Multiple platform build/check report for BioC 3.20 - BUILD results for Pirat on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4643
palomino6	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4414
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4442
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4391
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	3833
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 kunpeng2

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: 0.99.26

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

StartedAt: 2024-07-06 00:57:27 -0000 (Sat, 06 Jul 2024)

EndedAt: 2024-07-06 00:58:18 -0000 (Sat, 06 Jul 2024)

EllapsedTime: 51.1 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
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.17.0/Pirat/0.99.26/envPirat

  added / updated specs:
    - python=3.9.5


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-aarch64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-aarch64::_openmp_mutex-5.1-51_gnu
  ca-certificates    pkgs/main/linux-aarch64::ca-certificates-2024.3.11-hd43f75c_0
  ld_impl_linux-aar~ pkgs/main/linux-aarch64::ld_impl_linux-aarch64-2.38-h8131f2d_1
  libffi             pkgs/main/linux-aarch64::libffi-3.3-h7c1a80f_2
  libgcc-ng          pkgs/main/linux-aarch64::libgcc-ng-11.2.0-h1234567_1
  libgomp            pkgs/main/linux-aarch64::libgomp-11.2.0-h1234567_1
  libstdcxx-ng       pkgs/main/linux-aarch64::libstdcxx-ng-11.2.0-h1234567_1
  ncurses            pkgs/main/linux-aarch64::ncurses-6.4-h419075a_0
  openssl            pkgs/main/linux-aarch64::openssl-1.1.1w-h2f4d8fa_0
  pip                pkgs/main/linux-aarch64::pip-24.0-py39hd43f75c_0
  python             pkgs/main/linux-aarch64::python-3.9.5-hc137634_3
  readline           pkgs/main/linux-aarch64::readline-8.2-h998d150_0
  setuptools         pkgs/main/linux-aarch64::setuptools-69.5.1-py39hd43f75c_0
  sqlite             pkgs/main/linux-aarch64::sqlite-3.45.3-h998d150_0
  tk                 pkgs/main/linux-aarch64::tk-8.6.14-h987d8db_0
  tzdata             pkgs/main/noarch::tzdata-2024a-h04d1e81_0
  wheel              pkgs/main/linux-aarch64::wheel-0.43.0-py39hd43f75c_0
  xz                 pkgs/main/linux-aarch64::xz-5.4.6-h998d150_1
  zlib               pkgs/main/linux-aarch64::zlib-1.2.13-h998d150_1


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 24.5.0

Please update conda by running

    $ conda update -n base -c defaults conda



# All requested packages already installed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

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

  - pytorch=1.10.0

Current channels:

  - https://conda.anaconda.org/pytorch/linux-aarch64
  - https://conda.anaconda.org/pytorch/noarch
  - https://conda.anaconda.org/stable/linux-aarch64
  - https://conda.anaconda.org/stable/noarch
  - https://conda.anaconda.org/torch/linux-aarch64
  - https://conda.anaconda.org/torch/noarch
  - https://repo.anaconda.com/pkgs/main/linux-aarch64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-aarch64
  - https://repo.anaconda.com/pkgs/r/noarch

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 lines 71-72 [impute] (Pirat.Rmd)
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