BioC 3.3: CHECK report for ontoCAT on morelia

Package: ontoCAT

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.23.0.tar.gz

StartedAt: 2015-10-22 09:13:39 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 09:15:23 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 104.8 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_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ontoCAT.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.23.0’
* 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 ... [2s/2s] 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 ... [106s/74s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          58.420  0.880  33.738
getEFO                   6.922  0.096   5.842
showHierarchyDownToTerm  6.105  0.057   5.915
* 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-3.3-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	58.420	0.880	33.738
OntologyTerm-class	0.011	0.001	0.011
getAccession	0.005	0.000	0.005
getAllTermChildren	0.012	0.000	0.013
getAllTermIds	2.355	0.011	2.013
getAllTermParents	0.026	0.000	0.027
getAllTerms	4.215	0.050	3.705
getEFO	6.922	0.096	5.842
getEFOBranchRootIds	3.911	0.055	3.449
getLabel	0.005	0.001	0.005
getOntology	2.759	0.043	1.818
getOntologyAccession	0.003	0.000	0.003
getOntologyDescription	0.002	0.000	0.002
getRootIds	3.241	0.039	2.875
getRoots	3.275	0.038	3.100
getTermAndAllChildren	0.017	0.000	0.017
getTermById	0.006	0.000	0.006
getTermChildren	0.015	0.000	0.016
getTermDefinitions	0.014	0.000	0.014
getTermNameById	0.003	0.000	0.003
getTermParents	0.014	0.000	0.014
getTermSynonyms	0.034	0.001	0.035
hasTerm	0.01	0.00	0.01
isEFOBranchRoot	0.006	0.000	0.007
isRoot	2.943	0.026	2.846
ontoCAT-package	0.091	0.003	0.080
searchTerm	3.446	0.037	2.395
searchTermPrefix	2.549	0.021	2.269
showHierarchyDownToTerm	6.105	0.057	5.915
showPathsToTerm	3.034	0.026	2.950