Package: ontoCAT

Version: 1.6.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.6.0.tar.gz

StartedAt: 2012-03-24 01:47:51 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:55:54 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 483.2 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/ontoCAT.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘1.6.0’
* 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 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	34.242	0.552	48.187
OntologyTerm-class	0.024	0.000	0.023
getAccession	0.012	0.000	0.010
getAllTermChildren	4.340	0.028	4.398
getAllTermIds	16.569	0.020	16.628
getAllTermParents	0.064	0.000	0.065
getAllTerms	32.958	0.320	33.584
getEFO	7.661	0.036	7.795
getEFOBranchRootIds	2.040	0.004	2.079
getLabel	0.008	0.000	0.010
getOntology	45.047	0.056	45.368
getOntologyAccession	0.004	0.000	0.004
getOntologyDescription	0.004	0.000	0.004
getOntologyNoReasoning	47.811	0.100	48.574
getOntologyRelationNames	57.391	0.120	58.160
getRootIds	1.584	0.000	1.584
getRoots	1.620	0.000	1.589
getTermAndAllChildren	3.953	0.024	3.979
getTermById	0.012	0.000	0.011
getTermChildren	0.156	0.004	0.161
getTermDefinitions	0.020	0.000	0.021
getTermNameById	0.004	0.000	0.005
getTermParents	0.032	0.000	0.032
getTermRelationNames	57.155	0.080	57.430
getTermRelations	60.464	0.076	60.980
getTermSynonyms	0.052	0.000	0.052
hasTerm	0.012	0.000	0.011
isEFOBranchRoot	0.012	0.000	0.013
isRoot	1.540	0.000	1.547
ontoCAT-package	0.000	0.000	0.003
searchTerm	1.380	0.000	1.337
searchTermPrefix	1.352	0.004	1.358
showHierarchyDownToTerm	26.346	0.032	26.583
showPathsToTerm	25.605	0.024	26.139