Package: ontoCAT

Version: 1.4.2

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.4.2.tar.gz

StartedAt: 2011-07-07 01:40:25 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:46:45 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 379.9 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 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘1.4.2’
* 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 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	32.726	0.600	45.639
OntologyTerm-class	0.020	0.000	0.022
getAccession	0.012	0.000	0.010
getAllTermChildren	4.876	0.020	4.875
getAllTermIds	16.629	0.144	16.894
getAllTermParents	0.068	0.004	0.072
getAllTerms	33.858	0.232	34.188
getEFO	7.953	0.080	8.032
getEFOBranchRootIds	1.744	0.016	1.792
getLabel	0.008	0.000	0.010
getOntology	36.214	0.056	35.370
getOntologyAccession	0.004	0.000	0.004
getOntologyDescription	0.004	0.000	0.005
getOntologyNoReasoning	33.414	0.048	33.968
getOntologyRelationNames	37.254	0.048	37.228
getRootIds	1.408	0.000	1.374
getRoots	1.377	0.004	1.387
getTermAndAllChildren	4.800	0.024	4.836
getTermById	0.012	0.000	0.011
getTermChildren	0.148	0.000	0.147
getTermDefinitions	0.020	0.000	0.022
getTermNameById	0.004	0.000	0.005
getTermParents	0.032	0.000	0.031
getTermRelationNames	34.062	0.044	34.058
getTermRelations	41.727	0.036	42.274
getTermSynonyms	0.064	0.000	0.064
hasTerm	0.008	0.000	0.007
isEFOBranchRoot	0.012	0.000	0.012
isRoot	1.320	0.000	1.317
ontoCAT-package	0.000	0.000	0.003
searchTerm	1.200	0.004	1.154
searchTermPrefix	1.192	0.000	1.189
showHierarchyDownToTerm	17.237	0.000	17.222
showPathsToTerm	15.937	0.016	15.963