Build/check report for BioC 3.23 annotations - BUILD results for org.Mxanthus.db on nebbiolo1

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"	4875
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 org.Mxanthus.db on nebbiolo1

To the developers/maintainers of the org.Mxanthus.db package:
- 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: org.Mxanthus.db

Version: 1.0.27

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data org.Mxanthus.db

StartedAt: 2025-12-17 06:02:14 -0500 (Wed, 17 Dec 2025)

EndedAt: 2025-12-17 06:02:40 -0500 (Wed, 17 Dec 2025)

EllapsedTime: 26.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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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 org.Mxanthus.db
###
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* checking for file ‘org.Mxanthus.db/DESCRIPTION’ ... OK
* preparing ‘org.Mxanthus.db’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘org.Mxanthus.db.Rmd’ using rmarkdown

Quitting from org.Mxanthus.db.Rmd:109-115 [11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'clusterProfiler':
 object 'load_OrgDb' is not exported by 'namespace:GOSemSim'
---
Backtrace:
    ▆
 1. └─base::library(clusterProfiler)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'org.Mxanthus.db.Rmd' failed with diagnostics:
package or namespace load failed for 'clusterProfiler':
 object 'load_OrgDb' is not exported by 'namespace:GOSemSim'
--- failed re-building ‘org.Mxanthus.db.Rmd’

SUMMARY: processing the following file failed:
  ‘org.Mxanthus.db.Rmd’

Error: Vignette re-building failed.
Execution halted