BioC 2.12: CHECK report for ontoCAT on pelham

Package: ontoCAT

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.12.0.tar.gz

StartedAt: 2013-05-01 08:48:39 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:54:36 -0700 (Wed, 01 May 2013)

EllapsedTime: 357.6 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 Patched (2013-04-08 r62531)
* 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 '1.12.0'
* 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/8s] 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 ... [326s/292s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
getTermRelations        117.322  2.475 115.140
getTermRelationNames     90.582  2.422  88.990
Ontology-class           61.114  1.994  39.385
getEFO                    7.687  0.110   7.716
showHierarchyDownToTerm   6.348  0.100   6.388
showPathsToTerm           5.747  0.079   5.878
getTermAndAllChildren     5.417  0.079   5.549
getAllTermChildren        5.416  0.069   5.501
getOntology               5.103  0.072   4.711
* 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
** testing if installed package can be loaded
* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	61.114	1.994	39.385
OntologyTerm-class	0.032	0.002	0.035
getAccession	0.028	0.002	0.030
getAllTermChildren	5.416	0.069	5.501
getAllTermIds	1.131	0.017	1.131
getAllTermParents	0.090	0.007	0.097
getAllTerms	1.142	0.019	1.100
getEFO	7.687	0.110	7.716
getEFOBranchRootIds	1.143	0.020	1.110
getLabel	0.023	0.002	0.024
getOntology	5.103	0.072	4.711
getOntologyAccession	0.021	0.001	0.022
getOntologyDescription	0.024	0.003	0.028
getOntologyNoReasoning	0.631	0.014	0.589
getOntologyRelationNames	0.531	0.009	0.530
getRootIds	0.582	0.012	0.571
getRoots	0.506	0.008	0.511
getTermAndAllChildren	5.417	0.079	5.549
getTermById	0.027	0.001	0.028
getTermChildren	0.203	0.004	0.206
getTermDefinitions	0.048	0.002	0.051
getTermNameById	0.024	0.001	0.024
getTermParents	0.042	0.001	0.044
getTermRelationNames	90.582	2.422	88.990
getTermRelations	117.322	2.475	115.140
getTermSynonyms	0.067	0.002	0.070
hasTerm	0.014	0.001	0.045
isEFOBranchRoot	0.024	0.002	0.026
isRoot	0.511	0.008	0.510
ontoCAT-package	0.012	0.002	0.014
searchTerm	1.823	0.117	1.501
searchTermPrefix	1.433	0.058	1.232
showHierarchyDownToTerm	6.348	0.100	6.388
showPathsToTerm	5.747	0.079	5.878

Summary

Command output