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: 2011-06-22 04:27:16 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 04:41:33 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 857.4 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) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.4.2’
* 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	35.476	0.549	58.761
OntologyTerm-class	0.025	0.000	0.026
getAccession	0.019	0.000	0.018
getAllTermChildren	6.523	0.057	6.684
getAllTermIds	21.454	0.118	22.007
getAllTermParents	0.097	0.000	0.104
getAllTerms	39.869	0.328	40.725
getEFO	20.275	0.105	20.558
getEFOBranchRootIds	8.214	0.049	8.762
getLabel	0.016	0.001	0.017
getOntology	68.675	0.481	70.081
getOntologyAccession	0.006	0.000	0.005
getOntologyDescription	0.006	0.001	0.006
getOntologyNoReasoning	74.582	0.464	77.039
getOntologyRelationNames	90.674	0.560	93.439
getRootIds	6.463	0.017	6.595
getRoots	6.442	0.018	6.510
getTermAndAllChildren	6.505	0.053	6.804
getTermById	0.018	0.000	0.018
getTermChildren	0.226	0.003	0.241
getTermDefinitions	0.035	0.000	0.036
getTermNameById	0.01	0.00	0.01
getTermParents	0.049	0.001	0.049
getTermRelationNames	82.728	0.532	85.228
getTermRelations	102.640	0.554	105.216
getTermSynonyms	0.091	0.001	0.092
hasTerm	0.009	0.000	0.009
isEFOBranchRoot	0.018	0.001	0.018
isRoot	6.468	0.028	6.532
ontoCAT-package	0.004	0.001	0.004
searchTerm	5.404	0.023	5.468
searchTermPrefix	5.461	0.021	5.557
showHierarchyDownToTerm	84.883	0.322	86.343
showPathsToTerm	77.802	0.318	80.127