Package: ontoCAT

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.1.0.tar.gz

StartedAt: 2010-12-01 16:39:59 -0800 (Wed, 01 Dec 2010)

EndedAt: 2010-12-01 16:44:08 -0800 (Wed, 01 Dec 2010)

EllapsedTime: 248.9 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ontoCAT.Rcheck'
* using R version 2.13.0 Under development (unstable) (2010-11-28 r53696)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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	13.879	0.564	18.654
OntologyTerm-class	1.542	0.104	3.406
getAccession	1.569	0.116	2.604
getAllTermChildren	7.443	0.108	8.442
getAllTermIds	13.405	0.122	15.476
getAllTermParents	1.531	0.098	4.661
getAllTerms	24.058	0.262	26.009
getDefinitions	1.470	0.098	4.663
getEFOBranchRootIds	5.001	0.098	6.278
getEFOParser	6.578	0.176	7.499
getLabel	1.563	0.040	2.924
getOntologyAccession	1.603	0.046	2.610
getOntologyDescription	1.590	0.044	2.822
getOntologyParser	6.797	0.104	8.089
getRootIds	1.583	0.036	4.188
getRoots	1.643	0.088	2.480
getSynonyms	2.271	0.098	4.118
getTermAndAllChildrenIds	4.732	0.065	9.375
getTermById	1.668	0.037	7.906
getTermChildren	1.833	0.038	8.010
getTermNameById	1.734	0.038	6.258
getTermParents	2.348	0.065	7.820
getTreeDownTo	2.429	0.050	7.330
hasTerm	1.760	0.041	7.439
isEFOBranchRoot	1.698	0.037	5.486
isRoot	1.613	0.038	7.167
ontoCAT-package	1.629	0.039	7.815
searchTerm	3.830	0.078	7.760
searchTermPrefix	4.133	0.173	9.404