BioC 2.12: CHECK report for ontoCAT on george2

Package: ontoCAT

Version: 1.12.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.12.0.tar.gz

StartedAt: 2013-10-09 03:44:56 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:54:08 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 551.5 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 3.0.1 (2013-05-16)
* 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 ‘1.12.0’
* 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 ... [505s/499s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getTermRelations      229.799  0.812 240.340
getTermRelationNames  166.994  0.548 170.759
Ontology-class         69.736  1.432  51.799
getEFO                  7.952  0.048   7.972
getAllTermChildren      6.356  0.068   6.932
getOntology             5.060  0.004   4.209
getTermAndAllChildren   4.873  0.048   5.810
* 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
** testing if installed package can be loaded
* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	69.736	1.432	51.799
OntologyTerm-class	0.052	0.000	0.052
getAccession	0.040	0.000	0.036
getAllTermChildren	6.356	0.068	6.932
getAllTermIds	1.004	0.000	0.950
getAllTermParents	0.072	0.004	0.079
getAllTerms	0.881	0.008	0.974
getEFO	7.952	0.048	7.972
getEFOBranchRootIds	0.904	0.000	0.906
getLabel	0.032	0.000	0.029
getOntology	5.060	0.004	4.209
getOntologyAccession	0.016	0.000	0.015
getOntologyDescription	0.024	0.000	0.024
getOntologyNoReasoning	0.432	0.000	0.422
getOntologyRelationNames	0.412	0.000	0.430
getRootIds	0.34	0.00	0.34
getRoots	0.316	0.000	0.318
getTermAndAllChildren	4.873	0.048	5.810
getTermById	0.032	0.000	0.036
getTermChildren	0.344	0.000	0.351
getTermDefinitions	0.036	0.000	0.037
getTermNameById	0.020	0.000	0.017
getTermParents	0.044	0.000	0.046
getTermRelationNames	166.994	0.548	170.759
getTermRelations	229.799	0.812	240.340
getTermSynonyms	0.096	0.000	0.093
hasTerm	0.016	0.000	0.016
isEFOBranchRoot	0.020	0.000	0.021
isRoot	0.312	0.004	0.313
ontoCAT-package	0.012	0.000	0.011
searchTerm	0.876	0.004	0.833
searchTermPrefix	0.860	0.012	0.987
showHierarchyDownToTerm	0.756	0.000	0.753
showPathsToTerm	0.364	0.004	0.360