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: 2016-04-21 05:42:32 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:44:43 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 130.7 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 version 3.3.0 beta (2016-04-06 r70435)
* 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/6s] 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 ... [135s/99s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          71.513  0.977  43.451
showHierarchyDownToTerm  9.422  0.078   9.189
getEFO                   9.043  0.083   8.029
getAllTerms              5.909  0.086   4.705
getEFOBranchRootIds      5.086  0.047   4.612
* 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	71.513	0.977	43.451
OntologyTerm-class	0.012	0.000	0.012
getAccession	0.009	0.001	0.010
getAllTermChildren	0.036	0.001	0.021
getAllTermIds	2.688	0.022	2.156
getAllTermParents	0.03	0.00	0.03
getAllTerms	5.909	0.086	4.705
getEFO	9.043	0.083	8.029
getEFOBranchRootIds	5.086	0.047	4.612
getLabel	0.009	0.000	0.010
getOntology	3.033	0.030	2.482
getOntologyAccession	0.003	0.000	0.004
getOntologyDescription	0.003	0.001	0.003
getRootIds	4.695	0.041	4.345
getRoots	4.223	0.034	4.086
getTermAndAllChildren	0.015	0.000	0.015
getTermById	0.007	0.000	0.007
getTermChildren	0.015	0.001	0.015
getTermDefinitions	0.014	0.000	0.014
getTermNameById	0.003	0.000	0.003
getTermParents	0.018	0.001	0.019
getTermSynonyms	0.046	0.000	0.047
hasTerm	0.005	0.000	0.006
isEFOBranchRoot	0.007	0.000	0.007
isRoot	4.263	0.035	4.166
ontoCAT-package	0.167	0.004	0.117
searchTerm	3.809	0.041	3.266
searchTermPrefix	4.734	0.039	3.395
showHierarchyDownToTerm	9.422	0.078	9.189
showPathsToTerm	4.128	0.035	4.011