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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gemma.R_3.3.0.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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.3.0’
* 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                           7.540  0.377  12.599
get_dataset_processed_expression             1.096  0.044   5.656
get_dataset_expression                       0.815  0.069   9.769
get_gene_differential_expression_values      0.772  0.071   5.083
get_dataset_raw_expression                   0.646  0.046  11.727
get_dataset_differential_expression_analyses 0.472  0.052   6.320
* 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:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('testOrderSanity.R:3:5'): sample ordering in outputs ─────────────────
  Error in `.body(fname = fname, validators = validators, endpoint = endpoint, 
      envWhere = environment(), isFile = isFile, header = header, 
      raw = raw, overwrite = overwrite, file = file, attributes = TRUE, 
      open_api_name = open_api_name, .call = match.call())`: https://gemma.msl.ubc.ca/rest/v2/datasets/2/data/processed
  HTTP code 429
  Backtrace:
      ▆
   1. └─gemma.R::get_dataset_processed_expression(2) at testOrderSanity.R:3:5
   2.   └─gemma.R:::.body(...)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 191 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* 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.