BioC 3.2: CHECK report for ontoCAT on perceval

Package: ontoCAT

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.21.0.tar.gz

StartedAt: 2015-08-24 03:29:38 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:32:01 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 143.3 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 ontoCAT_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ontoCAT.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.21.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [148s/105s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          77.183  2.405  46.700
getEFO                  11.199  0.243   9.156
showHierarchyDownToTerm  8.392  0.188   8.103
getEFOBranchRootIds      6.599  0.136   5.366
getAllTerms              5.888  0.127   5.028
searchTerm               5.646  0.121   3.712
* 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
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-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	77.183	2.405	46.700
OntologyTerm-class	0.013	0.000	0.014
getAccession	0.007	0.001	0.008
getAllTermChildren	0.017	0.000	0.017
getAllTermIds	3.332	0.059	2.709
getAllTermParents	0.094	0.002	0.036
getAllTerms	5.888	0.127	5.028
getEFO	11.199	0.243	9.156
getEFOBranchRootIds	6.599	0.136	5.366
getLabel	0.009	0.000	0.009
getOntology	3.239	0.087	2.653
getOntologyAccession	0.003	0.000	0.003
getOntologyDescription	0.003	0.001	0.004
getRootIds	4.433	0.091	4.054
getRoots	4.070	0.086	3.906
getTermAndAllChildren	0.023	0.001	0.024
getTermById	0.011	0.000	0.011
getTermChildren	0.022	0.000	0.022
getTermDefinitions	0.018	0.000	0.019
getTermNameById	0.008	0.001	0.009
getTermParents	0.041	0.001	0.042
getTermSynonyms	0.059	0.001	0.056
hasTerm	0.006	0.000	0.006
isEFOBranchRoot	0.010	0.001	0.010
isRoot	4.055	0.087	3.933
ontoCAT-package	0.163	0.008	0.130
searchTerm	5.646	0.121	3.712
searchTermPrefix	4.068	0.080	3.569
showHierarchyDownToTerm	8.392	0.188	8.103
showPathsToTerm	3.986	0.082	3.857