Multiple platform build/check report for BioC 3.22 - BUILD results for Pirat on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4902
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4692
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4638
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 lconway

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: 1.4.0

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

StartedAt: 2025-11-03 18:15:21 -0500 (Mon, 03 Nov 2025)

EndedAt: 2025-11-03 18:16:10 -0500 (Mon, 03 Nov 2025)

EllapsedTime: 49.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat
###
##############################################################################
##############################################################################


* 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
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.22.0/Pirat/1.4.0/envPirat/lib/python3.9/site-packages (22.0.4)
Collecting pip
  Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.22.0/Pirat/1.4.0/envPirat/lib/python3.9/site-packages (58.1.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.1.0
    Uninstalling setuptools-58.1.0:
      Successfully uninstalled setuptools-58.1.0
  Attempting uninstall: pip
    Found existing installation: pip 22.0.4
    Uninstalling pip-22.0.4:
      Successfully uninstalled pip-22.0.4
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
Collecting numpy==1.20.2
  Using cached numpy-1.20.2-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.0 kB)
ERROR: Ignored the following versions that require a different python version: 2.1.0 Requires-Python >=3.10; 2.1.1 Requires-Python >=3.10; 2.1.2 Requires-Python >=3.10; 2.1.3 Requires-Python >=3.10; 2.2.0 Requires-Python >=3.10; 2.2.1 Requires-Python >=3.10; 2.2.2 Requires-Python >=3.10; 2.2.3 Requires-Python >=3.10; 2.2.4 Requires-Python >=3.10; 2.2.5 Requires-Python >=3.10; 2.2.6 Requires-Python >=3.10; 2.3.0 Requires-Python >=3.11; 2.3.1 Requires-Python >=3.11; 2.3.2 Requires-Python >=3.11; 2.3.3 Requires-Python >=3.11; 2.3.4 Requires-Python >=3.11
ERROR: Could not find a version that satisfies the requirement pytorch==1.12.0 (from versions: 0.1.2, 1.0.2)
ERROR: No matching distribution found for pytorch==1.12.0

Quitting from Pirat.Rmd:90-92 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'numpy==1.20.2'", "'pytorch==1.12.0'", "'cpuonly==2.0'"
---
Backtrace:
    ▆
 1. └─Pirat::my_pipeline_llkimpute(subbouyssie)
 2.   └─basilisk::basiliskStart(envPirat)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_create(...)
 6.           └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Pirat.Rmd' failed with diagnostics:
Error installing package(s): "'numpy==1.20.2'", "'pytorch==1.12.0'", "'cpuonly==2.0'"
--- failed re-building ‘Pirat.Rmd’

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

Error: Vignette re-building failed.
Execution halted