Multiple platform build/check report for BioC 3.22 - BUILD results for ORFik on taishan

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"	4883
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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 ORFik on taishan

To the developers/maintainers of the ORFik package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: ORFik

Version: 1.30.2

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ORFik

StartedAt: 2025-12-26 04:16:02 -0000 (Fri, 26 Dec 2025)

EndedAt: 2025-12-26 04:22:23 -0000 (Fri, 26 Dec 2025)

EllapsedTime: 380.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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

--- re-building ‘Importing_Data.Rmd’ using rmarkdown

Quitting from Importing_Data.Rmd:189-194 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `qs2::qs_save()`:
! nthreads > 1 requires TBB, see the readme and vignette for details.
---
Backtrace:
    ▆
 1. └─ORFik::makeTxdbFromGenome(...)
 2.   └─ORFik:::optimizeTranscriptRegions(txdb, optimized_path)
 3.     └─ORFik::save_RDSQS(...)
 4.       └─qs2::qs_save(object, file, nthread = nthread)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Importing_Data.Rmd' failed with diagnostics:
nthreads > 1 requires TBB, see the readme and vignette for details.
--- failed re-building ‘Importing_Data.Rmd’

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

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

--- re-building ‘Ribo-seq_pipeline-human.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-human.Rmd’

--- re-building ‘Ribo-seq_pipeline-yeast.Rmd’ using rmarkdown
--- finished re-building ‘Ribo-seq_pipeline-yeast.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted