Package: ontoCAT

Version: 1.4.2

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.4.2.tar.gz

StartedAt: 2011-10-20 13:46:37 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 13:52:10 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 332.6 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/ontoCAT.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘1.4.2’
* checking package namespace 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 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 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 ...
** testing if installed package can be loaded

* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	35.370	0.568	45.096
OntologyTerm-class	0.024	0.000	0.035
getAccession	0.012	0.000	0.022
getAllTermChildren	4.904	0.032	4.948
getAllTermIds	16.893	0.052	16.943
getAllTermParents	0.072	0.000	0.071
getAllTerms	33.730	0.196	34.055
getEFO	8.113	0.040	8.070
getEFOBranchRootIds	1.792	0.000	1.761
getLabel	0.012	0.000	0.011
getOntology	35.094	0.080	34.156
getOntologyAccession	0.004	0.000	0.004
getOntologyDescription	0.004	0.000	0.005
getOntologyRelationNames	33.346	0.036	34.083
getRootIds	1.404	0.000	1.415
getRoots	1.472	0.000	1.417
getTermAndAllChildren	4.873	0.032	4.908
getTermById	0.012	0.000	0.012
getTermChildren	0.172	0.000	0.174
getTermDefinitions	0.024	0.000	0.026
getTermNameById	0.008	0.000	0.007
getTermParents	0.036	0.000	0.035
getTermRelationNames	33.818	0.028	34.181
getTermRelations	33.694	0.044	34.373
getTermSynonyms	0.056	0.000	0.057
hasTerm	0.004	0.000	0.006
isEFOBranchRoot	0.016	0.000	0.013
isRoot	1.360	0.000	1.353
ontoCAT-package	0.004	0.000	0.003
searchTerm	1.220	0.004	1.192
searchTermPrefix	1.236	0.004	1.227
showHierarchyDownToTerm	17.661	0.032	18.016
showPathsToTerm	16.253	0.012	16.285