Package: ontoCAT

Version: 1.10.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.10.0.tar.gz

StartedAt: 2013-03-25 03:27:28 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:31:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 235.8 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ontoCAT.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-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 ‘1.10.0’
* 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 whether package ‘ontoCAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations      70.937  0.108  71.410
getTermRelationNames  57.359  0.392  57.769
Ontology-class        44.834  0.780  32.468
getEFO                 6.220  0.048   6.277
getTermAndAllChildren  5.056  0.024   5.076
getAllTermChildren     4.725  0.212   5.071
* 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

* 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	44.834	0.780	32.468
OntologyTerm-class	0.016	0.000	0.018
getAccession	0.008	0.000	0.010
getAllTermChildren	4.725	0.212	5.071
getAllTermIds	0.768	0.008	0.791
getAllTermParents	0.072	0.000	0.070
getAllTerms	0.760	0.000	0.743
getEFO	6.220	0.048	6.277
getEFOBranchRootIds	0.828	0.060	0.835
getLabel	0.012	0.000	0.010
getOntology	4.280	0.012	3.956
getOntologyAccession	0.004	0.000	0.004
getOntologyDescription	0.004	0.000	0.003
getOntologyNoReasoning	0.417	0.000	0.366
getOntologyRelationNames	0.332	0.000	0.322
getRootIds	0.388	0.000	0.327
getRoots	0.296	0.004	0.301
getTermAndAllChildren	5.056	0.024	5.076
getTermById	0.016	0.000	0.014
getTermChildren	0.152	0.000	0.152
getTermDefinitions	0.020	0.000	0.018
getTermNameById	0.004	0.000	0.005
getTermParents	0.036	0.000	0.034
getTermRelationNames	57.359	0.392	57.769
getTermRelations	70.937	0.108	71.410
getTermSynonyms	0.052	0.004	0.055
hasTerm	0.004	0.000	0.006
isEFOBranchRoot	0.012	0.000	0.033
isRoot	0.300	0.000	0.301
ontoCAT-package	0.004	0.000	0.002
searchTerm	0.672	0.000	0.673
searchTermPrefix	0.664	0.004	0.654
showHierarchyDownToTerm	3.868	0.012	3.905
showPathsToTerm	3.444	0.016	3.493