BioC 3.3: CHECK report for ontoCAT on linux2.bioconductor.org

Package: ontoCAT

Version: 1.23.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.23.0.tar.gz

StartedAt: 2015-10-27 06:27:53 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:29:36 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 103.3 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ontoCAT.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [102s/77s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          52.256  0.736  33.146
getEFO                   6.930  0.063   6.270
showHierarchyDownToTerm  6.492  0.020   6.372
getEFOBranchRootIds      5.856  0.020   3.636
* 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
  ‘/home/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	52.256	0.736	33.146
OntologyTerm-class	0.009	0.000	0.009
getAccession	0.005	0.000	0.005
getAllTermChildren	0.013	0.000	0.013
getAllTermIds	3.134	0.004	2.623
getAllTermParents	0.068	0.000	0.036
getAllTerms	4.419	0.004	4.084
getEFO	6.930	0.063	6.270
getEFOBranchRootIds	5.856	0.020	3.636
getLabel	0.005	0.000	0.005
getOntology	2.261	0.008	1.998
getOntologyAccession	0.003	0.000	0.004
getOntologyDescription	0.003	0.000	0.004
getRootIds	3.113	0.012	2.923
getRoots	3.875	0.016	3.853
getTermAndAllChildren	0.014	0.000	0.015
getTermById	0.007	0.000	0.006
getTermChildren	0.013	0.000	0.012
getTermDefinitions	0.012	0.000	0.012
getTermNameById	0.003	0.000	0.003
getTermParents	0.012	0.000	0.012
getTermSynonyms	0.026	0.004	0.030
hasTerm	0.004	0.000	0.003
isEFOBranchRoot	0.007	0.000	0.006
isRoot	3.229	0.020	3.134
ontoCAT-package	0.057	0.004	0.061
searchTerm	2.256	0.004	2.075
searchTermPrefix	3.370	0.000	3.141
showHierarchyDownToTerm	6.492	0.020	6.372
showPathsToTerm	3.159	0.008	3.110