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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gemma.R_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/gemma.R.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘1.2.0’
* 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 ‘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 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 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 ... NOTE
get_dataset_object : <anonymous>: no visible binding for global
  variable ‘contrast.id’
get_dataset_object : <anonymous>: no visible global function definition
  for ‘mutate’
Undefined global functions or variables:
  contrast.id mutate
* 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 ... ERROR
Running examples in ‘gemma.R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_dataset_differential_expression_analyses
> ### Title: Retrieve the differential analyses of a dataset
> ### Aliases: get_dataset_differential_expression_analyses
> ### Keywords: dataset
> 
> ### ** Examples
> 
> result <- get_dataset_differential_expression_analyses("GSE2018")
> get_differential_expression_values(resultSet = result$result.ID)
Error in if (is.na(dataset) == TRUE && is.na(resultSet) == FALSE) { : 
  missing value where TRUE/FALSE needed
Calls: get_differential_expression_values
Execution halted
* 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_gt(nrow(dat[[1]]), 10) at testConvenience.R:54:4
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::nrow(dat[[1]])
  ── Error ('testGeneEndpoints.R:46:5'): getGeneGO queries work ──────────────────
  Error in `eval(code, test_env)`: object 'term.Name' not found
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at testGeneEndpoints.R:46:4
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 4 | WARN 6 | SKIP 4 | PASS 112 ]
  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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/gemma.R.Rcheck/00check.log’
for details.