BioC 3.1: CHECK report for ontoCAT on petty

Package: ontoCAT

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.20.0.tar.gz

StartedAt: 2015-10-09 00:54:23 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:57:38 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 194.2 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_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ontoCAT.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.20.0’
* 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 ... [5s/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 ... [208s/142s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
Ontology-class          109.368  2.447  61.535
getEFO                   15.214  0.303  11.926
showHierarchyDownToTerm  12.635  0.255  11.964
getEFOBranchRootIds       8.655  0.157   6.686
getAllTerms               8.182  0.107   7.656
getRootIds                6.604  0.132   5.621
isRoot                    6.457  0.127   6.135
searchTerm                6.219  0.126   4.592
showPathsToTerm           6.100  0.116   5.797
getRoots                  5.848  0.107   5.528
searchTermPrefix          5.839  0.088   4.808
getOntology               5.207  0.065   3.503
* 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-3.1-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	109.368	2.447	61.535
OntologyTerm-class	0.019	0.001	0.019
getAccession	0.014	0.000	0.014
getAllTermChildren	0.027	0.000	0.026
getAllTermIds	4.796	0.057	3.779
getAllTermParents	0.056	0.001	0.057
getAllTerms	8.182	0.107	7.656
getEFO	15.214	0.303	11.926
getEFOBranchRootIds	8.655	0.157	6.686
getLabel	0.010	0.000	0.011
getOntology	5.207	0.065	3.503
getOntologyAccession	0.012	0.001	0.007
getOntologyDescription	0.011	0.000	0.006
getRootIds	6.604	0.132	5.621
getRoots	5.848	0.107	5.528
getTermAndAllChildren	0.037	0.001	0.037
getTermById	0.015	0.000	0.015
getTermChildren	0.033	0.000	0.033
getTermDefinitions	0.029	0.001	0.029
getTermNameById	0.006	0.000	0.006
getTermParents	0.028	0.001	0.027
getTermSynonyms	0.066	0.002	0.061
hasTerm	0.007	0.000	0.008
isEFOBranchRoot	0.013	0.000	0.014
isRoot	6.457	0.127	6.135
ontoCAT-package	0.212	0.005	0.157
searchTerm	6.219	0.126	4.592
searchTermPrefix	5.839	0.088	4.808
showHierarchyDownToTerm	12.635	0.255	11.964
showPathsToTerm	6.100	0.116	5.797