BioC 2.13: CHECK report for ontoCAT on perceval

Package: ontoCAT

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.14.0.tar.gz

StartedAt: 2014-04-05 03:07:00 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:14:29 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 449.1 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ontoCAT.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.14.0’
* 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/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ontoCAT.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [437s/397s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations     207.901  7.212 211.244
getTermRelationNames 151.408  6.638 144.443
Ontology-class        54.660  1.935  34.146
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	54.660	1.935	34.146
OntologyTerm-class	0.028	0.001	0.029
getAccession	0.020	0.000	0.021
getAllTermChildren	0.033	0.001	0.036
getAllTermIds	0.019	0.001	0.019
getAllTermParents	0.038	0.000	0.039
getAllTerms	0.021	0.001	0.023
getEFO	0.100	0.002	0.107
getEFOBranchRootIds	0.017	0.000	0.018
getLabel	0.019	0.000	0.019
getOntology	3.930	0.064	3.543
getOntologyAccession	0.015	0.001	0.017
getOntologyDescription	0.015	0.000	0.016
getOntologyNoReasoning	0.027	0.001	0.030
getOntologyRelationNames	0.029	0.001	0.031
getRootIds	0.110	0.002	0.116
getRoots	0.016	0.000	0.017
getTermAndAllChildren	0.024	0.000	0.024
getTermById	0.017	0.000	0.017
getTermChildren	0.023	0.000	0.024
getTermDefinitions	0.025	0.000	0.025
getTermNameById	0.01	0.00	0.01
getTermParents	0.030	0.001	0.031
getTermRelationNames	151.408	6.638	144.443
getTermRelations	207.901	7.212	211.244
getTermSynonyms	0.064	0.004	0.071
hasTerm	0.014	0.000	0.014
isEFOBranchRoot	0.019	0.000	0.019
isRoot	0.019	0.000	0.020
ontoCAT-package	0.082	0.001	0.092
searchTerm	0.017	0.000	0.017
searchTermPrefix	0.019	0.000	0.022
showHierarchyDownToTerm	0.021	0.000	0.024
showPathsToTerm	0.014	0.000	0.015