ontoCAT 1.30.0
Natalja Kurbatova
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ontoCAT |
| Branch: RELEASE_3_6 |
| Last Commit: 54c0085 |
| Last Changed Date: 2017-10-30 12:39:31 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ontoCAT.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-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 ‘1.30.0’
* 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 ... 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 ... 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()
INFO [ReasonedFileOntologyService] Classified the ontology http://www.ebi.ac.uk/efo/efo.owl
> getEFOBranchRootIds(ontology)
list()
> term <- getTermById(ontology,"EFO_0001221")
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
* 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
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/ontoCAT.Rcheck/00check.log’
for details.