BioC 2.12: CHECK report for rols on petty

Package: rols

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rols_1.2.2.tar.gz

StartedAt: 2013-10-08 23:46:14 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:51:25 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 311.2 seconds

RetCode: 0

Status:  OK

CheckDir: rols.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/rols.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '1.2.2'
* 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 'rols' can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
Found the following possibly unsafe calls:
File 'rols/R/queries.R':
  unlockBinding("ontologies", .rolsEnv)
* 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 examples ... [122s/180s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
allIds        110.334  0.671 139.995
olsQuery        2.469  0.021   5.431
CVParam-class   1.857  0.017   9.738
isIdObsolete    0.380  0.009   5.331
term            0.242  0.007   5.296
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/rols.Rcheck/00check.log'
for details.

* installing *source* package 'rols' ...
** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for S3 class "connection" in package 'BiocGenerics' seems equivalent to one from package 'SSOAP' and is not turning on duplicate class definitions for this class
* DONE (rols)

name	user	system	elapsed
CVParam-class	1.857	0.017	9.738
allIds	110.334	0.671	139.995
childrenRelations	0.124	0.006	0.517
isIdObsolete	0.380	0.009	5.331
olsQuery	2.469	0.021	5.431
olsVersion	0.044	0.004	0.404
ontologies	0.062	0.007	0.070
ontologyLoadDate	0.135	0.003	0.961
ontologyNames	0.036	0.003	0.038
parents	0.107	0.003	0.470
rootId	0.306	0.008	1.928
term	0.242	0.007	5.296
termMetadata	0.257	0.007	4.262