BioC 2.13: CHECK report for ontoCAT on zin1

Package: ontoCAT

Version: 1.14.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.14.0.tar.gz

StartedAt: 2014-04-05 02:49:01 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:53:34 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 273.6 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ontoCAT.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.14.0’
* 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 ... [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 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 ... [267s/245s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations     132.860  0.100 127.803
getTermRelationNames  93.578  0.112  88.956
Ontology-class        34.866  0.332  23.683
* 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
  ‘/home/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	34.866	0.332	23.683
OntologyTerm-class	0.016	0.000	0.018
getAccession	0.012	0.000	0.011
getAllTermChildren	0.024	0.000	0.022
getAllTermIds	0.016	0.000	0.014
getAllTermParents	0.024	0.000	0.024
getAllTerms	0.012	0.000	0.014
getEFO	0.06	0.00	0.06
getEFOBranchRootIds	0.012	0.000	0.040
getLabel	0.012	0.000	0.011
getOntology	3.408	0.016	2.731
getOntologyAccession	0.008	0.000	0.007
getOntologyDescription	0.008	0.000	0.008
getOntologyNoReasoning	0.016	0.000	0.016
getOntologyRelationNames	0.016	0.000	0.017
getRootIds	0.016	0.000	0.014
getRoots	0.012	0.000	0.013
getTermAndAllChildren	0.016	0.000	0.018
getTermById	0.012	0.000	0.012
getTermChildren	0.016	0.000	0.018
getTermDefinitions	0.020	0.000	0.021
getTermNameById	0.008	0.000	0.008
getTermParents	0.024	0.000	0.024
getTermRelationNames	93.578	0.112	88.956
getTermRelations	132.860	0.100	127.803
getTermSynonyms	0.048	0.000	0.048
hasTerm	0.044	0.000	0.045
isEFOBranchRoot	0.016	0.000	0.014
isRoot	0.016	0.000	0.014
ontoCAT-package	0.004	0.000	0.006
searchTerm	0.016	0.000	0.014
searchTermPrefix	0.016	0.000	0.013
showHierarchyDownToTerm	0.016	0.000	0.018
showPathsToTerm	0.012	0.000	0.012