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

To the developers/maintainers of the velociraptor package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/velociraptor.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: velociraptor

Version: 1.15.4

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

StartedAt: 2024-07-06 02:32:10 -0000 (Sat, 06 Jul 2024)

EndedAt: 2024-07-06 02:34:56 -0000 (Sat, 06 Jul 2024)

EllapsedTime: 166.2 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 velociraptor
###
##############################################################################
##############################################################################


* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* preparing ‘velociraptor’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘velociraptor.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/velociraptor/1.15.4/env

  added / updated specs:
    - python=3.8.6


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-2024.7.4-hcefe29a_0
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h9fc2d93_7
  libffi             conda-forge/linux-aarch64::libffi-3.3-h884eca8_2
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-14.1.0-he277a41_0
  libgomp            conda-forge/linux-aarch64::libgomp-14.1.0-he277a41_0
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.46.0-hf51ef55_0
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-14.1.0-h3f4de04_0
  libzlib            conda-forge/linux-aarch64::libzlib-1.2.13-h68df207_6
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-h0425590_0
  openssl            conda-forge/linux-aarch64::openssl-1.1.1w-h31becfc_0
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/linux-aarch64::python-3.8.6-h3bd6a85_5_cpython
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
  setuptools         conda-forge/noarch::setuptools-70.1.1-pyhd8ed1ab_0
  sqlite             conda-forge/linux-aarch64::sqlite-3.46.0-hdc7ab3c_0
  tk                 conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
  xz                 conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0
  zlib               conda-forge/linux-aarch64::zlib-1.2.13-h68df207_6


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:

  - anndata=0.7.4
  - stdlib-list=0.6.0
  - umap-learn=0.4.6

Current channels:

  - https://conda.anaconda.org/bioconda/linux-aarch64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/linux-aarch64
  - https://conda.anaconda.org/conda-forge/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 76-82 [unnamed-chunk-5] (velociraptor.Rmd)
Error: processing vignette 'velociraptor.Rmd' failed with diagnostics:
one or more Python packages failed to install [error code 1]
--- failed re-building ‘velociraptor.Rmd’

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

Error: Vignette re-building failed.
Execution halted