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This page was generated on 2025-06-19 12:06 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4493
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

Package 1252/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetMashR 1.3.0  (landing page)
Gavin Rhys Lloyd
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025)
git_url: https://git.bioconductor.org/packages/MetMashR
git_branch: devel
git_last_commit: 7cec1a9
git_last_commit_date: 2025-04-15 13:42:42 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for MetMashR on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: MetMashR
Version: 1.3.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data MetMashR
StartedAt: 2025-06-17 00:44:10 -0000 (Tue, 17 Jun 2025)
EndedAt: 2025-06-17 00:50:08 -0000 (Tue, 17 Jun 2025)
EllapsedTime: 358.1 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 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

Quitting from annotate_mixtures.Rmd:836-869 [unnamed-chunk-27]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. ├─struct::model_apply(SM, R)
  2. └─MetMashR::model_apply(SM, R)
  3.   └─MetMashR (local) .local(M, D, ...)
  4.     ├─struct::model_apply(M[i], D)
  5.     └─MetMashR::model_apply(M[i], D)
  6.       └─MetMashR (local) .local(M, D, ...)
  7.         ├─MetMashR::read_database(M$database)
  8.         └─MetMashR::read_database(M$database)
  9.           └─MetMashR (local) .local(obj, ...)
 10.             ├─methods::callNextMethod(obj)
 11.             │ └─base::eval(call, callEnv)
 12.             │   └─base::eval(call, callEnv)
 13.             └─MetMashR (local) .nextMethod(obj)
 14.               └─MetMashR (local) .local(obj, ...)
 15.                 └─MetMashR:::.get_cached_path(obj)
 16.                   ├─BiocFileCache::bfcdownload(...)
 17.                   └─BiocFileCache::bfcdownload(...)
 18.                     └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'annotate_mixtures.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘annotate_mixtures.Rmd’

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

Quitting from exploring_mtox.Rmd:107-119 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. ├─MetMashR::read_database(MT)
  2. └─MetMashR::read_database(MT)
  3.   └─MetMashR (local) .local(obj, ...)
  4.     ├─methods::callNextMethod(obj)
  5.     │ └─base::eval(call, callEnv)
  6.     │   └─base::eval(call, callEnv)
  7.     └─MetMashR (local) .nextMethod(obj)
  8.       └─MetMashR (local) .local(obj, ...)
  9.         └─MetMashR:::.get_cached_path(obj)
 10.           ├─BiocFileCache::bfcdownload(...)
 11.           └─BiocFileCache::bfcdownload(...)
 12.             └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'exploring_mtox.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘exploring_mtox.Rmd’

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

Quitting from using_MetMashR.Rmd:201-210 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
     ▆
  1. ├─MetMashR::read_source(MT)
  2. └─MetMashR::read_source(MT)
  3.   └─MetMashR (local) .local(obj, ...)
  4.     ├─MetMashR::read_database(obj)
  5.     └─MetMashR::read_database(obj)
  6.       └─MetMashR (local) .local(obj, ...)
  7.         ├─methods::callNextMethod(obj)
  8.         │ └─base::eval(call, callEnv)
  9.         │   └─base::eval(call, callEnv)
 10.         └─MetMashR (local) .nextMethod(obj)
 11.           └─MetMashR (local) .local(obj, ...)
 12.             └─MetMashR:::.get_cached_path(obj)
 13.               ├─BiocFileCache::bfcdownload(...)
 14.               └─BiocFileCache::bfcdownload(...)
 15.                 └─BiocFileCache:::.util_download_and_rename(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'using_MetMashR.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘using_MetMashR.Rmd’

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

Error: Vignette re-building failed.
Execution halted