Multiple platform build/check report for BioC 3.22 - BUILD results for biodbNcbi on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4553
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4595
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4537
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 biodbNcbi on kjohnson3

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

Version: 1.13.1

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

StartedAt: 2025-08-08 15:43:48 -0400 (Fri, 08 Aug 2025)

EndedAt: 2025-08-08 15:43:54 -0400 (Fri, 08 Aug 2025)

EllapsedTime: 6.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data biodbNcbi
###
##############################################################################
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* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* preparing ‘biodbNcbi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biodbNcbi.Rmd’ using rmarkdown
INFO  [15:43:52.874] Loading definitions from package biodb version 1.17.1.
INFO  [15:43:53.603] Loading definitions from package biodbChebi version 1.15.1.
INFO  [15:43:53.614] Loading definitions from package biodbHmdb version 1.15.1.
INFO  [15:43:53.625] Loading definitions from package biodbNcbi version 1.13.1.
INFO  [15:43:53.634] Loading definitions from package biodbNci version 1.13.1.
INFO  [15:43:53.637] Loading definitions from package biodbUniprot version 1.15.1.

Quitting from biodbNcbi.Rmd:72-74 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! 'BiodbUrl' is not an exported object from 'namespace:biodb'
---
Backtrace:
    ▆
 1. └─gene$getNbEntries()
 2.   └─private$doGetNbEntries(count = count)
 3.     └─self$wsEinfo(retfmt = "parsed")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbNcbi.Rmd' failed with diagnostics:
'BiodbUrl' is not an exported object from 'namespace:biodb'
--- failed re-building ‘biodbNcbi.Rmd’

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

Error: Vignette re-building failed.
Execution halted