BioC 2.11: CHECK report for ontoCAT on perceval

Package: ontoCAT

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.10.0.tar.gz

StartedAt: 2013-03-25 00:41:07 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:47:43 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 396.5 seconds

RetCode: 0

Status: OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ontoCAT.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.10.0'
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getTermRelations        144.005  0.701 146.686
getTermRelationNames     96.531  0.582  99.384
Ontology-class           30.204  0.553  32.285
showHierarchyDownToTerm  14.576  0.061  14.758
showPathsToTerm          13.161  0.041  13.283
getEFO                    9.661  0.074   9.784
* 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	30.204	0.553	32.285
OntologyTerm-class	0.022	0.001	0.023
getAccession	0.010	0.000	0.011
getAllTermChildren	4.316	0.043	4.366
getAllTermIds	2.511	0.011	2.524
getAllTermParents	0.065	0.001	0.065
getAllTerms	2.483	0.011	2.496
getEFO	9.661	0.074	9.784
getEFOBranchRootIds	2.500	0.011	2.528
getLabel	0.012	0.000	0.013
getOntology	4.510	0.028	4.549
getOntologyAccession	0.003	0.000	0.004
getOntologyDescription	0.004	0.000	0.005
getOntologyNoReasoning	1.099	0.003	1.104
getOntologyRelationNames	1.118	0.004	1.134
getRootIds	1.120	0.003	1.156
getRoots	1.111	0.003	1.117
getTermAndAllChildren	4.363	0.045	4.519
getTermById	0.015	0.001	0.016
getTermChildren	0.165	0.002	0.172
getTermDefinitions	0.023	0.000	0.024
getTermNameById	0.008	0.001	0.009
getTermParents	0.038	0.001	0.044
getTermRelationNames	96.531	0.582	99.384
getTermRelations	144.005	0.701	146.686
getTermSynonyms	0.065	0.001	0.067
hasTerm	0.007	0.001	0.007
isEFOBranchRoot	0.013	0.000	0.013
isRoot	1.140	0.006	1.154
ontoCAT-package	0.002	0.001	0.003
searchTerm	2.520	0.010	2.547
searchTermPrefix	2.522	0.010	2.553
showHierarchyDownToTerm	14.576	0.061	14.758
showPathsToTerm	13.161	0.041	13.283

Summary

Command output