Package: ontoCAT

Version: 1.4.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.4.0.tar.gz

StartedAt: 2011-05-09 13:31:55 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:37:53 -0700 (Mon, 09 May 2011)

EllapsedTime: 358.2 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ontoCAT.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.4.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 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 ...
*** tangling vignette sources ...
   ‘ontoCAT.Rnw’ 
** testing if installed package can be loaded

* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	31.054	0.716	83.072
OntologyTerm-class	0.024	0.000	0.025
getAccession	0.012	0.000	0.011
getAllTermChildren	5.244	0.056	5.374
getAllTermIds	14.781	0.104	15.014
getAllTermParents	0.080	0.000	0.081
getAllTerms	29.250	0.204	29.503
getEFO	7.952	0.060	8.146
getEFOBranchRootIds	1.820	0.004	1.830
getLabel	0.008	0.000	0.010
getOntology	4.737	0.228	33.261
getOntologyAccession	0.008	0.000	0.005
getOntologyDescription	0.004	0.004	0.006
getOntologyRelationNames	30.909	0.068	29.921
getRootIds	1.541	0.000	1.468
getRoots	1.448	0.000	1.439
getTermAndAllChildren	5.116	0.036	5.174
getTermById	0.016	0.000	0.016
getTermChildren	0.164	0.000	0.162
getTermDefinitions	0.024	0.004	0.029
getTermNameById	0.008	0.000	0.009
getTermParents	0.04	0.00	0.04
getTermRelationNames	29.286	0.028	29.070
getTermRelations	34.766	0.068	34.858
getTermSynonyms	0.060	0.000	0.059
hasTerm	0.008	0.000	0.006
isEFOBranchRoot	0.012	0.000	0.013
isRoot	1.428	0.000	1.416
ontoCAT-package	0.004	0.000	0.002
searchTerm	1.200	0.008	1.198
searchTermPrefix	1.236	0.000	1.221
showHierarchyDownToTerm	17.893	0.020	18.175
showPathsToTerm	17.085	0.060	17.495