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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biomaRt_2.66.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/biomaRt.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.66.0’
* 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 ‘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 loading without being on the library search path ... 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 ... 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
* 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:
    1. ├─testthat::expect_s3_class(...) at test_getBM.R:54:3
    2. │ └─testthat::quasi_label(enquo(object), 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(http_config)
    8.         └─biomaRt:::.getArchiveList(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)
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 156 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL biomaRt
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘biomaRt’ ...
** this is package ‘biomaRt’ version ‘2.66.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(biomaRt)
> 
> test_check("biomaRt")
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
Ensembl site unresponsive, trying www mirror
biomaRt cache uninitialized
- Location: /home/biocbuild/tmp/RtmpJYEBCB/biomart_cache_test
biomaRt cache
- Location: /home/biocbuild/tmp/RtmpJYEBCB/biomart_cache_test
- No. of files: 2
- Total size: 194 bytes
biomaRt cache
- Location: /home/biocbuild/tmp/RtmpJYEBCB/biomart_cache_test
- No. of files: 3
- Total size: 9.5 Kb
biomaRt cache
- Location: /home/biocbuild/tmp/RtmpJYEBCB/biomart_cache_test
- No. of files: 5
- Total size: 9.9 Kb
[ FAIL 1 | WARN 0 | SKIP 3 | PASS 156 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-exportFASTA.R:7:3', 'test-exportFASTA.R:18:3',
  'test_getBM.R:84:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_getBM.R:54:3'): 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 10000 milliseconds with 0 bytes received
Backtrace:
     ▆
  1. ├─testthat::expect_s3_class(...) at test_getBM.R:54:3
  2. │ └─testthat::quasi_label(enquo(object), 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(http_config)
  8.         └─biomaRt:::.getArchiveList(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)

[ FAIL 1 | WARN 0 | SKIP 3 | PASS 156 ]
Error: Test failures
Execution halted