Multiple platform build/check report for BioC 3.22 - BUILD results for biodbHmdb 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"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 biodbHmdb on taishan

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

Version: 1.16.0

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

StartedAt: 2025-11-18 00:02:32 -0000 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 00:03:31 -0000 (Tue, 18 Nov 2025)

EllapsedTime: 59.0 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 biodbHmdb
###
##############################################################################
##############################################################################


* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* preparing ‘biodbHmdb’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbHmdb.Rmd’ using rmarkdown
INFO  [00:03:28.265] Loading definitions from package biodb version 1.18.0.
INFO  [00:03:30.130] Loading definitions from package biodbChebi version 1.16.0.
INFO  [00:03:30.178] Loading definitions from package biodbHmdb version 1.16.0.
INFO  [00:03:30.229] Loading definitions from package biodbNcbi version 1.14.0.
INFO  [00:03:30.266] Loading definitions from package biodbNci version 1.14.0.
INFO  [00:03:30.278] Loading definitions from package biodbUniprot version 1.16.0.
INFO  [00:03:30.521] Extract whole database of hmdb.metabolites.
INFO  [00:03:30.522] Extracting content of downloaded',
                    ' HMDB metabolite database...

Quitting from biodbHmdb.Rmd:76-78 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `private$doExtractDownload()`:
! attempt to apply non-function
---
Backtrace:
    ▆
 1. └─conn$getNbEntries()
 2.   └─private$doGetNbEntries(count = count)
 3.     └─self$getEntryIds()
 4.       └─private$doGetEntryIds(max.results = max.results, ...)
 5.         └─self$download()
 6.           └─private$doExtractDownload()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbHmdb.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘biodbHmdb.Rmd’

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

Error: Vignette re-building failed.
Execution halted