Package: ontoCAT

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ontoCAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ontoCAT_1.32.0.tar.gz

StartedAt: 2018-10-16 23:03:31 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:04:09 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 38.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: ontoCAT.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ontoCAT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ontoCAT_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ontoCAT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.32.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'ontoCAT' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/ontoCAT.Rcheck/00install.out’ for details.
* 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 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ontoCAT.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ontoCAT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ontoCAT’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'ontoCAT' is deprecated and will be removed from Bioconductor
  version 3.8
* DONE (ontoCAT)

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