BioC 2.14: CHECK report for ontoCAT on petty

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: 2014-10-07 23:18:16 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:30:36 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 739.2 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-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 ‘1.16.0’
* 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 ... [7s/8s] 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 ... [12m/11m] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations     385.537  7.208 379.043
getTermRelationNames 244.587  6.927 233.168
Ontology-class        86.557  1.901  48.571
getOntology            6.027  0.035   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 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	86.557	1.901	48.571
OntologyTerm-class	0.065	0.001	0.035
getAccession	0.017	0.001	0.017
getAllTermChildren	0.033	0.001	0.035
getAllTermIds	0.020	0.000	0.021
getAllTermParents	0.050	0.000	0.053
getAllTerms	0.019	0.000	0.019
getEFO	0.113	0.002	0.118
getEFOBranchRootIds	0.017	0.000	0.018
getLabel	0.015	0.001	0.016
getOntology	6.027	0.035	5.682
getOntologyAccession	0.008	0.000	0.009
getOntologyDescription	0.008	0.000	0.009
getOntologyNoReasoning	0.023	0.001	0.023
getOntologyRelationNames	0.018	0.000	0.019
getRootIds	0.022	0.000	0.022
getRoots	0.020	0.001	0.021
getTermAndAllChildren	0.033	0.000	0.033
getTermById	0.023	0.000	0.023
getTermChildren	0.030	0.001	0.031
getTermDefinitions	0.029	0.000	0.029
getTermNameById	0.012	0.000	0.013
getTermParents	0.040	0.000	0.041
getTermRelationNames	244.587	6.927	233.168
getTermRelations	385.537	7.208	379.043
getTermSynonyms	0.114	0.001	0.117
hasTerm	0.016	0.000	0.016
isEFOBranchRoot	0.023	0.000	0.024
isRoot	0.021	0.000	0.022
ontoCAT-package	0.005	0.001	0.005
searchTerm	0.032	0.000	0.033
searchTermPrefix	0.03	0.00	0.03
showHierarchyDownToTerm	0.026	0.000	0.027
showPathsToTerm	0.023	0.000	0.023