BioC 2.12: CHECK report for ontoCAT on pelham

Package: ontoCAT

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.11.0.tar.gz

StartedAt: 2013-03-24 08:19:36 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:25:26 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 350.2 seconds

RetCode: 0

Status: OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ontoCAT.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ontoCAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ontoCAT' version '1.11.0'
* 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 ... [6s/7s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 examples ... [321s/290s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getTermRelations        113.794  1.886 111.808
getTermRelationNames     92.557  2.473  90.758
Ontology-class           60.792  1.907  40.643
getEFO                    7.567  0.112   7.560
showHierarchyDownToTerm   6.358  0.082   6.339
showPathsToTerm           5.875  0.056   5.910
getTermAndAllChildren     5.309  0.075   5.392
getAllTermChildren        5.268  0.083   5.351
getOntology               4.948  0.056   4.572
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
   'ontoCAT.Rnw' 
** testing if installed package can be loaded
* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	60.792	1.907	40.643
OntologyTerm-class	0.034	0.003	0.038
getAccession	0.021	0.001	0.021
getAllTermChildren	5.268	0.083	5.351
getAllTermIds	1.122	0.018	1.100
getAllTermParents	0.082	0.002	0.085
getAllTerms	1.156	0.021	1.115
getEFO	7.567	0.112	7.560
getEFOBranchRootIds	1.110	0.020	1.076
getLabel	0.027	0.002	0.030
getOntology	4.948	0.056	4.572
getOntologyAccession	0.016	0.002	0.019
getOntologyDescription	0.018	0.002	0.019
getOntologyNoReasoning	0.624	0.012	0.595
getOntologyRelationNames	0.537	0.013	0.541
getRootIds	0.591	0.012	0.600
getRoots	0.527	0.009	0.530
getTermAndAllChildren	5.309	0.075	5.392
getTermById	0.025	0.001	0.027
getTermChildren	0.211	0.003	0.214
getTermDefinitions	0.039	0.002	0.040
getTermNameById	0.015	0.001	0.016
getTermParents	0.043	0.002	0.044
getTermRelationNames	92.557	2.473	90.758
getTermRelations	113.794	1.886	111.808
getTermSynonyms	0.139	0.002	0.142
hasTerm	0.014	0.002	0.017
isEFOBranchRoot	0.020	0.001	0.022
isRoot	0.502	0.007	0.499
ontoCAT-package	0.011	0.000	0.012
searchTerm	1.099	0.015	1.077
searchTermPrefix	1.157	0.024	1.121
showHierarchyDownToTerm	6.358	0.082	6.339
showPathsToTerm	5.875	0.056	5.910

Summary

Command output