Package: ontoCAT

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.9.0.tar.gz

StartedAt: 2012-06-21 02:14:10 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 02:35:01 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 1251.5 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ontoCAT.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.9.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from '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
** installing vignettes
   'ontoCAT.Rnw' 
** testing if installed package can be loaded

* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	39.890	0.575	59.889
OntologyTerm-class	0.025	0.000	0.025
getAccession	0.013	0.000	0.014
getAllTermChildren	5.920	0.060	6.046
getAllTermIds	23.265	0.141	23.824
getAllTermParents	0.094	0.001	0.096
getAllTerms	45.923	0.394	46.760
getEFO	20.912	0.103	21.142
getEFOBranchRootIds	9.124	0.028	9.196
getLabel	0.014	0.000	0.015
getOntology	101.777	0.930	109.394
getOntologyAccession	0.005	0.000	0.005
getOntologyDescription	0.006	0.001	0.007
getOntologyNoReasoning	123.454	1.024	135.199
getOntologyRelationNames	154.656	0.691	158.172
getRootIds	7.349	0.020	7.475
getRoots	7.348	0.022	7.462
getTermAndAllChildren	5.707	0.050	5.844
getTermById	0.016	0.000	0.017
getTermChildren	0.216	0.002	0.227
getTermDefinitions	0.027	0.000	0.027
getTermNameById	0.008	0.000	0.009
getTermParents	0.050	0.001	0.061
getTermRelationNames	156.541	0.739	158.629
getTermRelations	168.379	0.814	172.973
getTermSynonyms	0.076	0.001	0.078
hasTerm	0.008	0.000	0.008
isEFOBranchRoot	0.015	0.000	0.015
isRoot	7.322	0.023	7.408
ontoCAT-package	0.003	0.001	0.018
searchTerm	6.011	0.018	6.091
searchTermPrefix	6.094	0.022	6.254
showHierarchyDownToTerm	125.253	0.407	127.421
showPathsToTerm	117.590	0.414	120.603