BioC 3.2: CHECK report for ontoCAT on oaxaca

Package: ontoCAT

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.22.0.tar.gz

StartedAt: 2016-04-23 02:47:10 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:49:31 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 141.4 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ontoCAT.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.22.0’
* 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 ... [142s/110s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          73.975  1.003  48.475
showHierarchyDownToTerm  9.771  0.073   9.611
getEFO                   9.008  0.066   8.379
getAllTerms              5.701  0.062   5.123
getEFOBranchRootIds      5.231  0.040   4.866
getRootIds               5.139  0.040   4.814
isRoot                   4.993  0.032   4.935
searchTerm               4.975  0.041   3.739
* 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	73.975	1.003	48.475
OntologyTerm-class	0.012	0.001	0.012
getAccession	0.005	0.000	0.006
getAllTermChildren	0.021	0.000	0.021
getAllTermIds	3.025	0.018	2.530
getAllTermParents	0.050	0.001	0.027
getAllTerms	5.701	0.062	5.123
getEFO	9.008	0.066	8.379
getEFOBranchRootIds	5.231	0.040	4.866
getLabel	0.007	0.000	0.007
getOntology	3.451	0.033	2.927
getOntologyAccession	0.004	0.000	0.004
getOntologyDescription	0.004	0.000	0.004
getRootIds	5.139	0.040	4.814
getRoots	4.940	0.033	4.826
getTermAndAllChildren	0.033	0.001	0.034
getTermById	0.011	0.000	0.012
getTermChildren	0.024	0.000	0.024
getTermDefinitions	0.018	0.000	0.018
getTermNameById	0.007	0.000	0.007
getTermParents	0.030	0.001	0.031
getTermSynonyms	0.064	0.001	0.061
hasTerm	0.008	0.000	0.009
isEFOBranchRoot	0.008	0.000	0.008
isRoot	4.993	0.032	4.935
ontoCAT-package	0.142	0.002	0.118
searchTerm	4.975	0.041	3.739
searchTermPrefix	3.751	0.026	3.520
showHierarchyDownToTerm	9.771	0.073	9.611
showPathsToTerm	4.781	0.033	4.712