##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialDE
###
##############################################################################
##############################################################################


* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* preparing ‘spatialDE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘spatialDE.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/1.20.0/spatialDE/1.14.1/env

  added / updated specs:
    - python=3.11


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/noarch::ca-certificates-2025.4.26-hbd8a1cb_0 
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4 
  libexpat           conda-forge/linux-aarch64::libexpat-2.7.0-h5ad3122_0 
  libffi             conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1 
  libgcc             conda-forge/linux-aarch64::libgcc-15.1.0-he277a41_2 
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_2 
  libgomp            conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_2 
  liblzma            conda-forge/linux-aarch64::liblzma-5.8.1-h86ecc28_1 
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.49.2-h5eb1b54_0 
  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-3.5.0-hd08dc88_1 
  pip                conda-forge/noarch::pip-25.1.1-pyh8b19718_0 
  python             conda-forge/linux-aarch64::python-3.11.12-h1683364_0_cpython 
  readline           conda-forge/linux-aarch64::readline-8.2-h8382b9d_2 
  setuptools         conda-forge/noarch::setuptools-80.8.0-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: 25.3.1

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

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

  - scipy=1.11.4*

Current channels:

  - 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 spatialDE.Rmd:122-125 [stabilize]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! one or more Python packages failed to install [error code 1]
---
Backtrace:
    ▆
 1. └─spatialDE::stabilize(Rep11_MOB_0)
 2.   └─basilisk::basiliskStart(spatialDE_env, testload = "scipy.optimize")
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::conda_install(...)
 6.           └─reticulate:::stopf(fmt, result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

Error: Vignette re-building failed.
Execution halted