Multiple platform build/check report for BioC 3.21 - BUILD results for Pirat on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4823
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4565
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4603
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4544
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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 Pirat on nebbiolo1

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

Version: 1.2.3

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat

StartedAt: 2025-08-03 18:39:08 -0400 (Sun, 03 Aug 2025)

EndedAt: 2025-08-03 18:39:38 -0400 (Sun, 03 Aug 2025)

EllapsedTime: 30.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat
###
##############################################################################
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* checking for file ‘Pirat/DESCRIPTION’ ... OK
* preparing ‘Pirat’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Pirat.Rmd’ using rmarkdown
/home/biocbuild/bbs-3.21-bioc/R/site-library/reticulate/python/rpytools/loader.py:120: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  return _find_and_load(name, import_)

Quitting from Pirat.Rmd:90-92 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_module_import()`:
! ImportError: /home/biocbuild/.cache/R/basilisk/1.20.0/Pirat/1.2.3/envPirat/lib/python3.9/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent
Run `reticulate::py_last_error()` for details.
---
Backtrace:
    ▆
 1. └─Pirat::my_pipeline_llkimpute(subbouyssie)
 2.   └─basilisk::basiliskRun(...)
 3.     └─Pirat (local) fun(...)
 4.       └─Pirat::pipeline_llkimpute(arg1, ...)
 5.         └─reticulate::import("PyPirat")
 6.           └─reticulate:::py_module_import(module, convert = convert)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Pirat.Rmd' failed with diagnostics:
ImportError: /home/biocbuild/.cache/R/basilisk/1.20.0/Pirat/1.2.3/envPirat/lib/python3.9/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘Pirat.Rmd’

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

Error: Vignette re-building failed.
Execution halted