BioC 2.14: CHECK report for rols on petty

Package: rols

Version: 1.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rols_1.6.1.tar.gz

StartedAt: 2014-10-07 23:54:56 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:58:19 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 203.0 seconds

RetCode: 0

Status:  OK

CheckDir: rols.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 rols_1.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/rols.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 ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘1.6.1’
* 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 ‘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
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 files in ‘vignettes’ ... OK
* checking examples ... [23s/90s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
allIds        13.422  0.058  16.268
CVParam-class  2.078  0.020  22.204
isIdObsolete   0.464  0.004  18.208
termMetadata   0.317  0.002   8.791
term           0.296  0.002  13.023
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/rols.Rcheck/00check.log’
for details.

* installing *source* package ‘rols’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘SSOAP’: 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
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘SSOAP’: not turning on duplicate class definitions for this class.
* DONE (rols)

name	user	system	elapsed
CVParam-class	2.078	0.020	22.204
allIds	13.422	0.058	16.268
childrenRelations	0.123	0.000	0.958
isIdObsolete	0.464	0.004	18.208
olsQuery	0.606	0.003	2.343
olsVersion	0.024	0.001	0.351
ontologies	0.057	0.001	0.058
ontologyLoadDate	0.166	0.002	0.828
ontologyNames	0.049	0.000	0.052
parents	0.145	0.001	0.497
rootId	0.394	0.002	2.036
term	0.296	0.002	13.023
termMetadata	0.317	0.002	8.791