Multiple platform build/check report for BioC 3.23 - BUILD results for anndataR on lconway

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"	4827
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4600
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4564
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 anndataR on lconway

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

Version: 1.1.0

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

StartedAt: 2025-11-18 16:03:00 -0500 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 16:05:57 -0500 (Tue, 18 Nov 2025)

EllapsedTime: 177.4 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data anndataR
###
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* checking for file ‘anndataR/DESCRIPTION’ ... OK
* preparing ‘anndataR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘anndataR.Rmd’ using rmarkdown
Warning: vignette 'usage_python' not found
--- finished re-building ‘anndataR.Rmd’

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

Quitting from usage_python.Rmd:59-62 [load_python_data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_call_impl()`:
! ModuleNotFoundError: No module named 'certifi'
Failed to open the url with default certificates. Please install `certifi` and try again.
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─sc$datasets$pbmc3k_processed()
 2.   └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'usage_python.Rmd' failed with diagnostics:
ModuleNotFoundError: No module named 'certifi'
Failed to open the url with default certificates. Please install `certifi` and try again.
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘usage_python.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted