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This page was generated on 2025-04-02 19:36 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1558/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pirat 1.0.3  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/Pirat
git_branch: RELEASE_3_20
git_last_commit: c6858d1
git_last_commit_date: 2025-03-03 06:28:00 -0400 (Mon, 03 Mar 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for Pirat on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Pirat
Version: 1.0.3
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat
StartedAt: 2025-04-01 01:36:01 -0000 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 01:37:21 -0000 (Tue, 01 Apr 2025)
EllapsedTime: 80.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/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
Channels:
 - pytorch
 - torch
 - conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/Pirat/1.0.3/envPirat

  added / updated specs:
    - python=3.9.5


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2025.1.31-hcefe29a_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4 
  libffi             conda-forge/linux-aarch64::libffi-3.3-h884eca8_2 
  libgcc             conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_2 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_2 
  libgomp            conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_2 
  liblzma            conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0 
  liblzma-devel      conda-forge/linux-aarch64::liblzma-devel-5.6.4-h86ecc28_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.46.0-hf51ef55_0 
  libstdcxx          conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_2 
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_2 
  libzlib            conda-forge/linux-aarch64::libzlib-1.2.13-h68df207_6 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 
  openssl            conda-forge/linux-aarch64::openssl-1.1.1w-h31becfc_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-aarch64::python-3.9.5-h4f4e160_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8382b9d_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 
  sqlite             conda-forge/linux-aarch64::sqlite-3.46.0-hdc7ab3c_0 
  tk                 conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 
  xz                 conda-forge/linux-aarch64::xz-5.6.4-h2dbfc1b_0 
  xz-gpl-tools       conda-forge/linux-aarch64::xz-gpl-tools-5.6.4-h2dbfc1b_0 
  xz-tools           conda-forge/linux-aarch64::xz-tools-5.6.4-h86ecc28_0 
  zlib               conda-forge/linux-aarch64::zlib-1.2.13-h68df207_6 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - pytorch
 - torch
 - conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 25.3.0

Please update conda by running

    $ conda update -n base -c conda-forge conda



# All requested packages already installed.

Channels:
 - pytorch
 - torch
 - conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pytorch=1.10.0*

Current channels:

  - https://conda.anaconda.org/pytorch
  - https://conda.anaconda.org/torch
  - https://conda.anaconda.org/conda-forge

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



Quitting from Pirat.Rmd:90-92 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! one or more Python packages failed to install [error code 1]
---
Backtrace:
    ▆
 1. └─Pirat::my_pipeline_llkimpute(subbouyssie)
 2.   └─basilisk::basiliskStart(envPirat)
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::conda_install(...)
 6.           └─reticulate:::stopf(fmt, result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Pirat.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building ‘Pirat.Rmd’

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

Error: Vignette re-building failed.
Execution halted