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CHECK report for ontoCAT on tokay2

This page was generated on 2018-10-17 08:34:59 -0400 (Wed, 17 Oct 2018).

Package 1028/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoCAT 1.32.0
Natalja Kurbatova
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ontoCAT
Branch: RELEASE_3_7
Last Commit: 896aa06
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: ontoCAT
Version: 1.32.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoCAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ontoCAT_1.32.0.tar.gz
StartedAt: 2018-10-17 03:46:04 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:46:57 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 53.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: ontoCAT.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ontoCAT.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ontoCAT_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ontoCAT.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-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 '1.32.0'
* 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 whether package 'ontoCAT' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'ontoCAT' is deprecated and will be removed from Bioconductor
See 'C:/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
* 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 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()
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
** 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()
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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/ontoCAT.Rcheck/00check.log'
for details.

Installation output

ontoCAT.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/ontoCAT_1.32.0.tar.gz && rm -rf ontoCAT.buildbin-libdir && mkdir ontoCAT.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ontoCAT.buildbin-libdir ontoCAT_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ontoCAT_1.32.0.zip && rm ontoCAT_1.32.0.tar.gz ontoCAT_1.32.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3485k  100 3485k    0     0  40.0M      0 --:--:-- --:--:-- --:--:-- 43.0M

install for i386

* installing *source* package 'ontoCAT' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ontoCAT'
    finding HTML links ... done
    Ontology-class                          html  
    OntologyTerm-class                      html  
    getAccession                            html  
    getAllTermChildren                      html  
    getAllTermChildrenById                  html  
    getAllTermIds                           html  
    getAllTermParents                       html  
    getAllTermParentsById                   html  
    getAllTerms                             html  
    getEFO                                  html  
    getEFOBranchRootIds                     html  
    getLabel                                html  
    getOntology                             html  
    getOntologyAccession                    html  
    getOntologyDescription                  html  
    getOntologyNoReasoning                  html  
    getOntologyRelationNames                html  
    getRootIds                              html  
    getRoots                                html  
    getTermAndAllChildren                   html  
    getTermAndAllChildrenById               html  
    getTermById                             html  
    getTermChildren                         html  
    getTermChildrenById                     html  
    getTermDefinitions                      html  
    getTermDefinitionsById                  html  
    getTermNameById                         html  
    getTermParents                          html  
    getTermParentsById                      html  
    getTermRelationNames                    html  
    getTermRelationNamesById                html  
    getTermRelations                        html  
    getTermRelationsById                    html  
    getTermSynonyms                         html  
    getTermSynonymsById                     html  
    hasTerm                                 html  
    isEFOBranchRoot                         html  
    isEFOBranchRootById                     html  
    isRoot                                  html  
    isRootById                              html  
    ontoCAT-package                         html  
    searchTerm                              html  
    searchTermPrefix                        html  
    showHierarchyDownToTerm                 html  
    showHierarchyDownToTermById             html  
    showPathsToTerm                         html  
    showPathsToTermById                     html  
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'ontoCAT' ...
** testing if installed package can be loaded
Warning: Package 'ontoCAT' is deprecated and will be removed from Bioconductor
  version 3.8
* MD5 sums
packaged installation of 'ontoCAT' as ontoCAT_1.32.0.zip
* DONE (ontoCAT)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ontoCAT' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

ontoCAT.Rcheck/examples_i386/ontoCAT-Ex.timings

nameusersystemelapsed

ontoCAT.Rcheck/examples_x64/ontoCAT-Ex.timings

nameusersystemelapsed