| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 206/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.14.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.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: biodbChebi |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi |
| StartedAt: 2025-10-13 20:04:06 -0400 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 20:04:22 -0400 (Mon, 13 Oct 2025) |
| EllapsedTime: 15.9 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 biodbChebi
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* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* preparing ‘biodbChebi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbChebi.Rmd’ using rmarkdown
INFO [20:04:17.661] Loading definitions from package biodb version 1.16.1.
INFO [20:04:21.079] Loading definitions from package biodbChebi version 1.14.0.
INFO [20:04:21.114] Loading definitions from package biodbHmdb version 1.14.0.
INFO [20:04:21.150] Loading definitions from package biodbNcbi version 1.12.0.
INFO [20:04:21.178] Loading definitions from package biodbNci version 1.12.0.
INFO [20:04:21.189] Loading definitions from package biodbUniprot version 1.14.0.
INFO [20:04:21.467] Load 3 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
Quitting from biodbChebi.Rmd:63-65 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! XML content does not seem to be XML: ''
---
Backtrace:
▆
1. └─chebi$getEntry(c("2528", "17053", "15440"))
2. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
3. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
4. └─self$createEntryFromContent(...)
5. └─entry$parseContent(single.content)
6. └─private$doParseContent(content)
7. └─XML::xmlInternalTreeParse(content, asText = TRUE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'biodbChebi.Rmd' failed with diagnostics:
XML content does not seem to be XML: ''
--- failed re-building ‘biodbChebi.Rmd’
SUMMARY: processing the following file failed:
‘biodbChebi.Rmd’
Error: Vignette re-building failed.
Execution halted