| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-10-23 11:30 -0400 (Thu, 23 Oct 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" | 3809 |
| 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 210/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
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To the developers/maintainers of the biodbHmdb package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.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: biodbHmdb |
| Version: 1.15.1 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodbHmdb |
| StartedAt: 2025-10-22 22:11:09 -0000 (Wed, 22 Oct 2025) |
| EndedAt: 2025-10-22 22:11:53 -0000 (Wed, 22 Oct 2025) |
| EllapsedTime: 44.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data biodbHmdb
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* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* preparing ‘biodbHmdb’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘biodbHmdb.Rmd’ using rmarkdown
INFO [22:11:48.593] Loading definitions from package biodb version 1.17.2.
INFO [22:11:51.669] Loading definitions from package biodbChebi version 1.15.1.
INFO [22:11:51.756] Loading definitions from package biodbHmdb version 1.15.1.
INFO [22:11:51.823] Loading definitions from package biodbNcbi version 1.13.1.
INFO [22:11:51.872] Loading definitions from package biodbNci version 1.13.1.
INFO [22:11:51.886] Loading definitions from package biodbUniprot version 1.15.1.
INFO [22:11:52.277] Extract whole database of hmdb.metabolites.
INFO [22:11:52.280] Extracting content of downloaded',
' HMDB metabolite database...
Quitting from biodbHmdb.Rmd:76-78 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `private$doExtractDownload()`:
! attempt to apply non-function
---
Backtrace:
▆
1. └─conn$getNbEntries()
2. └─private$doGetNbEntries(count = count)
3. └─self$getEntryIds()
4. └─private$doGetEntryIds(max.results = max.results, ...)
5. └─self$download()
6. └─private$doExtractDownload()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'biodbHmdb.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘biodbHmdb.Rmd’
SUMMARY: processing the following file failed:
‘biodbHmdb.Rmd’
Error: Vignette re-building failed.
Execution halted