BioC 2.14: CHECK report for ontoCAT on zin2

Package: ontoCAT

Version: 1.16.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.16.0.tar.gz

StartedAt: 2014-10-08 01:33:14 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:38:46 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 331.4 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ontoCAT.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ... [3s/3s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [322s/303s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations     168.931  0.256 165.630
getTermRelationNames 110.083  0.204 106.884
Ontology-class        37.966  0.252  26.084
* 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
  ‘/home/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	37.966	0.252	26.084
OntologyTerm-class	0.016	0.000	0.013
getAccession	0.008	0.000	0.008
getAllTermChildren	0.016	0.000	0.016
getAllTermIds	0.008	0.000	0.009
getAllTermParents	0.02	0.00	0.02
getAllTerms	0.016	0.000	0.013
getEFO	0.052	0.004	0.055
getEFOBranchRootIds	0.008	0.000	0.009
getLabel	0.012	0.000	0.010
getOntology	3.112	0.000	2.813
getOntologyAccession	0.004	0.000	0.004
getOntologyDescription	0.000	0.004	0.005
getOntologyNoReasoning	0.012	0.000	0.011
getOntologyRelationNames	0.012	0.000	0.013
getRootIds	0.008	0.000	0.011
getRoots	0.008	0.000	0.011
getTermAndAllChildren	0.02	0.00	0.02
getTermById	0.012	0.000	0.011
getTermChildren	0.016	0.000	0.017
getTermDefinitions	0.020	0.000	0.022
getTermNameById	0.004	0.000	0.006
getTermParents	0.024	0.000	0.023
getTermRelationNames	110.083	0.204	106.884
getTermRelations	168.931	0.256	165.630
getTermSynonyms	0.052	0.000	0.054
hasTerm	0.004	0.000	0.005
isEFOBranchRoot	0.008	0.000	0.015
isRoot	0.012	0.000	0.012
ontoCAT-package	0.004	0.000	0.003
searchTerm	0.012	0.000	0.012
searchTermPrefix	0.012	0.000	0.012
showHierarchyDownToTerm	0.012	0.000	0.012
showPathsToTerm	0.012	0.000	0.013