Build/check report for BioC 3.23 - BUILD results for destiny on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4428
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BUILD results for destiny on nebbiolo1

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

Version: 3.25.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data destiny

StartedAt: 2025-10-30 16:52:58 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 16:54:31 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 93.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data destiny
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* checking for file ‘destiny/DESCRIPTION’ ... OK
* preparing ‘destiny’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘DPT.Rmd’ using rmarkdown
--- finished re-building ‘DPT.Rmd’

--- re-building ‘Diffusion-Map-recap.Rmd’ using rmarkdown
--- finished re-building ‘Diffusion-Map-recap.Rmd’

--- re-building ‘Diffusion-Maps.Rmd’ using rmarkdown
--- finished re-building ‘Diffusion-Maps.Rmd’

--- re-building ‘Gene-Relevance.Rmd’ using rmarkdown

Quitting from Gene-Relevance.Rmd:60-67 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! error in evaluating the argument 'x' in selecting a method for function 'mapIds': there is no package called 'org.Mm.eg.db'
---
Backtrace:
    ▆
 1. ├─AnnotationDbi::mapIds(...)
 2. ├─base::loadNamespace(x)
 3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
 5. │ │   └─base (local) doWithOneRestart(return(expr), restart)
 6. │ └─base::stop(cond)
 7. └─base (local) `<fn>`(`<pckgNtFE>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Gene-Relevance.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'mapIds': there is no package called 'org.Mm.eg.db'
--- failed re-building ‘Gene-Relevance.Rmd’

--- re-building ‘Global-Sigma.Rmd’ using rmarkdown
--- finished re-building ‘Global-Sigma.Rmd’

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

SUMMARY: processing the following file failed:
  ‘Gene-Relevance.Rmd’

Error: Vignette re-building failed.
Execution halted