Pol Castellano-Escuder
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/fobitools |
| git_branch: devel |
| git_last_commit: f026ba6 |
| git_last_commit_date: 2025-10-29 11:06:08 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-21 11:38 -0500 (Fri, 21 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 767/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fobitools 1.19.0 (landing page) Pol Castellano-Escuder
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: fobitools |
| Version: 1.19.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fobitools |
| StartedAt: 2025-11-20 17:03:42 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 17:04:47 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 65.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data fobitools
###
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* checking for file ‘fobitools/DESCRIPTION’ ... OK
* preparing ‘fobitools’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Dietary_data_annotation.Rmd’ using rmarkdown
2025-11-20 17:04:07.578 R[80327:52784095] XType: Using static font registry.
Warning: ggrepel: 104 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 `curl::curl_fetch_memory()`:
! Timeout was reached [www.metabolomicsworkbench.org]:
Connection timed out after 10000 milliseconds
---
Backtrace:
▆
1. ├─metabolomicsWorkbenchR::do_query(...)
2. ├─metabolomicsWorkbenchR::do_query(...)
3. │ ├─metabolomicsWorkbenchR::do_query(...)
4. │ └─metabolomicsWorkbenchR::do_query(...)
5. │ ├─metabolomicsWorkbenchR::do_query(...)
6. │ └─metabolomicsWorkbenchR::do_query(...)
7. │ ├─metabolomicsWorkbenchR::do_query(...)
8. │ └─metabolomicsWorkbenchR::do_query(...)
9. │ └─metabolomicsWorkbenchR:::use_api(str, output_item, input_value)
10. │ └─httr::GET(url = str)
11. │ └─httr:::request_perform(req, hu$handle$handle)
12. │ ├─httr:::request_fetch(req$output, req$url, handle)
13. │ └─httr:::request_fetch.write_memory(req$output, req$url, handle)
14. │ └─curl::curl_fetch_memory(url, handle = handle)
15. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MW_ST000291_enrichment.Rmd' failed with diagnostics:
Timeout was reached [www.metabolomicsworkbench.org]:
Connection timed out after 10000 milliseconds
--- 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