Multiple platform build/check report for BioC 3.21 - BUILD results for biodbChebi on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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 biodbChebi on kjohnson1

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

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi

StartedAt: 2025-10-13 20:04:06 -0400 (Mon, 13 Oct 2025)

EndedAt: 2025-10-13 20:04:22 -0400 (Mon, 13 Oct 2025)

EllapsedTime: 15.9 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi
###
##############################################################################
##############################################################################


* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* preparing ‘biodbChebi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbChebi.Rmd’ using rmarkdown
INFO  [20:04:17.661] Loading definitions from package biodb version 1.16.1.
INFO  [20:04:21.079] Loading definitions from package biodbChebi version 1.14.0.
INFO  [20:04:21.114] Loading definitions from package biodbHmdb version 1.14.0.
INFO  [20:04:21.150] Loading definitions from package biodbNcbi version 1.12.0.
INFO  [20:04:21.178] Loading definitions from package biodbNci version 1.12.0.
INFO  [20:04:21.189] Loading definitions from package biodbUniprot version 1.14.0.
INFO  [20:04:21.467] Load 3 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.

Quitting from biodbChebi.Rmd:63-65 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! XML content does not seem to be XML: ''
---
Backtrace:
    ▆
 1. └─chebi$getEntry(c("2528", "17053", "15440"))
 2.   └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
 3.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 4.       └─self$createEntryFromContent(...)
 5.         └─entry$parseContent(single.content)
 6.           └─private$doParseContent(content)
 7.             └─XML::xmlInternalTreeParse(content, asText = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbChebi.Rmd' failed with diagnostics:
XML content does not seem to be XML: ''
--- failed re-building ‘biodbChebi.Rmd’

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

Error: Vignette re-building failed.
Execution halted