Multiple platform build/check report for BioC 3.21 - BUILD results for velociraptor on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4518
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: 1.17.0

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

StartedAt: 2025-03-28 03:16:22 -0000 (Fri, 28 Mar 2025)

EndedAt: 2025-03-28 03:18:24 -0000 (Fri, 28 Mar 2025)

EllapsedTime: 122.1 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 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
Channels:
 - 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/1.19.3/velociraptor/1.17.0/env

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu 
  bzip2              conda-forge/linux-aarch64::bzip2-1.0.8-h68df207_7 
  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 
  libexpat           conda-forge/linux-aarch64::libexpat-2.6.4-h5ad3122_0 
  libffi             conda-forge/linux-aarch64::libffi-3.4.6-he21f813_0 
  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 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.49.1-h5eb1b54_2 
  libuuid            conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0 
  libxcrypt          conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1 
  libzlib            conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 
  ncurses            conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 
  openssl            conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/linux-aarch64::python-3.12.8-h1683364_1_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8382b9d_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_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 


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
 - 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: 24.11.3
    latest version: 25.3.0

Please update conda by running

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



# All requested packages already installed.

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

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package pillow-10.0.0-py38hc8bea21_0 requires python_abi 3.8 *_pypy38_pp73, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ libtiff 4.5.1**  is requested and can be installed;
├─ pillow 10.0.0**  is installable with the potential options
│  ├─ pillow 10.0.0 would require
│  │  └─ python_abi 3.8 *_pypy38_pp73, which can be installed;
│  ├─ pillow 10.0.0 would require
│  │  └─ libtiff >=4.6.0,<4.8.0a0 , which conflicts with any installable versions previously reported;
│  ├─ pillow 10.0.0 would require
│  │  └─ python_abi 3.10.* *_cp310, which can be installed;
│  ├─ pillow 10.0.0 would require
│  │  └─ python_abi 3.11.* *_cp311, which can be installed;
│  ├─ pillow 10.0.0 would require
│  │  └─ python_abi 3.8.* *_cp38, which can be installed;
│  ├─ pillow 10.0.0 would require
│  │  └─ python_abi 3.9.* *_cp39, which can be installed;
│  └─ pillow 10.0.0 would require
│     └─ python_abi 3.9 *_pypy39_pp73, which can be installed;
└─ python 3.12.8**  is not installable because it conflicts with any installable versions previously reported.


Quitting from velociraptor.Rmd:75-82 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! one or more Python packages failed to install [error code 1]
---
Backtrace:
     ▆
  1. ├─velociraptor::scvelo(...)
  2. └─velociraptor::scvelo(...)
  3.   └─velociraptor (local) .local(x, ...)
  4.     ├─methods::callNextMethod(x, ..., sf.X = sf.X, dimred = dimred)
  5.     │ └─base::eval(call, callEnv)
  6.     │   └─base::eval(call, callEnv)
  7.     └─velociraptor (local) .nextMethod(x, ..., sf.X = sf.X, dimred = dimred)
  8.       └─velociraptor (local) .local(x, ...)
  9.         └─velociraptor:::.scvelo(...)
 10.           └─basilisk::basiliskRun(...)
 11.             └─basilisk::basiliskStart(...)
 12.               └─basilisk::obtainEnvironmentPath(env)
 13.                 └─basilisk::setupBasiliskEnv(...)
 14.                   └─reticulate::conda_install(...)
 15.                     └─reticulate:::stopf(fmt, result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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