Multiple platform build/check report for BioC 3.20 - BUILD results for gemma.R on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for gemma.R on nebbiolo2

To the developers/maintainers of the gemma.R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemma.R.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: gemma.R

Version: 3.2.1

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R

StartedAt: 2025-03-17 18:11:23 -0400 (Mon, 17 Mar 2025)

EndedAt: 2025-03-17 18:15:34 -0400 (Mon, 17 Mar 2025)

EllapsedTime: 251.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R
###
##############################################################################
##############################################################################


* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gemma.R.Rmd’ using rmarkdown

Quitting from gemma.R.Rmd:378-424 [diffExpr]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'head': ℹ In argument: `..1 = contrast_bipolar disorder has_modifier manic
  phase_pvalue`.
Caused by error:
! object 'contrast_bipolar disorder has_modifier manic phase_pvalue' not found
---
Backtrace:
     ▆
  1. ├─... %>% gemma_kable()
  2. ├─gemma.R::gemma_kable(.)
  3. │ └─base::ncol(table)
  4. ├─utils::head(., 10)
  5. ├─dplyr::select(...)
  6. ├─dplyr::arrange(., `contrast_bipolar disorder has_modifier manic phase_pvalue`)
  7. ├─dplyr:::arrange.data.frame(., `contrast_bipolar disorder has_modifier manic phase_pvalue`)
  8. │ └─dplyr:::arrange_rows(.data, dots = dots, locale = .locale)
  9. │   ├─dplyr::mutate(data, `:=`("{name}", !!dot), .keep = "none")
 10. │   └─dplyr:::mutate.data.frame(data, `:=`("{name}", !!dot), .keep = "none")
 11. │     └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 12. │       ├─base::withCallingHandlers(...)
 13. │       └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 14. │         └─mask$eval_all_mutate(quo)
 15. │           └─dplyr (local) eval()
 16. ├─base::.handleSimpleError(...)
 17. │ └─dplyr (local) h(simpleError(msg, call))
 18. │   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
 19. │     └─rlang:::signal_abort(cnd, .file)
 20. │       └─base::signalCondition(cnd)
 21. └─base (local) `<fn>`(`<dply:::_>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gemma.R.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'head': ℹ In argument: `..1 = contrast_bipolar disorder has_modifier manic
  phase_pvalue`.
Caused by error:
! object 'contrast_bipolar disorder has_modifier manic phase_pvalue' not found
--- failed re-building ‘gemma.R.Rmd’

--- re-building ‘metadata.Rmd’ using rmarkdown
--- finished re-building ‘metadata.Rmd’

--- re-building ‘metanalysis.Rmd’ using rmarkdown
--- finished re-building ‘metanalysis.Rmd’

SUMMARY: processing the following file failed:
  ‘gemma.R.Rmd’

Error: Vignette re-building failed.
Execution halted