Multiple platform build/check report for BioC 3.21 - BUILD results for biodbUniprot on merida1

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*

BUILD results for biodbUniprot on merida1

To the developers/maintainers of the biodbUniprot package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbUniprot.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: biodbUniprot

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbUniprot

StartedAt: 2025-10-13 17:26:32 -0400 (Mon, 13 Oct 2025)

EndedAt: 2025-10-13 17:27:02 -0400 (Mon, 13 Oct 2025)

EllapsedTime: 30.2 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 biodbUniprot
###
##############################################################################
##############################################################################


* checking for file ‘biodbUniprot/DESCRIPTION’ ... OK
* preparing ‘biodbUniprot’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbUniprot.Rmd’ using rmarkdown
INFO  [17:26:54.997] Loading definitions from package biodb version 1.16.1.
INFO  [17:26:59.968] Loading definitions from package biodbChebi version 1.14.0.
INFO  [17:27:00.057] Loading definitions from package biodbHmdb version 1.14.0.
INFO  [17:27:00.157] Loading definitions from package biodbNcbi version 1.12.0.
INFO  [17:27:00.230] Loading definitions from package biodbNci version 1.12.0.
INFO  [17:27:00.251] Loading definitions from package biodbUniprot version 1.14.0.
INFO  [17:27:00.623] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/uniprot-958d776f924f3e7a3bae586fa731b40c.

Quitting from biodbUniprot.Rmd:83-86 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `conn$wsSearch()`:
! object 'BiodbUrl' not found
---
Backtrace:
    ▆
 1. └─conn$wsSearch(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbUniprot.Rmd' failed with diagnostics:
object 'BiodbUrl' not found
--- failed re-building ‘biodbUniprot.Rmd’

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

Error: Vignette re-building failed.
Execution halted