ontoCAT 1.18.0
Natalja Kurbatova
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ontoCAT | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | ERROR | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | ERROR | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ontoCAT_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ontoCAT.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.18.0’
* 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 ... [4s/5s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ontoCAT-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Ontology-class
> ### Title: Class "Ontology"
> ### Aliases: Ontology-class getAllTermChildren,Ontology,OntologyTerm-method
> ### getAllTermChildrenById,Ontology,character-method
> ### getAllTermIds,Ontology-method
> ### getAllTermParents,Ontology,OntologyTerm-method
> ### getAllTermParentsById,Ontology,character-method
> ### getAllTerms,Ontology-method getEFOBranchRootIds,Ontology-method
> ### getOntologyAccession,Ontology-method
> ### getOntologyDescription,Ontology-method getRootIds,Ontology-method
> ### getRoots,Ontology-method
> ### getTermAndAllChildren,Ontology,OntologyTerm-method
> ### getTermAndAllChildrenById,Ontology,character-method
> ### getTermById,Ontology,character-method
> ### getTermChildren,Ontology,OntologyTerm-method
> ### getTermChildrenById,Ontology,character-method
> ### getTermDefinitions,Ontology,OntologyTerm-method
> ### getTermDefinitionsById,Ontology,character-method
> ### getTermNameById,Ontology,character-method
> ### getTermParents,Ontology,OntologyTerm-method
> ### getTermParentsById,Ontology,character-method
> ### getTermSynonyms,Ontology,OntologyTerm-method
> ### getTermSynonymsById,Ontology,character-method
> ### hasTerm,Ontology,character-method
> ### isEFOBranchRoot,Ontology,OntologyTerm-method
> ### isEFOBranchRootById,Ontology,character-method
> ### isRoot,Ontology,OntologyTerm-method
> ### isRootById,Ontology,character-method
> ### searchTerm,Ontology,character-method
> ### searchTermPrefix,Ontology,character-method
> ### showHierarchyDownToTerm,Ontology,OntologyTerm-method
> ### showHierarchyDownToTermById,Ontology,character-method
> ### showPathsToTerm,Ontology,OntologyTerm-method
> ### showPathsToTermById,Ontology,character-method
> ### getOntologyRelationNames,Ontology-method
> ### getTermRelationNames,Ontology,OntologyTerm-method
> ### getTermRelationNamesById,Ontology,character-method
> ### getTermRelations,Ontology,OntologyTerm,character-method
> ### getTermRelationsById,Ontology,character,character-method
> ### Keywords: classes
>
> ### ** Examples
>
> ontology <- getEFO()
WARN [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0000052>
WARN [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002215>
Sorry, can't create Ontology object for EFO by using URL "http://www.ebi.ac.uk/efo/efo.owl" or local file.
Sorry, can't create Ontology object for EFO by using URL "http://www.ebi.ac.uk/efo/efo.owl".
> getEFOBranchRootIds(ontology)
Sorry, can't get EFO branch root terms for ontology "null".
list()
> term <- getTermById(ontology,"EFO_0001221")
Sorry, can't find term "EFO_0001221" in ontology "null".
Error in validObject(.Object) :
invalid class “OntologyTerm” object: invalid object for slot "term" in class "OntologyTerm": got class "NULL", should be or extend class "jobjRef"
Calls: getTermById ... getTermById -> new -> initialize -> initialize -> validObject
Execution halted