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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rols_3.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rols.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘3.6.1’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
olsTerms      5.493  0.119  14.097
olsOntologies 0.648  0.104   5.090
OlsSearch     0.269  0.015   6.661
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL rols
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘rols’ ...
** this is package ‘rols’ version ‘3.6.1’
** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 3.6.1 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10585)
  response(s): 0 
Object of class 'olsOntologies' with 279 entries
   ADO, AfPO ... NULL, NULL 
Object of class 'olsOntologies' with 1 entries
ADO 
Object of class 'olsOntologies' with 2 entries
ADO, AfPO 
Object of class 'olsOntologies' with 3 entries
ADO, AfPO, AGRO 
Object of class 'olsOntologies' with 4 entries
ADO, AfPO, AGRO, AISM 
Object of class 'olsOntologies' with 5 entries
   ADO, AfPO ... AISM, AMPHX 
olsOntology: 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: 2025-12-14 Updated: 2025-12-14 Version: 2025-10-10 
   84388 terms  476 properties  48 individuals
Object of class 'olsProperties' with 92 entries
 From the SO ontology
  definition, IAO_0000231 ... label, deprecated 
Object of class 'olsProperties' with 164 entries
 From the UBERON ontology
  abdomen, endocrine system ... endothelial cell of periportal hepatic sinusoid, hepatic portal fibroblast 
A olsProperty from the UBERON ontology: UBERON:0000916 
 Label: abdomen
Object of class 'olsTerms' with 2747 entries
 From the SO ontology
  SO:0001943, SO:0001944 ... SO:0001941, SO:0001942 
A olsTerm from the GO ontology: GO:0032801 
 Label: receptor catabolic process
  The chemical reactions and pathways resulting in the breakdown of a
  receptor molecule, a macromolecule that undergoes combination with a
  hormone, neurotransmitter, drug or intracellular messenger to initiate
  a change in cell function.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 122 ]
> 
> proc.time()
   user  system elapsed 
 18.935   0.470  75.762