Package: ontoCAT

Version: 1.11.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.11.0.tar.gz

StartedAt: 2013-01-16 04:53:09 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:00:40 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 450.6 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/ontoCAT.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.11.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ontoCAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getAllTerms              74.900  0.532  75.358
Ontology-class           40.974  0.520  39.913
getAllTermIds            36.711  0.144  36.774
getOntology              36.003  0.112  34.617
getOntologyRelationNames 34.383  0.064  34.344
showHierarchyDownToTerm  31.930  0.016  31.896
getOntologyNoReasoning   30.513  0.108  30.023
getTermRelationNames     30.158  0.056  30.095
getTermRelations         29.558  0.100  29.574
showPathsToTerm          29.454  0.024  29.479
getEFO                   10.785  0.036  10.669
* 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	40.974	0.520	39.913
OntologyTerm-class	0.036	0.000	0.036
getAccession	0.02	0.00	0.02
getAllTermChildren	4.892	0.020	4.925
getAllTermIds	36.711	0.144	36.774
getAllTermParents	0.092	0.000	0.094
getAllTerms	74.900	0.532	75.358
getEFO	10.785	0.036	10.669
getEFOBranchRootIds	3.372	0.004	3.371
getLabel	0.024	0.000	0.025
getOntology	36.003	0.112	34.617
getOntologyAccession	0.012	0.000	0.011
getOntologyDescription	0.012	0.000	0.013
getOntologyNoReasoning	30.513	0.108	30.023
getOntologyRelationNames	34.383	0.064	34.344
getRootIds	2.524	0.000	2.524
getRoots	2.524	0.000	2.519
getTermAndAllChildren	4.236	0.032	4.266
getTermById	0.024	0.004	0.028
getTermChildren	0.208	0.000	0.209
getTermDefinitions	0.040	0.000	0.037
getTermNameById	0.012	0.000	0.013
getTermParents	0.036	0.000	0.035
getTermRelationNames	30.158	0.056	30.095
getTermRelations	29.558	0.100	29.574
getTermSynonyms	0.060	0.000	0.056
hasTerm	0.016	0.000	0.013
isEFOBranchRoot	0.016	0.000	0.017
isRoot	2.500	0.000	2.497
ontoCAT-package	0.012	0.000	0.010
searchTerm	2.236	0.000	2.219
searchTermPrefix	2.340	0.000	2.328
showHierarchyDownToTerm	31.930	0.016	31.896
showPathsToTerm	29.454	0.024	29.479