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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biomaRt.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biomaRt_2.57.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biomaRt.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘biomaRt/DESCRIPTION’ ... OK
* this is package ‘biomaRt’ version ‘2.57.0’
* 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 R 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:
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─biomaRt::useEnsemblGenomes("protists_mart", "bnatans_eg_gene")
    5.   └─biomaRt::listEnsemblGenomes(includeHosts = TRUE)
    6.     └─base::lapply(...)
    7.       └─biomaRt (local) FUN(X[[i]], ...)
    8.         ├─base::as.data.frame(...)
    9.         └─biomaRt:::.listMarts(...)
   10.           └─biomaRt:::bmRequest(...)
   11.             └─httr::stop_for_status(result)
  ── Failure ('test_ensembl_ssl_settings.R:71:5'): SSL settings are stored in the cache ──
  `httr_config <- .getEnsemblSSL()` produced messages.
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 146 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘accessing_ensembl.Rmd’ using ‘UTF-8’... OK
  ‘accessing_other_marts.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/biomaRt.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL biomaRt
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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)
> 
> test_check("biomaRt", encoding = "UTF-8")
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 146 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Linux (1)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_ensemblGenomes.R:23:5'): return type is correct ────────────────
<http_500/http_error/error/condition>
Error in `bmRequest(request = request, httr_config = httr_config, verbose = verbose)`: Internal Server Error (HTTP 500).
Backtrace:
     ▆
  1. ├─testthat::expect_is(...) at test_ensemblGenomes.R:23:4
  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)
  6.     └─base::lapply(...)
  7.       └─biomaRt (local) FUN(X[[i]], ...)
  8.         ├─base::as.data.frame(...)
  9.         └─biomaRt:::.listMarts(...)
 10.           └─biomaRt:::bmRequest(...)
 11.             └─httr::stop_for_status(result)
── Failure ('test_ensembl_ssl_settings.R:71:5'): SSL settings are stored in the cache ──
`httr_config <- .getEnsemblSSL()` produced messages.

[ FAIL 2 | WARN 0 | SKIP 1 | PASS 146 ]
Error: Test failures
Execution halted