BioC 3.5: CHECK report for ontoCAT on oaxaca

Package: ontoCAT

Version: 1.27.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.27.0.tar.gz

StartedAt: 2017-03-04 06:38:26 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 06:40:43 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 137.6 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_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ontoCAT.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.27.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          74.231  1.279  50.435
getEFO                   8.889  0.029   8.041
showHierarchyDownToTerm  7.861  0.031   7.767
getAllTerms              6.099  0.058   3.897
getRootIds               5.289  0.023   4.298
getEFOBranchRootIds      5.004  0.016   4.715
* 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-3.5-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	74.231	1.279	50.435
OntologyTerm-class	0.011	0.001	0.011
getAccession	0.087	0.000	0.046
getAllTermChildren	0.032	0.001	0.016
getAllTermIds	3.291	0.037	1.892
getAllTermParents	0.025	0.000	0.025
getAllTerms	6.099	0.058	3.897
getEFO	8.889	0.029	8.041
getEFOBranchRootIds	5.004	0.016	4.715
getLabel	0.008	0.001	0.009
getOntology	3.02	0.02	2.07
getOntologyAccession	0.005	0.000	0.003
getOntologyDescription	0.002	0.000	0.002
getRootIds	5.289	0.023	4.298
getRoots	4.392	0.014	4.250
getTermAndAllChildren	0.019	0.001	0.018
getTermById	0.013	0.000	0.012
getTermChildren	0.017	0.000	0.017
getTermDefinitions	0.015	0.001	0.015
getTermNameById	0.005	0.000	0.004
getTermParents	0.018	0.000	0.017
getTermSynonyms	0.042	0.000	0.041
hasTerm	0.005	0.000	0.004
isEFOBranchRoot	0.006	0.001	0.007
isRoot	4.524	0.011	4.452
ontoCAT-package	0.265	0.003	0.101
searchTerm	4.312	0.024	3.073
searchTermPrefix	3.332	0.011	3.045
showHierarchyDownToTerm	7.861	0.031	7.767
showPathsToTerm	4.019	0.011	3.992