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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gemma.R_3.4.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gemma.R.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.4.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘gemma.R’ 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 ... 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
get_dataset_object                           10.098  0.303  16.962
dot-get_gene_differential_expression_values   1.589  0.075   7.815
get_gene_differential_expression_values       1.543  0.108   9.843
get_dataset_processed_expression              1.400  0.016   9.201
get_dataset_expression                        0.968  0.055   5.261
update_result                                 0.722  0.016  17.726
get_dataset_raw_expression                    0.676  0.060   7.285
get_dataset_differential_expression_analyses  0.588  0.059  17.594
get_platform_annotations                      0.571  0.032  13.345
get_differential_expression_values            0.239  0.012  11.125
* 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:
    9. │         └─gemma.R:::processDEMatrix(ret)
   10. │           └─gemma.R::get_result_sets(resultSets = parent.frame(n = 2)$resultSet)
   11. │             ├─gemma.R:::.body(...)
   12. │             │ └─base::eval(requestExpr, envir = envWhere)
   13. │             │   └─base::eval(requestExpr, envir = envWhere)
   14. │             └─httr::GET(...)
   15. │               └─httr:::request_perform(req, hu$handle$handle)
   16. │                 ├─httr:::request_fetch(req$output, req$url, handle)
   17. │                 └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   18. │                   └─curl::curl_fetch_memory(url, handle = handle)
   19. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 171 ]
  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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gemma.R.Rcheck/00check.log’
for details.