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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:rols.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings rols_3.7.1.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rols.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘3.7.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Laurent Gatto <laurent.gatto@uclouvain.be>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Title field should be in title case. Current version is:
  ‘An R interface to the Ontology Lookup Service’
In title case that is:
  ‘An R Interface to the Ontology Lookup Service’
* 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 use of S3 registration ... 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
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rols.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL rols
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘rols’ ...
** this is package ‘rols’ version ‘3.7.1’
** 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 Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 3.7.1 

> 
> 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: 2025-12-16 Updated: 2025-12-16 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
  endocrine system, hepatobiliary system ... endothelial cell of periportal hepatic sinusoid, hepatic portal fibroblast 
A olsProperty from the UBERON ontology: UBERON:0000949 
 Label: endocrine system
Object of class 'olsTerms' with 2747 entries
 From the SO ontology
  SO:0001851, SO:0001852 ... SO:0001849, SO:0001850 
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 
  8.886   0.228  40.889