Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2025-03-20 12:08 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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 752/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fobitools 1.14.0  (landing page)
Pol Castellano-Escuder
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/fobitools
git_branch: RELEASE_3_20
git_last_commit: 4e8eee6
git_last_commit_date: 2024-10-29 10:55:26 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


BUILD results for fobitools on merida1

To the developers/maintainers of the fobitools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fobitools.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: fobitools
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fobitools
StartedAt: 2025-03-17 19:42:21 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 19:53:04 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 643.2 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 fobitools
###
##############################################################################
##############################################################################


* checking for file ‘fobitools/DESCRIPTION’ ... OK
* preparing ‘fobitools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Dietary_data_annotation.Rmd’ using rmarkdown
Warning: ggrepel: 95 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘Dietary_data_annotation.Rmd’

--- re-building ‘MW_ST000291_enrichment.Rmd’ using rmarkdown

Quitting from MW_ST000291_enrichment.Rmd:79-91 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': argument is not a matrix
---
Backtrace:
    ▆
 1. ├─metabolomicsWorkbenchR::do_query(...)
 2. ├─metabolomicsWorkbenchR::do_query(...)
 3. │ ├─metabolomicsWorkbenchR::do_query(...)
 4. │ └─metabolomicsWorkbenchR::do_query(...)
 5. │   ├─BiocGenerics::as.data.frame(t(df))
 6. │   ├─base::t(df)
 7. │   └─base::t.default(df)
 8. └─base::.handleSimpleError(...)
 9.   └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MW_ST000291_enrichment.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': argument is not a matrix
--- failed re-building ‘MW_ST000291_enrichment.Rmd’

--- re-building ‘MW_ST000629_enrichment.Rmd’ using rmarkdown
Warning: ggrepel: 7 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘MW_ST000629_enrichment.Rmd’

--- re-building ‘food_enrichment_analysis.Rmd’ using rmarkdown
Warning: ggrepel: 101 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘food_enrichment_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘MW_ST000291_enrichment.Rmd’

Error: Vignette re-building failed.
Execution halted