Multiple platform build/check report for BioC 3.22 - BUILD results for MetMashR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4615
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4562
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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 MetMashR on kjohnson3

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

Version: 1.3.0

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

StartedAt: 2025-08-29 16:56:35 -0400 (Fri, 29 Aug 2025)

EndedAt: 2025-08-29 16:58:45 -0400 (Fri, 29 Aug 2025)

EllapsedTime: 130.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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


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

Quitting from Extending_MetMashR.Rmd:534-553 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "openbabel_structure" object: The required package "ChemmineOB" is not installed.
---
Backtrace:
    ▆
 1. └─MetMashR::openbabel_structure(...)
 2.   └─struct::new_struct(...)
 3.     ├─BiocGenerics::do.call(new, L)
 4.     ├─base::do.call(new, L)
 5.     └─methods (local) `<fn>`(...)
 6.       ├─methods::initialize(value, ...)
 7.       └─methods::initialize(value, ...)
 8.         └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Extending_MetMashR.Rmd' failed with diagnostics:
invalid class "openbabel_structure" object: The required package "ChemmineOB" is not installed.
--- failed re-building ‘Extending_MetMashR.Rmd’

--- re-building ‘annotate_mixtures.Rmd’ using rmarkdown
2025-08-29 16:58:00.507 R[69035:122128768] XType: Using static font registry.
--- finished re-building ‘annotate_mixtures.Rmd’

--- re-building ‘exploring_mtox.Rmd’ using rmarkdown

Quitting from exploring_mtox.Rmd:148-170 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "openbabel_structure" object: The required package "ChemmineOB" is not installed.
---
Backtrace:
    ▆
 1. └─MetMashR::openbabel_structure(...)
 2.   └─struct::new_struct(...)
 3.     ├─BiocGenerics::do.call(new, L)
 4.     ├─base::do.call(new, L)
 5.     └─methods (local) `<fn>`(...)
 6.       ├─methods::initialize(value, ...)
 7.       └─methods::initialize(value, ...)
 8.         └─methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'exploring_mtox.Rmd' failed with diagnostics:
invalid class "openbabel_structure" object: The required package "ChemmineOB" is not installed.
--- failed re-building ‘exploring_mtox.Rmd’

--- re-building ‘using_MetMashR.Rmd’ using rmarkdown
--- finished re-building ‘using_MetMashR.Rmd’

SUMMARY: processing the following files failed:
  ‘Extending_MetMashR.Rmd’ ‘exploring_mtox.Rmd’

Error: Vignette re-building failed.
Execution halted