Multiple platform build/check report for BioC 3.23 - BUILD results for scFeatures 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
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4583
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 scFeatures on nebbiolo1

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

Version: 1.11.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scFeatures

StartedAt: 2025-12-15 19:43:36 -0500 (Mon, 15 Dec 2025)

EndedAt: 2025-12-15 19:45:53 -0500 (Mon, 15 Dec 2025)

EllapsedTime: 137.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scFeatures
###
##############################################################################
##############################################################################


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

Quitting from scFeatures_overview.Rmd:169-178 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'clusterProfiler':
 object 'load_OrgDb' is not exported by 'namespace:GOSemSim'
---
Backtrace:
     ▆
  1. └─scFeatures::run_association_study_report(scfeatures_result, output_folder)
  2.   ├─rmarkdown::render(...)
  3.   │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  4.   │   └─knitr:::process_file(text, output)
  5.   │     ├─xfun:::handle_error(...)
  6.   │     ├─base::withCallingHandlers(...)
  7.   │     └─knitr:::process_group(group)
  8.   │       └─knitr:::call_block(x)
  9.   │         └─knitr:::block_exec(params)
 10.   │           └─knitr:::eng_r(options)
 11.   │             ├─knitr:::in_input_dir(...)
 12.   │             │ └─knitr:::in_dir(input_dir(), expr)
 13.   │             └─knitr (local) evaluate(...)
 14.   │               └─evaluate::evaluate(...)
 15.   │                 ├─base::withRestarts(...)
 16.   │                 │ └─base (local) withRestartList(expr, restarts)
 17.   │                 │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 18.   │                 │   │ └─base (local) doWithOneRestart(return(expr), restart)
 19.   │                 │   └─base (local) withRestartList(expr, restarts[-nr])
 20.   │                 │     └─base (local) withOneRestart(expr, restarts[[1L]])
 21.   │                 │       └─base (local) doWithOneRestart(return(expr), restart)
 22.   │                 ├─evaluate:::with_handlers(...)
 23.   │                 │ ├─base::eval(call)
 24.   │                 │ │ └─base::eval(call)
 25.   │                 │ └─base::withCallingHandlers(...)
 26.   │                 ├─base::withVisible(eval(expr, envir))
 27.   │                 └─base::eval(expr, envir)
 28.   │                   └─base::eval(expr, envir)
 29.   └─base::library(clusterProfiler)
 30.     └─base::tryCatch(...)
 31.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 32.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 33.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted