Multiple platform build/check report for BioC 3.20 - BUILD results for fobitools on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4716
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4466
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4498
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4446
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4445
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 fobitools on kunpeng2

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

Version: 1.13.0

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

StartedAt: 2024-10-02 22:30:02 -0000 (Wed, 02 Oct 2024)

EndedAt: 2024-10-02 22:31:11 -0000 (Wed, 02 Oct 2024)

EllapsedTime: 69.1 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 fobitools
###
##############################################################################
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* checking for file ‘fobitools/DESCRIPTION’ ... OK
* preparing ‘fobitools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Dietary_data_annotation.Rmd’ using rmarkdown
Warning: ggrepel: 122 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘Dietary_data_annotation.Rmd’

--- re-building ‘MW_ST000291_enrichment.Rmd’ using rmarkdown

Quitting from lines 80-91 [unnamed-chunk-5] (MW_ST000291_enrichment.Rmd)
Error: processing vignette 'MW_ST000291_enrichment.Rmd' failed with diagnostics:
Timeout was reached: [www.metabolomicsworkbench.org] Resolving timed out after 10000 milliseconds
--- failed re-building ‘MW_ST000291_enrichment.Rmd’

--- re-building ‘MW_ST000629_enrichment.Rmd’ using rmarkdown

Quitting from lines 192-196 [unnamed-chunk-14] (MW_ST000629_enrichment.Rmd)
Error: processing vignette 'MW_ST000629_enrichment.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `logFC` doesn't exist.
--- failed re-building ‘MW_ST000629_enrichment.Rmd’

--- re-building ‘food_enrichment_analysis.Rmd’ using rmarkdown
Warning: ggrepel: 137 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘food_enrichment_analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘MW_ST000291_enrichment.Rmd’ ‘MW_ST000629_enrichment.Rmd’

Error: Vignette re-building failed.
Execution halted