Package: ontoCAT

Version: 1.8.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.8.0.tar.gz

StartedAt: 2012-09-24 02:37:07 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 02:46:15 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 548.2 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/ontoCAT.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.8.0’
* 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 whether package ‘ontoCAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* 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

* 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	36.210	0.592	60.182
OntologyTerm-class	0.016	0.000	0.017
getAccession	0.008	0.000	0.008
getAllTermChildren	4.728	0.060	4.780
getAllTermIds	19.097	0.028	19.188
getAllTermParents	0.072	0.000	0.072
getAllTerms	37.411	0.260	37.680
getEFO	7.928	0.024	7.899
getEFOBranchRootIds	2.132	0.004	2.113
getLabel	0.008	0.000	0.008
getOntology	50.447	0.040	49.348
getOntologyAccession	0.004	0.000	0.004
getOntologyDescription	0.004	0.000	0.005
getOntologyNoReasoning	54.620	0.044	54.809
getOntologyRelationNames	65.864	0.056	65.902
getRootIds	1.696	0.004	1.669
getRoots	1.648	0.000	1.718
getTermAndAllChildren	4.524	0.072	5.096
getTermById	0.012	0.004	0.013
getTermChildren	0.164	0.000	0.167
getTermDefinitions	0.024	0.000	0.026
getTermNameById	0.004	0.000	0.007
getTermParents	0.024	0.008	0.035
getTermRelationNames	63.756	0.072	63.996
getTermRelations	74.037	0.072	74.803
getTermSynonyms	0.056	0.000	0.057
hasTerm	0.008	0.000	0.006
isEFOBranchRoot	0.012	0.000	0.013
isRoot	1.648	0.000	1.671
ontoCAT-package	0.000	0.000	0.003
searchTerm	1.476	0.000	1.487
searchTermPrefix	1.468	0.012	1.533
showHierarchyDownToTerm	27.710	0.052	28.070
showPathsToTerm	26.398	0.016	26.338