##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
###
##############################################################################
##############################################################################


* checking for file ‘OSTA/DESCRIPTION’ ... OK
* preparing ‘OSTA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/41] index.qmd


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[ 2/41] pages/bkg-introduction.qmd


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[ 3/41] pages/bkg-spatial-omics.qmd


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[ 4/41] pages/bkg-infrastructure.qmd


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[ 5/41] pages/bkg-ecosystem.qmd


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[ 6/41] pages/bkg-importing-data.qmd


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output file: bkg-importing-data.knit.md

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[ 7/41] pages/bkg-example-datasets.qmd


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[ 8/41] pages/bkg-python-interoperability.qmd


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Channels:
 - conda-forge
 - bioconda
Platform: osx-arm64
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: 25.9.1

Please update conda by running

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



# All requested packages already installed.

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Channels:
 - conda-forge
 - bioconda
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop

  added / updated specs:
    - python=3.11


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libexpat-2.7.3             |       haf25636_0          66 KB  conda-forge
    ------------------------------------------------------------
                                           Total:          66 KB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-hd037594_8 
  ca-certificates    conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0 
  icu                conda-forge/osx-arm64::icu-75.1-hfee45f7_0 
  libexpat           conda-forge/osx-arm64::libexpat-2.7.3-haf25636_0 
  libffi             conda-forge/osx-arm64::libffi-3.5.2-he5f378a_0 
  liblzma            conda-forge/osx-arm64::liblzma-5.8.1-h39f12f2_2 
  libsqlite          conda-forge/osx-arm64::libsqlite-3.51.0-h8adb53f_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 
  ncurses            conda-forge/osx-arm64::ncurses-6.5-h5e97a16_3 
  openssl            conda-forge/osx-arm64::openssl-3.6.0-h5503f6c_0 
  pip                conda-forge/noarch::pip-25.3-pyh8b19718_0 
  python             conda-forge/osx-arm64::python-3.11.14-h18782d2_2_cpython 
  readline           conda-forge/osx-arm64::readline-8.2-h1d1bf99_2 
  setuptools         conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 
  tk                 conda-forge/osx-arm64::tk-8.6.13-h892fb3f_3 
  tzdata             conda-forge/noarch::tzdata-2025b-h78e105d_0 
  wheel              conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 


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 - nodefaults
 - bioconda
Platform: osx-arm64
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: 25.9.1

Please update conda by running

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



## Package Plan ##

  environment location: /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop

  added / updated specs:
    - libcxx
    - llvm-openmp
    - llvmlite
    - numba


The following NEW packages will be INSTALLED:

  libblas            conda-forge/osx-arm64::libblas-3.11.0-1_h51639a9_openblas 
  libcblas           conda-forge/osx-arm64::libcblas-3.11.0-1_hb0561ab_openblas 
  libcxx             conda-forge/osx-arm64::libcxx-21.1.6-hf598326_0 
  libgfortran        conda-forge/osx-arm64::libgfortran-15.2.0-hfcf01ff_1 
  libgfortran5       conda-forge/osx-arm64::libgfortran5-15.2.0-h742603c_1 
  liblapack          conda-forge/osx-arm64::liblapack-3.11.0-1_hd9741b5_openblas 
  libopenblas        conda-forge/osx-arm64::libopenblas-0.3.30-openmp_ha158390_3 
  llvm-openmp        conda-forge/osx-arm64::llvm-openmp-21.1.6-h4a912ad_0 
  llvmlite           conda-forge/osx-arm64::llvmlite-0.45.1-py311h27de090_0 
  numba              conda-forge/osx-arm64::numba-0.62.1-py311h922685c_0 
  numpy              conda-forge/osx-arm64::numpy-2.3.5-py311h8685306_0 
  python_abi         conda-forge/noarch::python_abi-3.11-8_cp311 
  zstd               conda-forge/osx-arm64::zstd-1.5.7-h6491c7d_2 



Downloading and Extracting Packages: ...working... done
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Collecting pytz>=2020.1 (from pandas>=2.1.0->squidpy==1.6.2)
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Collecting slicerator>=0.9.8 (from pims>=0.4.1->dask-image>=0.5.0->squidpy==1.6.2)
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Collecting charset_normalizer<4,>=2 (from requests>=2.24.0->omnipath>=1.0.7->squidpy==1.6.2)
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Collecting certifi>=2017.4.17 (from requests>=2.24.0->omnipath>=1.0.7->squidpy==1.6.2)
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Collecting pynndescent>=0.5.13 (from scanpy>=1.9.3->squidpy==1.6.2)
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INFO: pip is looking at multiple versions of spatialdata to determine which version is compatible with other requirements. This could take a while.
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Requirement already satisfied: setuptools in /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/lib/python3.11/site-packages (from spatialdata>=0.2.5->squidpy==1.6.2) (80.9.0)
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Collecting multiscale-spatial-image<2.0.0,>=1.0.0 (from spatialdata>=0.2.5->squidpy==1.6.2)
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Collecting pyogrio>=0.7.2 (from geopandas>=0.14->spatialdata>=0.2.5->squidpy==1.6.2)
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Collecting pyproj>=3.5.0 (from geopandas>=0.14->spatialdata>=0.2.5->squidpy==1.6.2)
  Using cached pyproj-3.7.2.tar.gz (226 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'error'
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [1 lines of output]
      ERROR: Minimum supported PROJ version is 9.4.0, installed version is 9.1.0. For more information see: https://pyproj4.github.io/pyproj/stable/installation.html
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed to build 'pyproj' when getting requirements to build wheel
Error: Error installing package(s): "'Dask==2024.12.1'", "'zarr==2.18.7'", "'squidpy==1.6.2'"

Quitting from bkg-python-interoperability.qmd:108-115 [deps-pypi]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'Dask==2024.12.1'", "'zarr==2.18.7'", "'squidpy==1.6.2'"
---
Backtrace:
    ▆
 1. └─reticulate::conda_install(...)
 2.   └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
make: *** [render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted