BioC 2.14: CHECK report for ontoCAT on morelia

Package: ontoCAT

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.16.0.tar.gz

StartedAt: 2014-10-08 00:27:27 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:34:10 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 402.6 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ontoCAT.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.16.0’
* 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 ... [4s/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 files in ‘vignettes’ ... OK
* checking examples ... [402s/358s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations     207.786  2.605 200.868
getTermRelationNames 129.226  2.321 120.566
Ontology-class        53.445  0.846  31.025
* 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	53.445	0.846	31.025
OntologyTerm-class	0.018	0.000	0.018
getAccession	0.011	0.001	0.012
getAllTermChildren	0.026	0.000	0.026
getAllTermIds	0.012	0.001	0.012
getAllTermParents	0.033	0.000	0.032
getAllTerms	0.012	0.000	0.012
getEFO	0.068	0.001	0.069
getEFOBranchRootIds	0.013	0.000	0.013
getLabel	0.01	0.00	0.01
getOntology	3.594	0.014	3.352
getOntologyAccession	0.006	0.000	0.006
getOntologyDescription	0.006	0.000	0.007
getOntologyNoReasoning	0.018	0.000	0.017
getOntologyRelationNames	0.011	0.001	0.010
getRootIds	0.012	0.000	0.012
getRoots	0.012	0.000	0.012
getTermAndAllChildren	0.018	0.001	0.018
getTermById	0.009	0.000	0.009
getTermChildren	0.023	0.000	0.023
getTermDefinitions	0.017	0.001	0.017
getTermNameById	0.006	0.000	0.006
getTermParents	0.024	0.000	0.024
getTermRelationNames	129.226	2.321	120.566
getTermRelations	207.786	2.605	200.868
getTermSynonyms	0.059	0.000	0.060
hasTerm	0.008	0.000	0.009
isEFOBranchRoot	0.013	0.000	0.013
isRoot	0.015	0.000	0.015
ontoCAT-package	0.003	0.000	0.003
searchTerm	0.009	0.000	0.010
searchTermPrefix	0.014	0.000	0.015
showHierarchyDownToTerm	0.017	0.000	0.017
showPathsToTerm	0.011	0.001	0.011