Build/check report for BioC 3.22 - BUILD results for MOSim on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4888
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BUILD results for MOSim on nebbiolo2

To the developers/maintainers of the MOSim package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOSim.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: MOSim

Version: 2.6.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 MOSim

StartedAt: 2026-02-03 18:36:00 -0500 (Tue, 03 Feb 2026)

EndedAt: 2026-02-03 18:38:18 -0500 (Tue, 03 Feb 2026)

EllapsedTime: 138.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 MOSim
###
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* checking for file ‘MOSim/DESCRIPTION’ ... OK
* preparing ‘MOSim’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MOSim.Rmd’ using rmarkdown

Quitting from MOSim.Rmd:391-411 [code11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! `group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
---
Backtrace:
     ▆
  1. ├─MOSim::mosim(omics = omics_list, omicsOptions = omics_options)
  2. │ ├─base::do.call(new, c(Class = "MOSimulation", simParams))
  3. │ └─methods (local) `<fn>`(Class = "MOSimulation", simulators = `<named list>`)
  4. │   ├─methods::initialize(value, ...)
  5. │   └─MOSim (local) initialize(value, ...)
  6. │     ├─base::suppressWarnings(...)
  7. │     │ └─base::withCallingHandlers(...)
  8. │     └─base::sapply(...)
  9. │       └─base::lapply(X = X, FUN = FUN, ...)
 10. │         └─MOSim (local) FUN(X[[i]], ...)
 11. │           └─dplyr::group_by(regTable[regDupsDE, ], ID) %>% ...
 12. ├─dplyr::do(., classifyDups(.))
 13. ├─dplyr:::do.grouped_df(., classifyDups(.))
 14. │ └─rlang::eval_tidy(args[[j]], mask)
 15. └─MOSim (local) classifyDups(.)
 16.   └─dplyr::group_by_(regGenes, .dots = dplyrGroup)
 17.     └─dplyr:::lazy_defunct("group_by")
 18.       └─lifecycle::deprecate_stop(...)
 19.         └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MOSim.Rmd' failed with diagnostics:
`group_by_()` was deprecated in dplyr 0.7.0 and is now defunct.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
--- failed re-building ‘MOSim.Rmd’

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

SUMMARY: processing the following file failed:
  ‘MOSim.Rmd’

Error: Vignette re-building failed.
Execution halted