BioC 2.13: CHECK report for rols on perceval

Package: rols

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rols_1.4.0.tar.gz

StartedAt: 2014-04-05 04:03:41 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:14:45 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 664.8 seconds

RetCode: 0

Status:  OK

CheckDir: rols.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/rols.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 ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘1.4.0’
* 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 ‘rols’ can be installed ... [9s/9s] 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
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getTermsByName’
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 ... 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 ... [529s/575s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
allIds        519.321  2.525 553.926
CVParam-class   1.381  0.025   7.527
* 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/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	1.381	0.025	7.527
allIds	519.321	2.525	553.926
childrenRelations	0.080	0.005	0.408
isIdObsolete	0.290	0.011	2.698
olsQuery	0.352	0.008	1.656
olsVersion	0.024	0.003	0.344
ontologies	0.042	0.007	0.050
ontologyLoadDate	0.108	0.006	0.752
ontologyNames	0.030	0.003	0.033
parents	0.085	0.007	0.409
rootId	0.250	0.009	1.216
term	0.198	0.008	1.228
termMetadata	0.186	0.006	0.843