Package: ontoCAT

Version: 1.1.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.1.0.tar.gz

StartedAt: 2010-12-01 19:43:56 -0800 (Wed, 01 Dec 2010)

EndedAt: 2010-12-01 19:46:33 -0800 (Wed, 01 Dec 2010)

EllapsedTime: 156.7 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 2.13.0 Under development (unstable) (2010-11-28 r53696)
* 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 ‘1.1.0’
* 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 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 package vignettes in ‘inst/doc’ ... 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
OntologyParser-class	14.808	0.332	13.117
OntologyTerm-class	1.213	0.012	2.414
getAccession	1.780	0.044	2.651
getAllTermChildren	5.460	0.064	7.392
getAllTermIds	11.013	0.068	13.061
getAllTermParents	0.896	0.020	4.282
getAllTerms	20.625	0.188	21.815
getDefinitions	0.904	0.012	3.547
getEFOBranchRootIds	2.204	0.060	3.416
getEFOParser	3.528	0.044	4.943
getLabel	0.897	0.004	2.409
getOntologyAccession	0.892	0.008	2.448
getOntologyDescription	0.912	0.004	2.360
getOntologyParser	5.952	0.036	6.750
getRootIds	1.052	0.004	2.539
getRoots	1.308	0.072	2.716
getSynonyms	1.900	0.016	3.025
getTermAndAllChildrenIds	3.156	0.016	5.843
getTermById	0.893	0.000	2.354
getTermChildren	1.404	0.012	2.558
getTermNameById	1.940	0.000	3.126
getTermParents	0.892	0.008	2.416
getTreeDownTo	1.500	0.024	2.772
hasTerm	1.036	0.012	2.411
isEFOBranchRoot	1.060	0.008	4.356
isRoot	2.256	0.016	3.497
ontoCAT-package	0.960	0.036	2.445
searchTerm	1.472	0.028	2.859
searchTermPrefix	1.964	0.008	3.406