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BioC 3.0: CHECK report for ontoCAT on moscato1

This page was generated on 2015-04-10 09:46:40 -0700 (Fri, 10 Apr 2015).

Package 625/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 

Summary

Package: ontoCAT
Version: 1.18.0
Command: rm -rf ontoCAT.buildbin-libdir ontoCAT.Rcheck && mkdir ontoCAT.buildbin-libdir ontoCAT.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ontoCAT.buildbin-libdir ontoCAT_1.18.0.tar.gz >ontoCAT.Rcheck\00install.out 2>&1 && cp ontoCAT.Rcheck\00install.out ontoCAT-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ontoCAT.buildbin-libdir --install="check:ontoCAT-install.out" --force-multiarch --no-vignettes --timings ontoCAT_1.18.0.tar.gz
StartedAt: 2015-04-10 03:49:41 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:51:03 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 82.0 seconds
RetCode: 1
Status:  ERROR  
CheckDir: ontoCAT.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ontoCAT.buildbin-libdir ontoCAT.Rcheck && mkdir ontoCAT.buildbin-libdir ontoCAT.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ontoCAT.buildbin-libdir ontoCAT_1.18.0.tar.gz >ontoCAT.Rcheck\00install.out 2>&1 && cp ontoCAT.Rcheck\00install.out ontoCAT-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=ontoCAT.buildbin-libdir --install="check:ontoCAT-install.out" --force-multiarch --no-vignettes --timings ontoCAT_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/ontoCAT.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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

ontoCAT.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'ontoCAT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ontoCAT' as ontoCAT_1.18.0.zip
* DONE (ontoCAT)

ontoCAT.Rcheck/examples_i386/ontoCAT-Ex.timings:

nameusersystemelapsed

ontoCAT.Rcheck/examples_x64/ontoCAT-Ex.timings:

nameusersystemelapsed