methods	1.223	0.103	1.362
incidence-methods	0.066	0.012	0.079