##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.1/spatialDE/1.13.0/env

  added / updated specs:
    - python=3.12.8


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-64::bzip2-1.0.8-hfdf4475_7 
  ca-certificates    conda-forge/osx-64::ca-certificates-2025.1.31-h8857fd0_0 
  libexpat           conda-forge/osx-64::libexpat-2.6.4-h240833e_0 
  libffi             conda-forge/osx-64::libffi-3.4.6-h281671d_0 
  liblzma            conda-forge/osx-64::liblzma-5.6.4-hd471939_0 
  libsqlite          conda-forge/osx-64::libsqlite-3.49.1-hdb6dae5_2 
  libzlib            conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 
  ncurses            conda-forge/osx-64::ncurses-6.5-h0622a9a_3 
  openssl            conda-forge/osx-64::openssl-3.4.1-hc426f3f_0 
  pip                conda-forge/noarch::pip-25.0.1-pyh8b19718_0 
  python             conda-forge/osx-64::python-3.12.8-h9ccd52b_1_cpython 
  readline           conda-forge/osx-64::readline-8.2-h7cca4af_2 
  setuptools         conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0 
  tk                 conda-forge/osx-64::tk-8.6.13-h1abcd95_1 
  tzdata             conda-forge/noarch::tzdata-2025a-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: osx-64
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: 25.1.1

Please update conda by running

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



# All requested packages already installed.

Channels:
 - conda-forge
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package scipy-1.9.3-py38hfb8b963_0 requires python_abi 3.8.* *_cp38, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ python 3.12.8**  is installable and it requires
│  └─ python_abi 3.12.* *_cp312, which can be installed;
└─ scipy 1.9.3**  is not installable because there are no viable options
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.8.* *_cp38, which conflicts with any installable versions previously reported;
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.10.* *_cp310, which conflicts with any installable versions previously reported;
   ├─ scipy 1.9.3 would require
   │  └─ python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
   └─ scipy 1.9.3 would require
      └─ python_abi 3.9.* *_cp39, which conflicts with any installable versions previously reported.


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