BioC 2.12: CHECK report for ontoCAT on george2

Package: ontoCAT

Version: 1.11.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.11.0.tar.gz

StartedAt: 2013-03-25 03:30:07 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:35:55 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 348.4 seconds

RetCode: 0

Status: OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ontoCAT.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ontoCAT’ version ‘1.11.0’
* 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 ‘ontoCAT’ can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [308s/289s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getTermRelations        110.867  0.404 114.589
getTermRelationNames     86.086  0.420  85.770
Ontology-class           62.876  1.220  41.812
getEFO                    7.949  0.068   7.991
getAllTermChildren        5.984  0.032   6.235
getTermAndAllChildren     5.720  0.088   5.851
getOntology               5.544  0.012   5.071
showHierarchyDownToTerm   5.036  0.020   5.787
showPathsToTerm           4.449  0.016   5.169
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/ontoCAT.Rcheck/00check.log’
for details.

* installing *source* package ‘ontoCAT’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘ontoCAT.Rnw’ 
** testing if installed package can be loaded
* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	62.876	1.220	41.812
OntologyTerm-class	0.060	0.000	0.059
getAccession	0.052	0.000	0.053
getAllTermChildren	5.984	0.032	6.235
getAllTermIds	0.968	0.008	0.878
getAllTermParents	0.092	0.004	0.096
getAllTerms	0.844	0.000	0.885
getEFO	7.949	0.068	7.991
getEFOBranchRootIds	0.920	0.000	0.907
getLabel	0.068	0.000	0.070
getOntology	5.544	0.012	5.071
getOntologyAccession	0.024	0.000	0.022
getOntologyDescription	0.024	0.000	0.026
getOntologyNoReasoning	0.560	0.000	0.393
getOntologyRelationNames	0.468	0.000	0.434
getRootIds	0.456	0.000	0.435
getRoots	0.444	0.000	0.437
getTermAndAllChildren	5.720	0.088	5.851
getTermById	0.032	0.000	0.032
getTermChildren	0.288	0.004	0.325
getTermDefinitions	0.048	0.004	0.054
getTermNameById	0.024	0.000	0.023
getTermParents	0.048	0.000	0.050
getTermRelationNames	86.086	0.420	85.770
getTermRelations	110.867	0.404	114.589
getTermSynonyms	0.088	0.000	0.109
hasTerm	0.016	0.000	0.017
isEFOBranchRoot	0.036	0.000	0.039
isRoot	0.408	0.004	0.497
ontoCAT-package	0.016	0.004	0.022
searchTerm	0.968	0.004	1.027
searchTermPrefix	0.904	0.000	1.102
showHierarchyDownToTerm	5.036	0.020	5.787
showPathsToTerm	4.449	0.016	5.169

Summary

Command output