Package: ontoCAT

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.4.0.tar.gz

StartedAt: 2011-05-09 16:03:49 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 16:15:47 -0700 (Mon, 09 May 2011)

EllapsedTime: 717.7 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) (2011-04-24 r55634)
* 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 ‘1.4.0’
* 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 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	35.924	0.812	92.204
OntologyTerm-class	0.029	0.000	0.030
getAccession	0.016	0.000	0.016
getAllTermChildren	6.736	0.067	7.070
getAllTermIds	21.238	0.111	22.476
getAllTermParents	0.097	0.000	0.098
getAllTerms	39.581	0.307	40.598
getEFO	20.065	0.090	20.315
getEFOBranchRootIds	8.117	0.025	8.212
getLabel	0.017	0.000	0.017
getOntology	6.143	0.266	38.126
getOntologyAccession	0.006	0.000	0.005
getOntologyDescription	0.006	0.000	0.006
getOntologyRelationNames	65.224	0.475	67.587
getRootIds	6.489	0.022	6.552
getRoots	6.526	0.030	6.966
getTermAndAllChildren	6.655	0.051	6.800
getTermById	0.026	0.001	0.028
getTermChildren	0.230	0.002	0.237
getTermDefinitions	0.033	0.000	0.033
getTermNameById	0.009	0.001	0.009
getTermParents	0.048	0.000	0.049
getTermRelationNames	65.283	0.393	66.996
getTermRelations	84.127	0.494	86.036
getTermSynonyms	0.091	0.000	0.092
hasTerm	0.012	0.001	0.013
isEFOBranchRoot	0.021	0.000	0.021
isRoot	6.497	0.019	6.546
ontoCAT-package	0.004	0.000	0.004
searchTerm	5.428	0.020	5.505
searchTermPrefix	5.508	0.020	5.619
showHierarchyDownToTerm	84.258	0.250	85.425
showPathsToTerm	77.704	0.363	80.266