BioC 2.12: CHECK report for ontoCAT on petty

Package: ontoCAT

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.12.0.tar.gz

StartedAt: 2013-10-08 23:19:40 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:30:03 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 623.2 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ontoCAT.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ontoCAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ontoCAT' version '1.12.0'
* 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 ... [7s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [619s/545s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getTermRelations      277.626  6.732 271.304
getTermRelationNames  186.825  6.162 181.336
Ontology-class         94.590  1.940  49.614
getEFO                  9.357  0.107   9.308
getAllTermChildren      6.804  0.060   6.865
getTermAndAllChildren   6.697  0.063   6.814
getOntology             6.577  0.061   5.682
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ontoCAT.Rcheck/00check.log'
for details.

* installing *source* package 'ontoCAT' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	94.590	1.940	49.614
OntologyTerm-class	0.035	0.001	0.035
getAccession	0.026	0.000	0.027
getAllTermChildren	6.804	0.060	6.865
getAllTermIds	1.283	0.024	1.212
getAllTermParents	0.045	0.001	0.045
getAllTerms	1.308	0.024	1.213
getEFO	9.357	0.107	9.308
getEFOBranchRootIds	1.369	0.025	1.313
getLabel	0.024	0.001	0.025
getOntology	6.577	0.061	5.682
getOntologyAccession	0.018	0.001	0.019
getOntologyDescription	0.020	0.000	0.021
getOntologyNoReasoning	0.529	0.009	0.503
getOntologyRelationNames	0.576	0.008	0.495
getRootIds	0.495	0.006	0.496
getRoots	0.487	0.009	0.502
getTermAndAllChildren	6.697	0.063	6.814
getTermById	0.024	0.001	0.024
getTermChildren	0.296	0.006	0.305
getTermDefinitions	0.047	0.001	0.048
getTermNameById	0.018	0.001	0.019
getTermParents	0.047	0.001	0.047
getTermRelationNames	186.825	6.162	181.336
getTermRelations	277.626	6.732	271.304
getTermSynonyms	0.107	0.001	0.109
hasTerm	0.032	0.000	0.033
isEFOBranchRoot	0.036	0.001	0.037
isRoot	0.571	0.007	0.554
ontoCAT-package	0.014	0.000	0.015
searchTerm	1.388	0.024	1.339
searchTermPrefix	1.377	0.023	1.305
showHierarchyDownToTerm	1.135	0.023	0.968
showPathsToTerm	0.465	0.008	0.458