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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_3.3.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/rols.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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 ‘3.3.0’
* 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 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 ... ERROR
Running examples in ‘rols-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CVParam
> ### Title: Controlled Vocabulary
> ### Aliases: CVParam charIsCVParam cvCharToCVPar as.character.CVParam
> ###   show,CVParam-method rep,CVParam-method
> 
> ### ** Examples
> 
> 
> ## User param
> CVParam(name = "A user param", value = "the value")
[, , A user param, the value] 
> ## CVParam ESI from PSI's Mass Spectrometry ontology
> Term("MS", "MS:1000073")
Error in if (grepl("ebi.ac.uk", loc)) { : argument is of length zero
Calls: Term -> Term -> .local -> Term -> Term -> .local
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:
  ── Error ('test_Terms.R:2:1'): (code run outside of `test_that()`) ─────────────
  Error in `if (grepl("ebi.ac.uk", loc)) {
      uri <- sub("/[a-zA-z]+\\.owl$", "", loc)
  } else if (grepl("purl.obolibrary.org", loc)) {
      uri <- "http://purl.obolibrary.org/obo"
  } else stop("Unknown fileLocation")`: argument is of length zero
  Backtrace:
      ▆
   1. ├─rols::Term(go, "GO:0032801") at test_Terms.R:2:1
   2. └─rols::Term(go, "GO:0032801")
   3.   └─rols (local) .local(object, ...)
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 74 ]
  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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/rols.Rcheck/00check.log’
for details.

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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-devel_2024-11-24/site-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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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 3.3.0 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10483)
  response(s): 0 
Object of class 'Ontologies' with 267 entries
   ADO, AfPO ... CPONT, LIFESTYLEFACTORS 
Object of class 'Ontologies' with 1 entries
ADO 
Object of class 'Ontologies' with 2 entries
ADO, AfPO 
Object of class 'Ontologies' with 3 entries
ADO, AfPO, AGRO 
Object of class 'Ontologies' with 4 entries
ADO, AfPO, AGRO, AISM 
Object of class 'Ontologies' with 5 entries
   ADO, AfPO ... AISM, AMPHX 
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: 2025-01-27 Updated: 2025-01-27 Version: 2024-11-03 
   84016 terms  369 properties  19 individuals
Object of class 'Properties' with 92 entries
 From the SO ontology
  definition, IAO_0000231 ... label, deprecated 
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 74 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_CVParam.R:6:15'): User param creation ──────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': argument is of length zero
Backtrace:
     ▆
  1. ├─testthat::expect_warning(as("[MS, MS:1000073, ESI, ]", "CVParam")) at test_CVParam.R:6:15
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─methods::as("[MS, MS:1000073, ESI, ]", "CVParam")
  7. │ └─rols (local) asMethod(object)
  8. │   ├─base::lapply(from, cvCharToCVPar)
  9. │   └─base::lapply(from, cvCharToCVPar)
 10. │     └─rols (local) FUN(X[[i]], ...)
 11. │       └─rols::CVParam(label = from[1], accession = from[2])
 12. │         ├─rols::termLabel(Term(label, accession))
 13. │         ├─rols::Term(label, accession)
 14. │         └─rols::Term(label, accession)
 15. │           └─rols (local) .local(object, ...)
 16. │             ├─rols::Term(Ontology(object), id)
 17. │             └─rols::Term(Ontology(object), id)
 18. │               └─rols (local) .local(object, ...)
 19. └─base::.handleSimpleError(...)
 20.   └─base (local) h(simpleError(msg, call))
── Error ('test_CVParam.R:20:15'): CVParam creation and coercion ───────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': argument is of length zero
Backtrace:
     ▆
  1. ├─rols::CVParam(label = "MS", accession = "MS:1000073") at test_CVParam.R:20:15
  2. │ ├─rols::termLabel(Term(label, accession))
  3. │ ├─rols::Term(label, accession)
  4. │ └─rols::Term(label, accession)
  5. │   └─rols (local) .local(object, ...)
  6. │     ├─rols::Term(Ontology(object), id)
  7. │     └─rols::Term(Ontology(object), id)
  8. │       └─rols (local) .local(object, ...)
  9. └─base::.handleSimpleError(...)
 10.   └─base (local) h(simpleError(msg, call))
── Error ('test_CVParam.R:39:15'): Convert char to CVParam ─────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'termLabel': argument is of length zero
Backtrace:
     ▆
  1. ├─methods::as(x, "CVParam") at test_CVParam.R:39:15
  2. │ └─rols (local) asMethod(object)
  3. │   ├─base::lapply(from, cvCharToCVPar)
  4. │   └─base::lapply(from, cvCharToCVPar)
  5. │     └─rols (local) FUN(X[[i]], ...)
  6. │       └─rols::CVParam(label = from[1], accession = from[2])
  7. │         ├─rols::termLabel(Term(label, accession))
  8. │         ├─rols::Term(label, accession)
  9. │         └─rols::Term(label, accession)
 10. │           └─rols (local) .local(object, ...)
 11. │             ├─rols::Term(Ontology(object), id)
 12. │             └─rols::Term(Ontology(object), id)
 13. │               └─rols (local) .local(object, ...)
 14. └─base::.handleSimpleError(...)
 15.   └─base (local) h(simpleError(msg, call))
── Error ('test_OlsSearch.R:41:5'): OlsSearch coercion ─────────────────────────
Error in `asMethod(object)`: No result retrieved. This might be due to a temporary network issue.
Backtrace:
    ▆
 1. └─methods::as(res, "Terms") at test_OlsSearch.R:41:5
 2.   └─rols (local) asMethod(object)
── Error ('test_Properties.R:11:5'): Property constructors ─────────────────────
Error in `if (grepl("ebi.ac.uk", loc)) {
    uri <- sub("/[a-zA-z]+\\.owl$", "", loc)
} else if (grepl("purl.obolibrary.org", loc)) {
    uri <- "http://purl.obolibrary.org/obo"
} else stop("Unknown fileLocation")`: argument is of length zero
Backtrace:
    ▆
 1. ├─rols::Term("uberon", "UBERON_0002107") at test_Properties.R:11:5
 2. └─rols::Term("uberon", "UBERON_0002107")
 3.   └─rols (local) .local(object, ...)
 4.     ├─rols::Term(Ontology(object), id)
 5.     └─rols::Term(Ontology(object), id)
 6.       └─rols (local) .local(object, ...)
── Error ('test_Properties.R:30:5'): Property/ies show ─────────────────────────
Error in `if (grepl("ebi.ac.uk", loc)) {
    uri <- sub("/[a-zA-z]+\\.owl$", "", loc)
} else if (grepl("purl.obolibrary.org", loc)) {
    uri <- "http://purl.obolibrary.org/obo"
} else stop("Unknown fileLocation")`: argument is of length zero
Backtrace:
    ▆
 1. ├─rols::Term("uberon", "UBERON_0002107") at test_Properties.R:30:5
 2. └─rols::Term("uberon", "UBERON_0002107")
 3.   └─rols (local) .local(object, ...)
 4.     ├─rols::Term(Ontology(object), id)
 5.     └─rols::Term(Ontology(object), id)
 6.       └─rols (local) .local(object, ...)
── Error ('test_Terms.R:2:1'): (code run outside of `test_that()`) ─────────────
Error in `if (grepl("ebi.ac.uk", loc)) {
    uri <- sub("/[a-zA-z]+\\.owl$", "", loc)
} else if (grepl("purl.obolibrary.org", loc)) {
    uri <- "http://purl.obolibrary.org/obo"
} else stop("Unknown fileLocation")`: argument is of length zero
Backtrace:
    ▆
 1. ├─rols::Term(go, "GO:0032801") at test_Terms.R:2:1
 2. └─rols::Term(go, "GO:0032801")
 3.   └─rols (local) .local(object, ...)

[ FAIL 7 | WARN 0 | SKIP 0 | PASS 74 ]
Error: Test failures
Execution halted