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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings rols_2.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/rols.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘2.27.0’
* 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: Term-class
> ### Title: Class '"Term"'
> ### Aliases: Term class:Term Term-class Terms class:Terms Terms-class
> ###   termLabel termLabel,Term-method termLabel,Terms-method termNamespace
> ###   termNamespace,Term-method termNamespace,Terms-method termOntology
> ###   termOntology,Term-method termOntology,Terms-method termSynonym
> ###   termSynonym,Term-method termSynonym,Terms-method termDesc
> ###   termDesc,Term-method termDesc,Terms-method termPrefix
> ###   termPrefix,Term-method termPrefix,Terms-method show,Term-method
> ###   show,Terms-method termId termId,Term-method termId,Terms-method
> ###   isObsolete isObsolete,Term-method isObsolete,Terms-method isRoot
> ###   isRoot,Term-method isRoot,Terms-method coerce,Term,data.frame-method
> ###   coerce,Terms,data.frame-method as.Term.data.frame as.Terms.data.frame
> ###   terms term term,Ontology,character-method
> ###   term,character,character-method terms,Ontology-method
> ###   terms,character-method children parents ancestors descendants partOf
> ###   derivesFrom unique,Terms-method length,Terms-method
> ###   lapply,Terms-method [,Terms-method [[,Terms-method
> ###   all.equal,Term,Term-method all.equal,Terms,Terms-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> 
> ## (all) terms
> (gotrms <- terms("go", pagesize = 10000))
Error in curl::curl_fetch_memory(url, handle = handle) : 
  GnuTLS recv error (-110): The TLS connection was non-properly terminated.
Calls: terms ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rols
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘rols’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘rols’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rols)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # setting R_TESTS to empty string because of 
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> library("testthat")
> library("rols")

This is 'rols' version 2.27.0 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 4093)
  response(s): 0 
Object of class 'Ontologies' with 280 entries
   SBO, RS ... REPR, VBO 
Object of class 'Ontologies' with 1 entries
SBO 
Object of class 'Ontologies' with 2 entries
SBO, RS 
Object of class 'Ontologies' with 3 entries
SBO, RS, TGMA 
Object of class 'Ontologies' with 4 entries
SBO, RS, TGMA, UBERON 
Object of class 'Ontologies' with 5 entries
   SBO, RS ... UBERON, TTO 
Ontology: Gene Ontology (go)  
  The Gene Ontology (GO) provides a framework and set of concepts for
  describing the functions of gene products from all organisms.
   Loaded: 2023-01-04 Updated: 2023-01-04 Version: 2022-12-04 
   51052 terms  68 properties  0 individuals
Object of class 'Properties' with 92 entries
 From the SO ontology
  partial_evidence_for_feature, evidence_for_feature ... variant_of, DBVAR 
Object of class 'Properties' with 147 entries
 From the UBERON ontology
  digestive system gland, abdomen element ... hepatic immune response, glycogen catabolic process 
A Property from the UBERON ontology: UBERON:0006925 
 Label: digestive system gland
Object of class 'Terms' with 2729 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000071, SO:0000070 
Object of class 'Terms' with 1 entries
 From the SO ontology
SO:0000579 
Object of class 'Terms' with 2 entries
 From the SO ontology
SO:0000579, SO:0000833 
Object of class 'Terms' with 3 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578 
Object of class 'Terms' with 4 entries
 From the SO ontology
SO:0000579, SO:0000833, SO:0000578, SO:0000011 
Object of class 'Terms' with 5 entries
 From the SO ontology
  SO:0000579, SO:0000833 ... SO:0000011, SO:0001430 
A Term from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  No description
Testing term SO:0001212 
Testing term SO:0000180 
Testing term SO:0005849 
Testing term SO:0001387 
Testing term SO:0000879 
Testing term SO:0001965 
Testing term SO:0000932 
Testing term SO:0000935 
Testing term SO:0001344 
Testing term SO:0000237