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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) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘3.7.1’
* 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 13829)
  response(s): 0 
> 
> ## Exact matches
> OlsSearch(q = "trans-golgi", exact = TRUE)
Object of class 'OlsSearch':
  query: trans-golgi 
  requested: 20 (out of 328)
  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 41)
  response(s): 0 
> OlsSearch(q = "trans-golgi", exact = TRUE, ontology = "GO")
Object of class 'OlsSearch':
  ontolgy: GO 
  query: trans-golgi 
  requested: 20 (out of 41)
  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 45)
  response(s): 0 
> 
> ## Testing different ESI queries
> OlsSearch(q = "electrospray", ontology = "MS")
Object of class 'OlsSearch':
  ontolgy: MS 
  query: electrospray 
  requested: 20 (out of 7)
  response(s): 0 
> OlsSearch(q = "ionization", ontology = "MS")
Object of class 'OlsSearch':
  ontolgy: MS 
  query: ionization 
  requested: 20 (out of 51)
  response(s): 0 
> OlsSearch(q = "electrospray ionization", ontology = "MS")
Object of class 'OlsSearch':
  ontolgy: MS 
  query: electrospray ionization 
  requested: 20 (out of 52)
  response(s): 0 
> OlsSearch(q = "electrospray ionization", ontology = "MS", exact=TRUE)
Object of class 'OlsSearch':
  ontolgy: MS 
  query: electrospray ionization 
  requested: 20 (out of 6)
  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 4091)
  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 4091)
  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 4091)
  response(s): 0 
> olsRows(res) <- 5
> res
Object of class 'OlsSearch':
  ontolgy: go 
  query: plasma,membrane 
  requested: 5 (out of 4091)
  response(s): 0 
> 
> ## all results
> res <- allRows(res)
> res
Object of class 'OlsSearch':
  ontolgy: go 
  query: plasma,membrane 
  requested: 4091 (out of 4091)
  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 537)
  response(s): 0 
> res <- olsSearch(res)
> res
Object of class 'OlsSearch':
  ontolgy: go 
  query: trans-golgi 
  requested: 5 (out of 537)
  response(s): 5 
> as(res, "data.frame")
                                        iri ontology_name related_synonyms
1 http://purl.obolibrary.org/obo/GO_0032588            go     Golgi tr....
2 http://purl.obolibrary.org/obo/GO_0160282            go                 
3 http://purl.obolibrary.org/obo/GO_0160289            go                 
4 http://purl.obolibrary.org/obo/GO_0000301            go                 
5 http://purl.obolibrary.org/obo/GO_0005802            go     Golgi tr....
  ontology_prefix short_form  description
1              GO GO_0032588 The lipi....
2              GO GO_0160282 The memb....
3              GO GO_0160289 The memb....
4              GO GO_0000301 The retr....
5              GO GO_0005802 The netw....
                                                 label     obo_id  type
1                         trans-Golgi network membrane GO:0032588 class
2         lumenal side of trans-Golgi network membrane GO:0160282 class
3       lumenal side of trans-Golgi cisternae membrane GO:0160289 class
4 retrograde transport, vesicle recycling within Golgi GO:0000301 class
5                                  trans-Golgi network GO:0005802 class
  exact_synonyms broad_synonyms
1   trans Go....               
2   lumenal ....               
3   lumenal ....               
4   retrogra....               
5   TGN, tra....     trans face
> trms <- as(res, "olsTerms")
> trms
Object of class 'olsTerms' with 5 entries
 From the GO ontology
  GO:0032588, GO:0160282 ... GO:0000301, GO:0005802 
> termPrefix(trms)
GO:0032588 GO:0160282 GO:0160289 GO:0000301 GO:0005802 
      "GO"       "GO"       "GO"       "GO"       "GO" 
> termId(trms)
  GO:0032588   GO:0160282   GO:0160289   GO:0000301   GO:0005802 
"GO:0032588" "GO:0160282" "GO:0160289" "GO:0000301" "GO:0005802" 
> 
> ## Setting rows and start parameters
> tg1 <- OlsSearch(q = "trans-golgi", rows = 5, start = 0) |>
+                  olsSearch() |>
+                  as("data.frame")
> tg2 <- OlsSearch(q = "trans-golgi", rows = 5, start = 5) |>
+                  olsSearch() |>
+                  as("data.frame")
> tg3 <- OlsSearch(q = "trans-golgi", rows = 10, start = 0) |>
+                  olsSearch() |>
+                  as("data.frame")
> 
> ## The two consecutive small results are identical
> ## to the larger on.
> identical(rbind(tg1, tg2), tg3)
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Calls: identical -> rbind -> rbind
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 ... 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
  ‘/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-arm64/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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 10360)
  response(s): 0 
Object of class 'olsOntologies' with 274 entries
   ADO, AfPO ... hgnc.genegroup, PREFER 
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: 2026-01-22 Updated: 2026-01-22 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
  digestive system, abdomen ... endothelial cell of periportal hepatic sinusoid, hepatic portal fibroblast 
A olsProperty from the UBERON ontology: UBERON:0001007 
 Label: digestive system
Object of class 'olsTerms' with 2747 entries
 From the SO ontology
  SO:0001739, SO:0001740 ... SO:0001453, SO:0001454 
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 
  5.591   0.339  76.195