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This page was generated on 2025-10-02 11:40 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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 206/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-29 13:40 -0400 (Mon, 29 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_21
git_last_commit: b8d718f
git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for biodbChebi on kjohnson1

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.

raw results


Summary

Package: biodbChebi
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi
StartedAt: 2025-09-29 20:09:39 -0400 (Mon, 29 Sep 2025)
EndedAt: 2025-09-29 20:09:54 -0400 (Mon, 29 Sep 2025)
EllapsedTime: 15.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbChebi
###
##############################################################################
##############################################################################


* 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  [20:09:50.952] Loading definitions from package biodb version 1.16.1.
INFO  [20:09:53.142] Loading definitions from package biodbChebi version 1.14.0.
INFO  [20:09:53.176] Loading definitions from package biodbHmdb version 1.14.0.
INFO  [20:09:53.211] Loading definitions from package biodbNcbi version 1.12.0.
INFO  [20:09:53.238] Loading definitions from package biodbNci version 1.12.0.
INFO  [20:09:53.247] Loading definitions from package biodbUniprot version 1.14.0.
INFO  [20:09:53.484] 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