Package: ontoCAT

Version: 1.0.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.0.0.tar.gz

StartedAt: 2010-12-02 07:49:44 -0800 (Thu, 02 Dec 2010)

EndedAt: 2010-12-02 07:52:34 -0800 (Thu, 02 Dec 2010)

EllapsedTime: 169.7 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/ontoCAT.Rcheck’
* using R version 2.12.0 Patched (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 ‘1.0.0’
* 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	14.640	0.340	15.178
OntologyTerm-class	1.281	0.012	3.655
getAccession	1.796	0.052	2.747
getAllTermChildren	5.452	0.092	6.950
getAllTermIds	11.689	0.040	13.801
getAllTermParents	0.896	0.016	3.034
getAllTerms	21.937	0.188	25.551
getDefinitions	0.892	0.016	2.936
getEFOBranchRootIds	3.056	0.076	4.163
getEFOParser	3.113	0.048	4.566
getLabel	0.812	0.016	2.439
getOntologyAccession	1.232	0.024	3.700
getOntologyDescription	2.216	0.020	3.392
getOntologyParser	4.868	0.052	5.814
getRootIds	1.180	0.064	2.465
getRoots	1.140	0.036	2.508
getSynonyms	1.940	0.024	4.551
getTermAndAllChildrenIds	2.945	0.024	5.395
getTermById	1.088	0.000	2.526
getTermChildren	1.376	0.008	3.606
getTermNameById	1.716	0.004	3.831
getTermParents	1.004	0.000	2.629
getTreeDownTo	1.560	0.012	3.010
hasTerm	0.876	0.000	2.385
isEFOBranchRoot	1.140	0.012	2.738
isRoot	0.980	0.012	2.412
ontoCAT-package	2.012	0.016	3.683
searchTerm	1.396	0.060	3.191
searchTermPrefix	1.993	0.012	3.385