Multiple platform build/check report for BioC 3.21 - BUILD results for VariantAnnotation on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4547
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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 VariantAnnotation on kunpeng2

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

Version: 1.53.1

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

StartedAt: 2025-03-22 03:26:52 -0000 (Sat, 22 Mar 2025)

EndedAt: 2025-03-22 03:30:21 -0000 (Sat, 22 Mar 2025)

EllapsedTime: 209.1 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 VariantAnnotation
###
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* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* preparing ‘VariantAnnotation’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘VariantAnnotation.Rmd’ using rmarkdown
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
--- finished re-building ‘VariantAnnotation.Rmd’

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

Quitting from ensemblVEP.Rmd:53-58 [lksnv]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `post_Hs_region()`:
! Bad Gateway (HTTP 502).
---
Backtrace:
    ▆
 1. └─VariantAnnotation::vep_by_region(...)
 2.   └─VariantAnnotation::post_Hs_region(...)
 3.     └─httr::stop_for_status(ans)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ensemblVEP.Rmd' failed with diagnostics:
Bad Gateway (HTTP 502).
--- failed re-building ‘ensemblVEP.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted