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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rols.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rols_3.7.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/rols.Rcheck’
* using R Under development (unstable) (2026-03-20 r89666)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-21 05:00:37 UTC
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘3.7.1’
* 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 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 ... ERROR
Running examples in ‘rols-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OlsSearch
> ### Title: Querying OLS
> ### Aliases: OlsSearch .OlsSearch olsSearch olsRows 'olsRows<-' allRows
> ###   as.data.frame.OlsSearch show,OlsSearch-method olsRows<-
> 
> ### ** Examples
> 
> 
> ## Many results across all ontologies
> OlsSearch(q = "trans-golgi")
Object of class 'OlsSearch':
  query: trans-golgi 
  requested: 20 (out of 0)
  response(s): 0 
> 
> ## Exact matches
> OlsSearch(q = "trans-golgi", exact = TRUE)
Object of class 'OlsSearch':
  query: trans-golgi 
  requested: 20 (out of 0)
  response(s): 0 
> 
> ## Exact match in the gene ontology (go or GO) only
> OlsSearch(q = "trans-golgi", exact = TRUE, ontology = "go")
Object of class 'OlsSearch':
  ontolgy: go 
  query: trans-golgi 
  requested: 20 (out of 0)
  response(s): 0 
> OlsSearch(q = "trans-golgi", exact = TRUE, ontology = "GO")
Object of class 'OlsSearch':
  ontolgy: GO 
  query: trans-golgi 
  requested: 20 (out of 0)
  response(s): 0 
> 
> ## Exact match in the GO and Uberon
> OlsSearch(q = "trans-golgi", exact = TRUE,
+           ontology = c("GO", "Uberon"))
Object of class 'OlsSearch':
  ontolgies: GO, Uberon 
  query: trans-golgi 
  requested: 20 (out of 0)
  response(s): 0 
> 
> ## Testing different ESI queries
> OlsSearch(q = "electrospray", ontology = "MS")
Object of class 'OlsSearch':
  ontolgy: MS 
  query: electrospray 
  requested: 20 (out of 0)
  response(s): 0 
> OlsSearch(q = "ionization", ontology = "MS")
Object of class 'OlsSearch':
  ontolgy: MS 
  query: ionization 
  requested: 20 (out of 0)
  response(s): 0 
> OlsSearch(q = "electrospray ionization", ontology = "MS")
Object of class 'OlsSearch':
  ontolgy: MS 
  query: electrospray ionization 
  requested: 20 (out of 1)
  response(s): 0 
> OlsSearch(q = "electrospray ionization", ontology = "MS", exact=TRUE)
Object of class 'OlsSearch':
  ontolgy: MS 
  query: electrospray ionization 
  requested: 20 (out of 1)
  response(s): 0 
> 
> ## Request 5 results instead of 20 (default)
> OlsSearch(q = "plasma,membrane", ontology = "go", rows = 5)
Object of class 'OlsSearch':
  ontolgy: go 
  query: plasma,membrane 
  requested: 5 (out of 0)
  response(s): 0 
> ## Same as above
> OlsSearch(q = "plasma membrane", ontology = "go", rows = 5)
Object of class 'OlsSearch':
  ontolgy: go 
  query: plasma membrane 
  requested: 5 (out of 4)
  response(s): 0 
> 
> ## or, once the object was created
> (res <- OlsSearch(q = "plasma,membrane", ontology = "go"))
Object of class 'OlsSearch':
  ontolgy: go 
  query: plasma,membrane 
  requested: 20 (out of 0)
  response(s): 0 
> olsRows(res) <- 5
> res
Object of class 'OlsSearch':
  ontolgy: go 
  query: plasma,membrane 
  requested: 5 (out of 0)
  response(s): 0 
> 
> ## all results
> res <- allRows(res)
> res
Object of class 'OlsSearch':
  ontolgy: go 
  query: plasma,membrane 
  requested: 0 (out of 0)
  response(s): 0 
> 
> res <- OlsSearch(q = "trans-golgi", ontology = "go", rows = 5)
> res
Object of class 'OlsSearch':
  ontolgy: go 
  query: trans-golgi 
  requested: 5 (out of 0)
  response(s): 0 
> res <- olsSearch(res)
> res
Object of class 'OlsSearch':
  ontolgy: go 
  query: trans-golgi 
  requested: 5 (out of 0)
  response(s): 0 
> as(res, "data.frame")
 [1] id                   iri                  short_form          
 [4] obo_id               label                description         
 [7] ontology_name        ontology_prefix      type                
[10] is_defining_ontology
<0 rows> (or 0-length row.names)
> trms <- as(res, "olsTerms")
Error in asMethod(object) : 
  No result retrieved. This might be due to a temporary network issue.
Calls: as -> asMethod
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Failure ('test_OlsSearch.R:25:5'): OlsSearch rows ───────────────────────────
  Expected `nrow(olsSearch(res)@response)` to equal 108L.
  Differences:
  1/1 mismatches
  [1] 5 - 108 == -103
  ── Failure ('test_OlsSearch.R:31:5'): OlsSearch rows ───────────────────────────
  Expected `nrow(res@response)` to equal 1000.
  Differences:
  1/1 mismatches
  [1] 5 - 1000 == -995
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 117 ]
  Error:
  ! Test failures.
  Execution halted
* 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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/rols.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL rols
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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) (2026-03-20 r89666) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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] 
Saving _problems/test_OlsSearch-4.R
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 5)
  response(s): 0 
Saving _problems/test_OlsSearch-16.R
Saving _problems/test_OlsSearch-19.R
Saving _problems/test_OlsSearch-25.R
Saving _problems/test_OlsSearch-31.R
Object of class 'olsOntologies' with 270 entries
   ADDICTO, ADO ... ZFA, ZP 
Object of class 'olsOntologies' with 1 entries
ADDICTO 
Object of class 'olsOntologies' with 2 entries
ADDICTO, ADO 
Object of class 'olsOntologies' with 3 entries
ADDICTO, ADO, AEO 
Object of class 'olsOntologies' with 4 entries
ADDICTO, ADO, AEO, AFO 
Object of class 'olsOntologies' with 5 entries
   ADDICTO, ADO ... AFO, AfPO 
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: 2026-03-18 Updated: 2026-03-18 Version: 2026-01-23 
   84443 terms  480 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
  hepatobiliary system, exocrine gland ... quadrate lobe of liver, hepatic portal fibroblast 
A olsProperty from the UBERON ontology: UBERON:0002423 
 Label: hepatobiliary system
Object of class 'olsTerms' with 2747 entries
 From the SO ontology
  BS:00003, BS:0000338 ... SO:2000061, SO:3000000 
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 5 | WARN 0 | SKIP 0 | PASS 117 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_OlsSearch.R:4:5'): OlsSearch tgn ─────────────────────────────
Expected `tgnpw@numFound` to equal 4L.
Differences:
1/1 mismatches
[1] 0 - 4 == -4
── Failure ('test_OlsSearch.R:16:5'): OlsSearch rows ───────────────────────────
Expected `nrow(olsSearch(res)@response)` to equal 20L.
Differences:
1/1 mismatches
[1] 5 - 20 == -15
── Failure ('test_OlsSearch.R:19:5'): OlsSearch rows ───────────────────────────
Expected `nrow(olsSearch(res)@response)` to equal 32L.
Differences:
1/1 mismatches
[1] 5 - 32 == -27
── Failure ('test_OlsSearch.R:25:5'): OlsSearch rows ───────────────────────────
Expected `nrow(olsSearch(res)@response)` to equal 108L.
Differences:
1/1 mismatches
[1] 5 - 108 == -103
── Failure ('test_OlsSearch.R:31:5'): OlsSearch rows ───────────────────────────
Expected `nrow(res@response)` to equal 1000.
Differences:
1/1 mismatches
[1] 5 - 1000 == -995

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 117 ]
Error:
! Test failures.
Execution halted