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BioC 2.14: CHECK report for ontoCAT on zin2

This page was generated on 2014-10-08 08:48:54 -0700 (Wed, 08 Oct 2014).

Package 553/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoCAT 1.16.0
Natalja Kurbatova
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ontoCAT
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: ontoCAT
Version: 1.16.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.16.0.tar.gz
StartedAt: 2014-10-08 01:33:14 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:38:46 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 331.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ontoCAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/ontoCAT.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.16.0’
* 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 ... [3s/3s] 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 ... [322s/303s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations     168.931  0.256 165.630
getTermRelationNames 110.083  0.204 106.884
Ontology-class        37.966  0.252  26.084
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/ontoCAT.Rcheck/00check.log’
for details.

ontoCAT.Rcheck/00install.out:

* 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)

ontoCAT.Rcheck/ontoCAT-Ex.timings:

nameusersystemelapsed
Ontology-class37.966 0.25226.084
OntologyTerm-class0.0160.0000.013
getAccession0.0080.0000.008
getAllTermChildren0.0160.0000.016
getAllTermIds0.0080.0000.009
getAllTermParents0.020.000.02
getAllTerms0.0160.0000.013
getEFO0.0520.0040.055
getEFOBranchRootIds0.0080.0000.009
getLabel0.0120.0000.010
getOntology3.1120.0002.813
getOntologyAccession0.0040.0000.004
getOntologyDescription0.0000.0040.005
getOntologyNoReasoning0.0120.0000.011
getOntologyRelationNames0.0120.0000.013
getRootIds0.0080.0000.011
getRoots0.0080.0000.011
getTermAndAllChildren0.020.000.02
getTermById0.0120.0000.011
getTermChildren0.0160.0000.017
getTermDefinitions0.0200.0000.022
getTermNameById0.0040.0000.006
getTermParents0.0240.0000.023
getTermRelationNames110.083 0.204106.884
getTermRelations168.931 0.256165.630
getTermSynonyms0.0520.0000.054
hasTerm0.0040.0000.005
isEFOBranchRoot0.0080.0000.015
isRoot0.0120.0000.012
ontoCAT-package0.0040.0000.003
searchTerm0.0120.0000.012
searchTermPrefix0.0120.0000.012
showHierarchyDownToTerm0.0120.0000.012
showPathsToTerm0.0120.0000.013