BioC 2.12: CHECK report for ontoCAT on petty

Package: ontoCAT

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.11.0.tar.gz

StartedAt: 2013-03-25 03:51:59 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:00:05 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 485.8 seconds

RetCode: 0

Status: OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ontoCAT.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.11.0'
* 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 ... [5s/5s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [431s/432s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getTermRelations        186.211  0.395 186.446
getTermRelationNames    116.116  0.378 116.284
Ontology-class           32.200  0.427  34.183
showHierarchyDownToTerm  19.845  0.027  19.867
showPathsToTerm          18.282  0.025  18.305
getEFO                   12.917  0.050  12.972
getAllTermChildren        5.907  0.047   5.969
* 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	32.200	0.427	34.183
OntologyTerm-class	0.027	0.007	0.035
getAccession	0.017	0.006	0.023
getAllTermChildren	5.907	0.047	5.969
getAllTermIds	4.120	0.011	4.131
getAllTermParents	0.102	0.007	0.110
getAllTerms	3.013	0.009	3.023
getEFO	12.917	0.050	12.972
getEFOBranchRootIds	2.745	0.010	2.756
getLabel	0.019	0.005	0.025
getOntology	4.737	0.024	4.763
getOntologyAccession	0.013	0.005	0.018
getOntologyDescription	0.013	0.006	0.019
getOntologyNoReasoning	1.555	0.009	1.564
getOntologyRelationNames	1.565	0.008	1.574
getRootIds	1.452	0.007	1.459
getRoots	1.654	0.007	1.662
getTermAndAllChildren	4.865	0.039	4.903
getTermById	0.030	0.006	0.037
getTermChildren	0.264	0.010	0.273
getTermDefinitions	0.048	0.008	0.056
getTermNameById	0.026	0.008	0.033
getTermParents	0.065	0.008	0.075
getTermRelationNames	116.116	0.378	116.284
getTermRelations	186.211	0.395	186.446
getTermSynonyms	0.071	0.007	0.078
hasTerm	0.025	0.008	0.033
isEFOBranchRoot	0.039	0.008	0.047
isRoot	1.697	0.011	1.708
ontoCAT-package	0.014	0.009	0.022
searchTerm	3.229	0.014	3.251
searchTermPrefix	3.253	0.010	3.264
showHierarchyDownToTerm	19.845	0.027	19.867
showPathsToTerm	18.282	0.025	18.305

Summary

Command output