CHECK report for rols on malbec2
This page was generated on 2019-10-16 12:01:14 -0400 (Wed, 16 Oct 2019).
rols 2.12.2
Laurent Gatto
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rols |
| Branch: RELEASE_3_9 |
| Last Commit: b191259 |
| Last Changed Date: 2019-10-12 16:19:25 -0400 (Sat, 12 Oct 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Command output
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings rols_2.12.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/rols.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘2.12.2’
* package encoding: UTF-8
* 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 ‘rols’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rols-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:Ontology Ontology-class Ontologies
> ### class:Ontologies Ontologies-class Ontologies,missing-method
> ### Ontologies,numeric-method Ontology,Ontology-method
> ### Ontology,character-method olsDesc olsDesc,character-method
> ### olsDesc,Ontology-method olsDesc,Ontologies-method olsPrefix
> ### olsPrefix,character-method olsPrefix,Ontology-method
> ### olsPrefix,Ontologies-method olsStatus olsStatus,character-method
> ### olsStatus,Ontology-method olsStatus,Ontologies-method olsNamespace
> ### olsNamespace,character-method olsNamespace,Ontology-method
> ### olsNamespace,Ontologies-method olsRoot olsRoot,character-method
> ### olsRoot,Ontology-method olsRoot,Ontologies-method olsTitle
> ### olsTitle,character-method olsTitle,Ontology-method
> ### olsTitle,Ontologies-method olsVersion olsVersion,Ontology-method
> ### olsVersion,character-method olsVersion,Ontologies-method olsLoaded
> ### olsLoaded,Ontology-method olsLoaded,character-method
> ### olsLoaded,Ontologies-method olsUpdated olsUpdated,Ontology-method
> ### olsUpdated,character-method olsUpdated,Ontologies-method
> ### show,Ontology-method show,Ontologies-method length,Ontologies-method
> ### lapply,Ontologies-method [,Ontologies-method [[,Ontologies-method
> ### coerce,Ontologies,data.frame-method coerce,Ontologies,list-method
> ### all.equal,Ontologies,Ontologies-method
> ### all.equal,Ontology,Ontology-method
> ### Keywords: classes
>
> ### ** Examples
>
> ## Get all ontolgies
> ol <- Ontologies()
> ol
Object of class 'Ontologies' with 239 entries
AEO, MIAPA ... SEP, SEPIO
>
> head(as(ol, "data.frame"))
Prefix Namespace
aeo AEO aeo
miapa MIAPA miapa
micro MICRO micro
mirnao MIRNAO mirnao
miro MIRO miro
mmo MMO mmo
Title
aeo Anatomical Entity Ontology
miapa Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology
micro Ontology of Prokaryotic Phenotypic and Metabolic Characters
mirnao microRNA Ontology
miro Mosquito insecticide resistance
mmo Measurement method ontology
> length(ol)
[1] 239
>
> ## Individual ontologies
> (go <- ol[["go"]])
Ontology: Gene Ontology (go)
An ontology for describing the function of genes and gene products
Loaded: 2019-10-10 Updated: 2019-10-15 Version: 2019-10-07
49992 terms 60 properties 0 individuals
> (efo <- ol[["efo"]])
Ontology: Experimental Factor Ontology (efo)
The Experimental Factor Ontology (EFO) provides a systematic
description of many experimental variables available in EBI databases,
and for external projects such as the NHGRI GWAS catalogue. It combines
parts of several biological ontologies, such as anatomy, disease and
chemical compounds. The scope of EFO is to support the annotation,
analysis and visualization of data handled by many groups at the EBI
and as the core ontology for OpenTargets.org
Loaded: 2019-09-16 Updated: 2019-10-15 Version: 3.10.0
36759 terms 230 properties 0 individuals
>
> ## some basic information
> olsVersion(go)
[1] "2019-10-07"
> olsDesc(go)
[1] "An ontology for describing the function of genes and gene products"
> olsTitle(go)
[1] "Gene Ontology"
> olsPrefix(go)
[1] "GO"
> olsNamespace(go)
[1] "go"
>
> olsRoot(go)
Error in .local(object, ...) : Internal Server Error (HTTP 500).
Calls: olsRoot ... .local -> olsRoot -> olsRoot -> .local -> stop_for_status
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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
See
‘/home/biocbuild/bbs-3.9-bioc/meat/rols.Rcheck/00check.log’
for details.
Installation output
rols.Rcheck/00install.out
Tests output
rols.Rcheck/tests/testthat.Rout
Example timings
rols.Rcheck/rols-Ex.timings