Build/check report for BioC 3.24 - BUILD results for MetaboAnnotation on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4844
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 MetaboAnnotation on nebbiolo2

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

Version: 1.17.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 MetaboAnnotation

StartedAt: 2026-05-04 18:41:42 -0400 (Mon, 04 May 2026)

EndedAt: 2026-05-04 18:43:05 -0400 (Mon, 04 May 2026)

EllapsedTime: 83.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 MetaboAnnotation
###
##############################################################################
##############################################################################


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

Quitting from MetaboAnnotation.Rmd:727-732 [unnamed-chunk-41]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'target' in selecting a method for function 'matchSpectra': unable to open database file
---
Backtrace:
     ▆
  1. ├─MetaboAnnotation::matchSpectra(...)
  2. ├─MetaboAnnotation::matchSpectra(...)
  3. │ └─MetaboAnnotation (local) .local(query, target, param, ...)
  4. │   ├─MetaboAnnotation::matchSpectra(...)
  5. │   ├─Spectra::Spectra(db)
  6. │   └─CompoundDb::Spectra(db)
  7. │     └─CompoundDb (local) .local(object, ...)
  8. │       ├─ProtGenerics::backendInitialize(...)
  9. │       └─CompoundDb::backendInitialize(...)
 10. │         └─CompoundDb (local) .local(object, ...)
 11. │           └─CompoundDb:::.fetch_data(...)
 12. │             ├─DBI::dbGetQuery(...)
 13. │             └─DBI::dbGetQuery(...)
 14. │               └─DBI (local) .local(conn, statement, ...)
 15. │                 ├─DBI::dbFetch(rs, n = n, ...)
 16. │                 └─RSQLite::dbFetch(rs, n = n, ...)
 17. │                   └─RSQLite (local) .local(res, n, ...)
 18. │                     └─RSQLite:::result_fetch(res@ptr, n = n)
 19. └─base::.handleSimpleError(...)
 20.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MetaboAnnotation.Rmd' failed with diagnostics:
error in evaluating the argument 'target' in selecting a method for function 'matchSpectra': unable to open database file
--- failed re-building ‘MetaboAnnotation.Rmd’

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

Error: Vignette re-building failed.
Execution halted