Back to Multiple platform build/check report for BioC 3.23:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-11-21 11:38 -0500 (Fri, 21 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4829
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4602
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4566
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

Package 1585/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pirat 1.5.5  (landing page)
Lucas Etourneau
Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025)
git_url: https://git.bioconductor.org/packages/Pirat
git_branch: devel
git_last_commit: ad69e4a
git_last_commit_date: 2025-11-19 13:05:34 -0500 (Wed, 19 Nov 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES

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: 1.5.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat
StartedAt: 2025-11-20 18:12:47 -0500 (Thu, 20 Nov 2025)
EndedAt: 2025-11-20 18:13:40 -0500 (Thu, 20 Nov 2025)
EllapsedTime: 52.7 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 (it is needed 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/1.23.0/Pirat/1.5.5/envPirat/lib/python3.10/site-packages (23.0.1)
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/1.23.0/Pirat/1.5.5/envPirat/lib/python3.10/site-packages (79.0.1)
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 79.0.1
    Uninstalling setuptools-79.0.1:
      Successfully uninstalled setuptools-79.0.1
  Attempting uninstall: pip
    Found existing installation: pip 23.0.1
    Uninstalling pip-23.0.1:
      Successfully uninstalled pip-23.0.1
Successfully installed pip-25.3 setuptools-80.9.0 wheel-0.45.1
ERROR: Could not find a version that satisfies the requirement torch==2.5.1 (from versions: 1.11.0, 1.12.0, 1.12.1, 1.13.0, 1.13.1, 2.0.0, 2.0.1, 2.1.0, 2.1.1, 2.1.2, 2.2.0, 2.2.1, 2.2.2)
ERROR: No matching distribution found for torch==2.5.1

Quitting from Pirat.Rmd:90-92 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'torch==2.5.1'", "'numpy==1.24'"
---
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): "'torch==2.5.1'", "'numpy==1.24'"
--- failed re-building ‘Pirat.Rmd’

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

Error: Vignette re-building failed.
Execution halted