Multiple platform build/check report for BioC 3.22 - BUILD results for Pirat on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4818
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4596
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4538
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4535
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 kjohnson3

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: 1.3.2

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

StartedAt: 2025-08-15 17:15:44 -0400 (Fri, 15 Aug 2025)

EndedAt: 2025-08-15 17:19:10 -0400 (Fri, 15 Aug 2025)

EllapsedTime: 206.4 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 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
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.10.0.tar.xz...
-> https://www.python.org/ftp/python/3.10.0/Python-3.10.0.tar.xz
Installing Python-3.10.0...
patching file aclocal.m4
patching file configure
patching file 'Misc/NEWS.d/next/Build/2021-10-11-16-27-38.bpo-45405.iSfdW5.rst'
patching file configure
patching file configure.ac
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from homebrew
Installed Python-3.10.0 to /Users/biocbuild/.pyenv/versions/3.10.0
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/Pirat/1.3.2/envPirat/lib/python3.10/site-packages (21.2.3)
Collecting pip
  Using cached pip-25.2-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/1.21.5/Pirat/1.3.2/envPirat/lib/python3.10/site-packages (57.4.0)
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 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Collecting numpy==1.24.1
  Downloading numpy-1.24.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (5.6 kB)
ERROR: Ignored the following versions that require a different python version: 2.3.0 Requires-Python >=3.11; 2.3.1 Requires-Python >=3.11; 2.3.2 Requires-Python >=3.11
ERROR: Could not find a version that satisfies the requirement pytorch==1.13 (from versions: 0.1.2, 1.0.2)
ERROR: No matching distribution found for pytorch==1.13

Quitting from Pirat.Rmd:90-92 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'numpy==1.24.1'", "'pytorch==1.13'", "'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==1.24.1'", "'pytorch==1.13'", "'cpuonly==2.0'"
--- failed re-building ‘Pirat.Rmd’

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

Error: Vignette re-building failed.
Execution halted