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BioC 2.13: CHECK report for ontoCAT on zin1

This page was generated on 2014-04-05 09:47:57 -0700 (Sat, 05 Apr 2014).

Package 498/750HostnameOS / ArchBUILDCHECKBUILD BIN
ontoCAT 1.14.0
Natalja Kurbatova
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ontoCAT
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ontoCAT
Version: 1.14.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.14.0.tar.gz
StartedAt: 2014-04-05 02:49:01 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:53:34 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 273.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ontoCAT.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/ontoCAT.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.14.0’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ontoCAT.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [267s/245s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
getTermRelations     132.860  0.100 127.803
getTermRelationNames  93.578  0.112  88.956
Ontology-class        34.866  0.332  23.683
* 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 were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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-class34.866 0.33223.683
OntologyTerm-class0.0160.0000.018
getAccession0.0120.0000.011
getAllTermChildren0.0240.0000.022
getAllTermIds0.0160.0000.014
getAllTermParents0.0240.0000.024
getAllTerms0.0120.0000.014
getEFO0.060.000.06
getEFOBranchRootIds0.0120.0000.040
getLabel0.0120.0000.011
getOntology3.4080.0162.731
getOntologyAccession0.0080.0000.007
getOntologyDescription0.0080.0000.008
getOntologyNoReasoning0.0160.0000.016
getOntologyRelationNames0.0160.0000.017
getRootIds0.0160.0000.014
getRoots0.0120.0000.013
getTermAndAllChildren0.0160.0000.018
getTermById0.0120.0000.012
getTermChildren0.0160.0000.018
getTermDefinitions0.0200.0000.021
getTermNameById0.0080.0000.008
getTermParents0.0240.0000.024
getTermRelationNames93.578 0.11288.956
getTermRelations132.860 0.100127.803
getTermSynonyms0.0480.0000.048
hasTerm0.0440.0000.045
isEFOBranchRoot0.0160.0000.014
isRoot0.0160.0000.014
ontoCAT-package0.0040.0000.006
searchTerm0.0160.0000.014
searchTermPrefix0.0160.0000.013
showHierarchyDownToTerm0.0160.0000.018
showPathsToTerm0.0120.0000.012