Package: ontoCAT

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.4.2.tar.gz

StartedAt: 2011-10-20 16:21:29 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 16:34:19 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 769.8 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/ontoCAT.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ontoCAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ontoCAT' version '1.4.2'
* checking package namespace 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 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 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 ...
** testing if installed package can be loaded

* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	36.366	0.560	58.467
OntologyTerm-class	0.028	0.000	0.038
getAccession	0.016	0.000	0.016
getAllTermChildren	6.687	0.057	6.967
getAllTermIds	24.094	0.119	24.562
getAllTermParents	0.101	0.001	0.101
getAllTerms	45.840	0.345	46.499
getEFO	20.765	0.108	21.479
getEFOBranchRootIds	8.339	0.027	8.507
getLabel	0.015	0.001	0.016
getOntology	70.953	0.478	72.307
getOntologyAccession	0.006	0.001	0.005
getOntologyDescription	0.006	0.000	0.006
getOntologyRelationNames	79.538	0.541	82.618
getRootIds	6.701	0.027	6.969
getRoots	6.690	0.026	6.998
getTermAndAllChildren	6.673	0.054	7.034
getTermById	0.021	0.000	0.036
getTermChildren	0.271	0.004	0.307
getTermDefinitions	0.034	0.000	0.034
getTermNameById	0.01	0.00	0.01
getTermParents	0.048	0.001	0.049
getTermRelationNames	81.810	0.472	83.685
getTermRelations	88.308	0.475	89.450
getTermSynonyms	0.088	0.000	0.088
hasTerm	0.012	0.000	0.012
isEFOBranchRoot	0.018	0.000	0.018
isRoot	6.745	0.014	6.763
ontoCAT-package	0.004	0.001	0.004
searchTerm	5.590	0.017	5.616
searchTermPrefix	5.662	0.021	5.705
showHierarchyDownToTerm	86.485	0.289	88.818
showPathsToTerm	80.004	0.316	82.540