Package: ontoCAT

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.4.2.tar.gz

StartedAt: 2011-07-07 04:46:22 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:01:27 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 905.5 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/ontoCAT.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* 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 '1.4.2'
* 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 sizes of PDF files under 'inst/doc' ... 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	36.522	0.587	58.533
OntologyTerm-class	0.028	0.000	0.030
getAccession	0.016	0.000	0.016
getAllTermChildren	6.793	0.067	7.163
getAllTermIds	24.196	0.133	24.806
getAllTermParents	0.102	0.001	0.103
getAllTerms	45.830	0.403	46.705
getEFO	21.206	0.120	21.648
getEFOBranchRootIds	8.319	0.047	8.436
getLabel	0.017	0.000	0.018
getOntology	71.591	0.543	73.067
getOntologyAccession	0.006	0.000	0.005
getOntologyDescription	0.005	0.000	0.006
getOntologyNoReasoning	78.713	0.583	81.357
getOntologyRelationNames	96.955	0.681	100.473
getRootIds	6.698	0.033	7.028
getRoots	6.734	0.048	7.325
getTermAndAllChildren	6.721	0.057	6.984
getTermById	0.020	0.000	0.021
getTermChildren	0.232	0.003	0.244
getTermDefinitions	0.034	0.000	0.035
getTermNameById	0.009	0.000	0.010
getTermParents	0.049	0.000	0.049
getTermRelationNames	86.395	0.549	89.249
getTermRelations	110.880	0.738	113.776
getTermSynonyms	0.090	0.001	0.092
hasTerm	0.010	0.000	0.011
isEFOBranchRoot	0.018	0.001	0.018
isRoot	6.715	0.031	6.837
ontoCAT-package	0.004	0.000	0.004
searchTerm	5.547	0.031	5.641
searchTermPrefix	5.623	0.029	5.986
showHierarchyDownToTerm	86.753	0.376	88.537
showPathsToTerm	80.356	0.405	83.097