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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biomaRt_2.62.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biomaRt.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.62.1’
* 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 ‘biomaRt’ 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘AnnotationDbi:::smartKeys’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.shrinkDatasetName: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* 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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Caused by error in `curl::curl_fetch_memory()`:
  ! Timeout was reached [www.ensembl.org]: Operation timed out after 10003 milliseconds with 0 bytes received
  Backtrace:
      ▆
   1. └─biomaRt:::.createHash(ensembl, attributes, filters, values) at test_z_cache.R:28:1
   2.   └─biomaRt:::.listEnsemblArchives(http_config = martHTTPConfig(mart))
   3.     └─biomaRt:::.checkArchiveList(https, http_config)
   4.       └─biomaRt:::.getArchiveList(https = https, http_config = http_config)
   5.         └─httr2::req_perform(html_request)
   6.           └─httr2:::handle_resp(req, resp, error_call = error_call)
   7.             └─rlang::cnd_signal(resp)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 140 ]
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biomaRt
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biomaRt’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (biomaRt)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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.

> library(testthat)
> library(mockery)
> library(biomaRt)
> library(httptest2)
> 
> test_check("biomaRt", encoding = "UTF-8")
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 140 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_ensemblGenomes.R:23:5'): return type is correct ────────────────
<httr2_http_500/httr2_http/httr2_error/rlang_error/rlang_error/error/condition>
Error in `req_perform(request)`: HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. ├─testthat::expect_is(...) at test_ensemblGenomes.R:23:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─biomaRt::useEnsemblGenomes("protists_mart", "bnatans_eg_gene")
  5.   └─biomaRt::listEnsemblGenomes(includeHosts = TRUE, host = host)
  6.     └─base::lapply(...)
  7.       └─biomaRt (local) FUN(X[[i]], ...)
  8.         ├─base::as.data.frame(...)
  9.         └─biomaRt:::.listMarts(...)
 10.           └─biomaRt:::bmRequest(...)
 11.             └─httr2::req_perform(request)
 12.               └─httr2:::handle_resp(req, resp, error_call = error_call)
 13.                 └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 14.                   ├─rlang::catch_cnd(...)
 15.                   │ ├─rlang::eval_bare(...)
 16.                   │ ├─base::tryCatch(...)
 17.                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 18.                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 19.                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 20.                   │ └─base::force(expr)
 21.                   └─rlang::abort(...)
── Error ('test_getBM.R:50:5'): getBM returns sensible things ──────────────────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `req_perform(html_request)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]: Operation timed out after 10002 milliseconds with 0 bytes received
Backtrace:
     ▆
  1. ├─testthat::expect_is(...) at test_getBM.R:50:5
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─biomaRt::getBM(...)
  5.   └─biomaRt:::.createHash(...)
  6.     └─biomaRt:::.listEnsemblArchives(http_config = martHTTPConfig(mart))
  7.       └─biomaRt:::.checkArchiveList(https, http_config)
  8.         └─biomaRt:::.getArchiveList(https = https, http_config = http_config)
  9.           └─httr2::req_perform(html_request)
 10.             └─httr2:::handle_resp(req, resp, error_call = error_call)
 11.               └─rlang::cnd_signal(resp)
── Error ('test_z_cache.R:16:4'): Hashing is order insensitive ─────────────────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `req_perform(html_request)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]: Operation timed out after 10003 milliseconds with 0 bytes received
Backtrace:
     ▆
  1. ├─testthat::expect_identical(...) at test_z_cache.R:16:4
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. └─biomaRt:::.createHash(ensembl, attributes, filters, values)
  5.   └─biomaRt:::.listEnsemblArchives(http_config = martHTTPConfig(mart))
  6.     └─biomaRt:::.checkArchiveList(https, http_config)
  7.       └─biomaRt:::.getArchiveList(https = https, http_config = http_config)
  8.         └─httr2::req_perform(html_request)
  9.           └─httr2:::handle_resp(req, resp, error_call = error_call)
 10.             └─rlang::cnd_signal(resp)
── Error ('test_z_cache.R:28:1'): (code run outside of `test_that()`) ──────────
<httr2_failure/httr2_error/rlang_error/error/condition>
Error in `req_perform(html_request)`: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]: Operation timed out after 10003 milliseconds with 0 bytes received
Backtrace:
    ▆
 1. └─biomaRt:::.createHash(ensembl, attributes, filters, values) at test_z_cache.R:28:1
 2.   └─biomaRt:::.listEnsemblArchives(http_config = martHTTPConfig(mart))
 3.     └─biomaRt:::.checkArchiveList(https, http_config)
 4.       └─biomaRt:::.getArchiveList(https = https, http_config = http_config)
 5.         └─httr2::req_perform(html_request)
 6.           └─httr2:::handle_resp(req, resp, error_call = error_call)
 7.             └─rlang::cnd_signal(resp)

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 140 ]
Error: Test failures
Execution halted