##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rols.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rols_3.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/rols.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rols/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rols' version '3.1.0'
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Terms      5.35   0.14   12.19
Properties 1.33   0.03    5.43
* 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:
   15. │       │     └─methods::initialize(value, ...)
   16. │       ├─httr2::resp_body_json(req_perform(request(url)))
   17. │       │ └─httr2:::check_response(resp)
   18. │       │   └─httr2:::is_response(resp)
   19. │       └─httr2::req_perform(request(url))
   20. │         └─httr2:::handle_resp(req, resp, error_call = error_call)
   21. │           └─httr2:::resp_abort(resp, req, body, call = error_call)
   22. │             └─rlang::abort(...)
   23. │               └─rlang:::signal_abort(cnd, .file)
   24. │                 └─base::signalCondition(cnd)
   25. └─base (local) `<fn>`(`<ht2__500>`)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]
  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: 1 ERROR
See
  'F:/biocbuild/bbs-3.20-bioc/meat/rols.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rols
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 3.1.0 

> 
> test_check("rols")
[, , Hello, World] 
Object of class 'OlsSearch':
  ontolgy: GO 
  query: cell 
  requested: 20 (out of 10498)
  response(s): 0 
Object of class 'Ontologies' with 257 entries
   ADO, AfPO ... CCF, CPONT 
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: 2024-07-14 Updated: 2024-07-14 Version: 2024-06-17 
   83855 terms  367 properties  18 individuals
Object of class 'Properties' with 91 entries
 From the SO ontology
  definition, IAO_0000231 ... label, deprecated 
Object of class 'Properties' with 160 entries
 From the UBERON ontology
  hepatobiliary system, exocrine system ... liver subserosa, ventral liver lobe 
A Property from the UBERON ontology: UBERON:0002423 
 Label: hepatobiliary system
Object of class 'Terms' with 2736 entries
 From the SO ontology
  SO:1000050, SO:1000054 ... SO:1000048, SO:1000049 
A Term 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 1 | WARN 0 | SKIP 0 | PASS 119 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_Terms.R:41:5'): constructors different URIs (issue 42) ─────────
Error in `(function (cond) 
.Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "HTTP 500 Internal Server Error.", 
    trace = structure(list(call = list(expect_is(Term("efo", 
        "EFO:0001200"), "Term"), quasi_label(enquo(object), label, 
        arg = "object"), eval_bare(expr, quo_get_env(quo)), Term("efo", 
        "EFO:0001200"), Term("efo", "EFO:0001200"), .local(object, 
        ...), Term(Ontology(object), id), Ontology(object), Ontology(object), 
        makeOntology(url), ontologyFromJson(resp_body_json(req_perform(request(url)))), 
        .Ontology(languages = x[["languages"]], lang = x[["lang"]], 
            ontologyId = x[["ontologyId"]], loaded = x[["loaded"]], 
            updated = x[["updated"]], status = x[["status"]], 
            message = x[["message"]], version = x[["version"]], 
            numberOfTerms = x[["numberOfTerms"]], numberOfProperties = x[["numberOfProperties"]], 
            numberOfIndividuals = x[["numberOfIndividuals"]], 
            config = x[["config"]], links = x[["_links"]]), new(`<chr>`, 
            ...), initialize(value, ...), initialize(value, ...), 
        resp_body_json(req_perform(request(url))), check_response(resp), 
        is_response(resp), req_perform(request(url)), handle_resp(req, 
            resp, error_call = error_call), resp_abort(resp, 
            req, body, call = error_call), abort(c(message, resp_auth_message(resp), 
            info), status = status, resp = resp, class = c(glue("httr2_http_{status}"), 
            "httr2_http", "httr2_error"), request = req, call = call)), 
        parent = c(0L, 1L, 2L, 0L, 0L, 5L, 6L, 6L, 6L, 9L, 10L, 
        11L, 12L, 13L, 13L, 10L, 16L, 17L, 10L, 19L, 20L, 21L
        ), visible = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
        TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, 
        TRUE, TRUE, TRUE, FALSE, FALSE, FALSE), namespace = c("testthat", 
        "testthat", "rlang", "rols", "rols", "rols", "rols", 
        "BiocGenerics", "rols", "rols", "rols", "rols", "methods", 
        "methods", "methods", "httr2", "httr2", "httr2", "httr2", 
        "httr2", "httr2", "rlang"), scope = c("::", "::", "::", 
        "::", "::", "local", "::", "::", "::", ":::", ":::", 
        ":::", "::", "::", "::", "::", ":::", ":::", "::", ":::", 
        ":::", "::"), error_frame = c(FALSE, FALSE, FALSE, FALSE, 
        FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, 
        FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, 
        FALSE, FALSE)), row.names = c(NA, -22L), version = 2L, class = c("rlang_trace", 
    "rlib_trace", "tbl", "data.frame")), parent = NULL, status = 500L, 
    resp = structure(list(method = "GET", url = "https://www.ebi.ac.uk/ols4/api/ontologies/efo", 
        status_code = 500L, headers = structure(list(Vary = "Origin", 
            Vary = "Access-Control-Request-Method", Vary = "Access-Control-Request-Headers", 
            `Content-Type` = "application/json", `Strict-Transport-Security` = "max-age=0", 
            Date = "Tue, 16 Jul 2024 08:00:54 GMT", `Transfer-Encoding` = "chunked", 
            Connection = "close"), class = "httr2_headers"), 
        body = as.raw(c(0x7b, 0x0a, 0x20, 0x20, 0x22, 0x74, 0x69, 
        0x6d, 0x65, 0x73, 0x74, 0x61, 0x6d, 0x70, 0x22, 0x20, 
        0x3a, 0x20, 0x22, 0x32, 0x30, 0x32, 0x34, 0x2d, 0x30, 
        0x37, 0x2d, 0x31, 0x36, 0x54, 0x30, 0x38, 0x3a, 0x30, 
        0x30, 0x3a, 0x35, 0x35, 0x2e, 0x36, 0x37, 0x33, 0x2b, 
        0x30, 0x30, 0x3a, 0x30, 0x30, 0x22, 0x2c, 0x0a, 0x20, 
        0x20, 0x22, 0x73, 0x74, 0x61, 0x74, 0x75, 0x73, 0x22, 
        0x20, 0x3a, 0x20, 0x35, 0x30, 0x30, 0x2c, 0x0a, 0x20, 
        0x20, 0x22, 0x65, 0x72, 0x72, 0x6f, 0x72, 0x22, 0x20, 
        0x3a, 0x20, 0x22, 0x49, 0x6e, 0x74, 0x65, 0x72, 0x6e, 
        0x61, 0x6c, 0x20, 0x53, 0x65, 0x72, 0x76, 0x65, 0x72, 
        0x20, 0x45, 0x72, 0x72, 0x6f, 0x72, 0x22, 0x2c, 0x0a, 
        0x20, 0x20, 0x22, 0x70, 0x61, 0x74, 0x68, 0x22, 0x20, 
        0x3a, 0x20, 0x22, 0x2f, 0x6f, 0x6c, 0x73, 0x34, 0x2f, 
        0x61, 0x70, 0x69, 0x2f, 0x6f, 0x6e, 0x74, 0x6f, 0x6c, 
        0x6f, 0x67, 0x69, 0x65, 0x73, 0x2f, 0x65, 0x66, 0x6f, 
        0x22, 0x0a, 0x7d)), request = structure(list(url = "https://www.ebi.ac.uk/ols4/api/ontologies/efo", 
            method = NULL, headers = list(), body = NULL, fields = list(), 
            options = list(), policies = list()), class = "httr2_request"), 
        cache = <environment>), class = "httr2_response"), request = structure(list(
        url = "https://www.ebi.ac.uk/ols4/api/ontologies/efo", 
        method = NULL, headers = list(), body = NULL, fields = list(), 
        options = list(), policies = list()), class = "httr2_request"), 
    rlang = list(inherit = TRUE), call = req_perform(request(url))), class = c("httr2_http_500", 
"httr2_http", "httr2_error", "rlang_error", "error", "condition"
)))`: error in evaluating the argument 'object' in selecting a method for function 'Term': HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. ├─testthat::expect_is(Term("efo", "EFO:0001200"), "Term") at test_Terms.R:41:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─rols::Term("efo", "EFO:0001200")
  5. ├─rols::Term("efo", "EFO:0001200")
  6. │ └─rols (local) .local(object, ...)
  7. │   ├─rols::Term(Ontology(object), id)
  8. │   ├─BiocGenerics::Ontology(object)
  9. │   └─rols::Ontology(object)
 10. │     └─rols:::makeOntology(url)
 11. │       ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url))))
 12. │       │ └─rols:::.Ontology(...)
 13. │       │   └─methods::new(`<chr>`, ...)
 14. │       │     ├─methods::initialize(value, ...)
 15. │       │     └─methods::initialize(value, ...)
 16. │       ├─httr2::resp_body_json(req_perform(request(url)))
 17. │       │ └─httr2:::check_response(resp)
 18. │       │   └─httr2:::is_response(resp)
 19. │       └─httr2::req_perform(request(url))
 20. │         └─httr2:::handle_resp(req, resp, error_call = error_call)
 21. │           └─httr2:::resp_abort(resp, req, body, call = error_call)
 22. │             └─rlang::abort(...)
 23. │               └─rlang:::signal_abort(cnd, .file)
 24. │                 └─base::signalCondition(cnd)
 25. └─base (local) `<fn>`(`<ht2__500>`)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]
Error: Test failures
Execution halted