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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 MSstatsBioNet on kunpeng2

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

Version: 1.0.0

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

StartedAt: 2025-04-18 00:44:58 -0000 (Fri, 18 Apr 2025)

EndedAt: 2025-04-18 00:45:27 -0000 (Fri, 18 Apr 2025)

EllapsedTime: 29.0 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 MSstatsBioNet
###
##############################################################################
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* checking for file ‘MSstatsBioNet/DESCRIPTION’ ... OK
* preparing ‘MSstatsBioNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MSstatsBioNet.Rmd’ using rmarkdown

Quitting from MSstatsBioNet.Rmd:108-112 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `statement$data`:
! $ operator is invalid for atomic vectors
---
Backtrace:
    ▆
 1. └─MSstatsBioNet::getSubnetworkFromIndra(annotated_df, pvalueCutoff = 0.05)
 2.   └─MSstatsBioNet:::.filterIndraResponse(...)
 3.     └─base::Filter(...)
 4.       ├─base::unlist(lapply(x, f))
 5.       └─base::lapply(x, f)
 6.         └─MSstatsBioNet (local) FUN(X[[i]], ...)
 7.           └─statement$data$stmt_type %in% interaction_types
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MSstatsBioNet.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘MSstatsBioNet.Rmd’

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

Error: Vignette re-building failed.
Execution halted