Multiple platform build/check report for BioC 3.22 - BUILD results for scviR 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"	4813
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4550
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4592
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4534
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 scviR on kjohnson3

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

Version: 1.9.11

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

StartedAt: 2025-08-05 17:36:22 -0400 (Tue, 05 Aug 2025)

EndedAt: 2025-08-05 17:37:01 -0400 (Tue, 05 Aug 2025)

EllapsedTime: 39.4 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 scviR
###
##############################################################################
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* checking for file ‘scviR/DESCRIPTION’ ... OK
* preparing ‘scviR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘citeseq_tut.Rmd’ using rmarkdown
--- finished re-building ‘citeseq_tut.Rmd’

--- re-building ‘compch12.Rmd’ using rmarkdown
/Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/scviR/1.9.11/bsklenv/lib/python3.10/site-packages/anndata/__init__.py:42: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
  warnings.warn(
2025-08-05 17:36:50.571 R[95619:461781466] XType: Using static font registry.
--- finished re-building ‘compch12.Rmd’

--- re-building ‘new_citeseq.Rmd’ using rmarkdown

Quitting from new_citeseq.Rmd:41-48 [doe44]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_module_import()`:
! OSError: Could not find/load shared object file
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─scviR::muonR()
 2.   └─basilisk::basiliskRun(...)
 3.     └─scviR (local) fun(...)
 4.       └─reticulate::import("muon")
 5.         └─reticulate:::py_module_import(module, convert = convert)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'new_citeseq.Rmd' failed with diagnostics:
OSError: Could not find/load shared object file
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘new_citeseq.Rmd’

--- re-building ‘scviR.Rmd’ using rmarkdown
--- finished re-building ‘scviR.Rmd’

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

Error: Vignette re-building failed.
Execution halted