Multiple platform build/check report for BioC 3.22 - BUILD results for biodbHmdb on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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 nebbiolo2

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.

raw results

Summary

Package: biodbHmdb

Version: 1.15.1

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 biodbHmdb

StartedAt: 2025-08-08 16:19:02 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 16:19:41 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 39.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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  [16:19:39.237] Loading definitions from package biodb version 1.17.1.
INFO  [16:19:40.719] Loading definitions from package biodbChebi version 1.15.1.
INFO  [16:19:40.750] Loading definitions from package biodbHmdb version 1.15.1.
INFO  [16:19:40.780] Loading definitions from package biodbNcbi version 1.13.1.
INFO  [16:19:40.803] Loading definitions from package biodbNci version 1.13.1.
INFO  [16:19:40.810] Loading definitions from package biodbUniprot version 1.15.1.
INFO  [16:19:40.972] Extract whole database of hmdb.metabolites.
INFO  [16:19:40.973] 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