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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4894
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4684
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4629
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4642
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 MsDataHub on taishan

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

Version: 1.9.0

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

StartedAt: 2025-10-21 01:31:25 -0000 (Tue, 21 Oct 2025)

EndedAt: 2025-10-21 01:32:15 -0000 (Tue, 21 Oct 2025)

EllapsedTime: 50.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data MsDataHub
###
##############################################################################
##############################################################################


* checking for file ‘MsDataHub/DESCRIPTION’ ... OK
* preparing ‘MsDataHub’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MsDataHub.Rmd’ using rmarkdown

Quitting from MsDataHub.Rmd:70-73 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error: Can not open file /home/biocbuild/.cache/R/ExperimentHub/3bc43e5654645f_7862! Original error was: Error in eval(expr, envir): [SAXParser::parse()] Empty tag at offset 23330813.

---
Backtrace:
     ▆
  1. ├─Spectra::Spectra(f)
  2. └─Spectra::Spectra(f)
  3.   └─Spectra (local) .local(object, ...)
  4.     └─Spectra:::.create_spectra(...)
  5.       ├─ProtGenerics::backendInitialize(...)
  6.       └─Spectra::backendInitialize(...)
  7.         └─Spectra (local) .local(object, ...)
  8.           ├─base::do.call(...)
  9.           ├─BiocParallel::bplapply(...)
 10.           └─BiocParallel::bplapply(...)
 11.             └─BiocParallel:::.bpinit(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MsDataHub.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error: Can not open file /home/biocbuild/.cache/R/ExperimentHub/3bc43e5654645f_7862! Original error was: Error in eval(expr, envir): [SAXParser::parse()] Empty tag at offset 23330813.


--- failed re-building ‘MsDataHub.Rmd’

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

Error: Vignette re-building failed.
Execution halted