############################################################################## ############################################################################## ### ### 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/  [ 1/43] index.qmd  processing file: index.qmd 1/4 [unnamed-chunk-1] 2/4 3/4 [carousel] 4/4 output file: index.knit.md  [ 2/43] pages/bkg-introduction.qmd  processing file: bkg-introduction.qmd 1/5 2/5 [unnamed-chunk-1] 3/5 4/5 [unnamed-chunk-2] 5/5 output file: bkg-introduction.knit.md  [ 3/43] pages/bkg-spatial-omics.qmd  processing file: bkg-spatial-omics.qmd 1/5 2/5 [unnamed-chunk-1] 3/5 4/5 [unnamed-chunk-2] 5/5 output file: bkg-spatial-omics.knit.md  [ 4/43] pages/bkg-infrastructure.qmd  processing file: bkg-infrastructure.qmd 1/9 2/9 [unnamed-chunk-1] 3/9 4/9 [fig-spatialexperiment] 5/9 6/9 [fig-spatialdata] 7/9 8/9 [unnamed-chunk-2] 9/9 output file: bkg-infrastructure.knit.md  [ 5/43] pages/bkg-ecosystem.qmd  processing file: bkg-ecosystem.qmd 1/23 2/23 [unnamed-chunk-1] 3/23 4/23 [unnamed-chunk-2] 5/23 6/23 [unnamed-chunk-3] 7/23 8/23 [unnamed-chunk-4] 9/23 10/23 [unnamed-chunk-5] 11/23 12/23 [unnamed-chunk-6] 2025-12-17 06:50:02.097 R[15823:429947391] XType: Using static font registry. 13/23 14/23 [unnamed-chunk-7] 15/23 16/23 [unnamed-chunk-8] 17/23 18/23 [unnamed-chunk-9] 19/23 20/23 [unnamed-chunk-10] 21/23 22/23 [unnamed-chunk-11] 23/23 output file: bkg-ecosystem.knit.md  [ 6/43] pages/bkg-importing-data.qmd  processing file: bkg-importing-data.qmd 1/13 2/13 [unnamed-chunk-1] 3/13 4/13 [unnamed-chunk-2] 5/13 6/13 [unnamed-chunk-3] 7/13 8/13 [unnamed-chunk-4] 9/13 10/13 [unnamed-chunk-5] 11/13 12/13 [unnamed-chunk-6] 13/13 output file: bkg-importing-data.knit.md  [ 7/43] pages/bkg-example-datasets.qmd  processing file: bkg-example-datasets.qmd 1/13 2/13 [unnamed-chunk-1] 3/13 4/13 [bfc] 5/13 6/13 [list-data] 7/13 8/13 [list-stexampledata] 9/13 10/13 [clean-biocfilecache] 11/13 12/13 [unnamed-chunk-2] 13/13 output file: bkg-example-datasets.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [ 8/43] pages/bkg-python-interoperability.qmd  processing file: bkg-python-interoperability.qmd 1/51 2/51 [unnamed-chunk-1] 3/51 4/51 [libraries] 5/51 6/51 [conda-settings] 7/51 8/51 [install-miniconda] 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: 25.11.1 Please update conda by running $ conda update -n base -c conda-forge conda  # All requested packages already installed. 9/51 10/51 [conda-create] 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 ---------------------------|----------------- readline-8.3 | h46df422_0 307 KB conda-forge ------------------------------------------------------------ Total: 307 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 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-3.51.1-h9a5124b_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-8.3-h46df422_0 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-2025c-h8577fbf_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done 11/51 12/51 [conda-list] 13/51 14/51 [deps-conda-forge] Channels: - conda-forge - 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: 25.11.1 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 - proj[version='>=9.4'] - pyproj[version='>=3.7'] The following packages will be downloaded: package | build ---------------------------|----------------- libblas-3.11.0 |5_h51639a9_openblas 18 KB conda-forge libcblas-3.11.0 |5_hb0561ab_openblas 18 KB conda-forge libcxx-21.1.8 | hf598326_0 556 KB conda-forge liblapack-3.11.0 |5_hd9741b5_openblas 18 KB conda-forge llvm-openmp-21.1.8 | h4a912ad_0 279 KB conda-forge numba-0.63.1 | py311had9367a_0 5.6 MB conda-forge ------------------------------------------------------------ Total: 6.4 MB The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/osx-arm64::_openmp_mutex-4.5-7_kmp_llvm c-ares conda-forge/osx-arm64::c-ares-1.34.6-hc919400_0 certifi conda-forge/noarch::certifi-2025.11.12-pyhd8ed1ab_0 krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 lerc conda-forge/osx-arm64::lerc-4.0.0-hd64df32_1 libblas conda-forge/osx-arm64::libblas-3.11.0-5_h51639a9_openblas libcblas conda-forge/osx-arm64::libcblas-3.11.0-5_hb0561ab_openblas libcurl conda-forge/osx-arm64::libcurl-8.17.0-hdece5d2_1 libcxx conda-forge/osx-arm64::libcxx-21.1.8-hf598326_0 libdeflate conda-forge/osx-arm64::libdeflate-1.25-hc11a715_0 libedit conda-forge/osx-arm64::libedit-3.1.20250104-pl5321hafb1f1b_0 libev conda-forge/osx-arm64::libev-4.33-h93a5062_2 libgcc conda-forge/osx-arm64::libgcc-15.2.0-hcbb3090_16 libgfortran conda-forge/osx-arm64::libgfortran-15.2.0-h07b0088_16 libgfortran5 conda-forge/osx-arm64::libgfortran5-15.2.0-hdae7583_16 libjpeg-turbo conda-forge/osx-arm64::libjpeg-turbo-3.1.2-hc919400_0 liblapack conda-forge/osx-arm64::liblapack-3.11.0-5_hd9741b5_openblas libnghttp2 conda-forge/osx-arm64::libnghttp2-1.67.0-hc438710_0 libopenblas conda-forge/osx-arm64::libopenblas-0.3.30-openmp_ha158390_3 libssh2 conda-forge/osx-arm64::libssh2-1.11.1-h1590b86_0 libtiff conda-forge/osx-arm64::libtiff-4.7.1-h4030677_1 libwebp-base conda-forge/osx-arm64::libwebp-base-1.6.0-h07db88b_0 llvm-openmp conda-forge/osx-arm64::llvm-openmp-21.1.8-h4a912ad_0 llvmlite conda-forge/osx-arm64::llvmlite-0.46.0-py311h27de090_0 numba conda-forge/osx-arm64::numba-0.63.1-py311had9367a_0 numpy conda-forge/osx-arm64::numpy-2.3.5-py311h8685306_0 proj conda-forge/osx-arm64::proj-9.7.1-h46dec42_0 pyproj conda-forge/osx-arm64::pyproj-3.7.2-py311h55f0a08_2 python_abi conda-forge/noarch::python_abi-3.11-8_cp311 sqlite conda-forge/osx-arm64::sqlite-3.51.1-he8f07e4_0 zstd conda-forge/osx-arm64::zstd-1.5.7-hbf9d68e_6 Downloading and Extracting Packages: ...working... numba-0.63.1 | 5.6 MB | | 0% libcxx-21.1.8 | 556 KB | | 0%  llvm-openmp-21.1.8 | 279 KB | | 0%  liblapack-3.11.0 | 18 KB | | 0%  libcblas-3.11.0 | 18 KB | | 0%  libblas-3.11.0 | 18 KB | | 0%  liblapack-3.11.0 | 18 KB | ########8 | 88%  liblapack-3.11.0 | 18 KB | ########## | 100%  liblapack-3.11.0 | 18 KB | ########## | 100%  llvm-openmp-21.1.8 | 279 KB | 5 | 6%  numba-0.63.1 | 5.6 MB | | 0% libcxx-21.1.8 | 556 KB | 2 | 3%  libcblas-3.11.0 | 18 KB | ########8 | 88%  libcblas-3.11.0 | 18 KB | ########## | 100%  libcblas-3.11.0 | 18 KB | ########## | 100%  llvm-openmp-21.1.8 | 279 KB | ########## | 100%  llvm-openmp-21.1.8 | 279 KB | ########## | 100%  llvm-openmp-21.1.8 | 279 KB | ########## | 100%  numba-0.63.1 | 5.6 MB | 6 | 6% libcxx-21.1.8 | 556 KB | #####7 | 58%  libcxx-21.1.8 | 556 KB | ########## | 100%  libblas-3.11.0 | 18 KB | ########8 | 88%  libblas-3.11.0 | 18 KB | ########## | 100%  libcxx-21.1.8 | 556 KB | ########## | 100%  libblas-3.11.0 | 18 KB | ########## | 100%  numba-0.63.1 | 5.6 MB | ##4 | 25% numba-0.63.1 | 5.6 MB | #########4 | 94% numba-0.63.1 | 5.6 MB | ########## | 100% numba-0.63.1 | 5.6 MB | ########## | 100%      done Preparing transaction: - done Verifying transaction: | / - \ | / - done Executing transaction: | / - \ | / - \ | / - \ | / - \ | / done 15/51 16/51 [deps-pypi] + . /Users/biocbuild/Library/r-miniconda-arm64/bin/activate + conda activate 'py-interop' + '/Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/bin/python' -m pip install --upgrade --no-user 'Dask==2024.12.1' 'zarr==2.18.7' 'squidpy==1.6.2' Collecting Dask==2024.12.1 Using cached dask-2024.12.1-py3-none-any.whl.metadata (3.7 kB) Collecting zarr==2.18.7 Using cached zarr-2.18.7-py3-none-any.whl.metadata (5.8 kB) Collecting squidpy==1.6.2 Using cached squidpy-1.6.2-py3-none-any.whl.metadata (8.8 kB) Collecting click>=8.1 (from Dask==2024.12.1) Using cached click-8.3.1-py3-none-any.whl.metadata (2.6 kB) Collecting cloudpickle>=3.0.0 (from Dask==2024.12.1) Using cached cloudpickle-3.1.2-py3-none-any.whl.metadata (7.1 kB) Collecting fsspec>=2021.09.0 (from Dask==2024.12.1) Using cached fsspec-2025.12.0-py3-none-any.whl.metadata (10 kB) Collecting packaging>=20.0 (from Dask==2024.12.1) Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB) Collecting partd>=1.4.0 (from Dask==2024.12.1) Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB) Collecting pyyaml>=5.3.1 (from Dask==2024.12.1) Using cached pyyaml-6.0.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.4 kB) Collecting toolz>=0.10.0 (from Dask==2024.12.1) Using cached toolz-1.1.0-py3-none-any.whl.metadata (5.1 kB) Collecting importlib_metadata>=4.13.0 (from Dask==2024.12.1) Using cached importlib_metadata-8.7.0-py3-none-any.whl.metadata (4.8 kB) Collecting asciitree (from zarr==2.18.7) Using cached asciitree-0.3.3-py3-none-any.whl Requirement already satisfied: numpy>=1.24 in /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/lib/python3.11/site-packages (from zarr==2.18.7) (2.3.5) Collecting fasteners (from zarr==2.18.7) Using cached fasteners-0.20-py3-none-any.whl.metadata (4.8 kB) Collecting numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0 (from zarr==2.18.7) Using cached numcodecs-0.15.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.9 kB) Collecting aiohttp>=3.8.1 (from squidpy==1.6.2) Using cached aiohttp-3.13.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (8.1 kB) Collecting anndata>=0.9 (from squidpy==1.6.2) Downloading anndata-0.12.7-py3-none-any.whl.metadata (9.9 kB) Collecting cycler>=0.11.0 (from squidpy==1.6.2) Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting dask-image>=0.5.0 (from squidpy==1.6.2) Using cached dask_image-2025.11.0-py3-none-any.whl.metadata (2.8 kB) Collecting docrep>=0.3.1 (from squidpy==1.6.2) Using cached docrep-0.3.2-py3-none-any.whl Collecting leidenalg>=0.8.2 (from squidpy==1.6.2) Using cached leidenalg-0.11.0-cp38-abi3-macosx_11_0_arm64.whl.metadata (10 kB) Collecting matplotlib-scalebar>=0.8.0 (from squidpy==1.6.2) Using cached matplotlib_scalebar-0.9.0-py3-none-any.whl.metadata (18 kB) Collecting matplotlib>=3.3 (from squidpy==1.6.2) Using cached matplotlib-3.10.8-cp311-cp311-macosx_11_0_arm64.whl.metadata (52 kB) Collecting networkx>=2.6.0 (from squidpy==1.6.2) Using cached networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB) Requirement already satisfied: numba>=0.56.4 in /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/lib/python3.11/site-packages (from squidpy==1.6.2) (0.63.1) Collecting omnipath>=1.0.7 (from squidpy==1.6.2) Using cached omnipath-1.0.12-py3-none-any.whl.metadata (7.0 kB) Collecting pandas>=2.1.0 (from squidpy==1.6.2) Using cached pandas-2.3.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB) Collecting pillow>=8.0.0 (from squidpy==1.6.2) Using cached pillow-12.0.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (8.8 kB) Collecting scanpy>=1.9.3 (from squidpy==1.6.2) Using cached scanpy-1.11.5-py3-none-any.whl.metadata (9.3 kB) Collecting scikit-image>=0.20 (from squidpy==1.6.2) Using cached scikit_image-0.25.2-cp311-cp311-macosx_12_0_arm64.whl.metadata (14 kB) Collecting scikit-learn>=0.24.0 (from squidpy==1.6.2) Using cached scikit_learn-1.8.0-cp311-cp311-macosx_12_0_arm64.whl.metadata (11 kB) Collecting spatialdata>=0.2.5 (from squidpy==1.6.2) Using cached spatialdata-0.6.1-py3-none-any.whl.metadata (10 kB) Collecting statsmodels>=0.12.0 (from squidpy==1.6.2) Using cached statsmodels-0.14.6-cp311-cp311-macosx_11_0_arm64.whl.metadata (9.5 kB) Collecting tifffile!=2022.4.22 (from squidpy==1.6.2) Using cached tifffile-2025.12.12-py3-none-any.whl.metadata (31 kB) Collecting tqdm>=4.50.2 (from squidpy==1.6.2) Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) Collecting validators>=0.18.2 (from squidpy==1.6.2) Using cached validators-0.35.0-py3-none-any.whl.metadata (3.9 kB) Collecting xarray<2024.10.0,>=0.16.1 (from squidpy==1.6.2) Using cached xarray-2024.9.0-py3-none-any.whl.metadata (11 kB) Collecting deprecated (from numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0->zarr==2.18.7) Using cached deprecated-1.3.1-py2.py3-none-any.whl.metadata (5.9 kB) Collecting aiohappyeyeballs>=2.5.0 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB) Collecting aiosignal>=1.4.0 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB) Collecting attrs>=17.3.0 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached attrs-25.4.0-py3-none-any.whl.metadata (10 kB) Collecting frozenlist>=1.1.1 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached frozenlist-1.8.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (20 kB) Collecting multidict<7.0,>=4.5 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached multidict-6.7.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.3 kB) Collecting propcache>=0.2.0 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached propcache-0.4.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (13 kB) Collecting yarl<2.0,>=1.17.0 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached yarl-1.22.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (75 kB) Collecting idna>=2.0 (from yarl<2.0,>=1.17.0->aiohttp>=3.8.1->squidpy==1.6.2) Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB) Collecting typing-extensions>=4.2 (from aiosignal>=1.4.0->aiohttp>=3.8.1->squidpy==1.6.2) Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB) Collecting array-api-compat>=1.7.1 (from anndata>=0.9->squidpy==1.6.2) Using cached array_api_compat-1.12.0-py3-none-any.whl.metadata (2.5 kB) Collecting h5py>=3.8 (from anndata>=0.9->squidpy==1.6.2) Using cached h5py-3.15.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (3.0 kB) Collecting legacy-api-wrap (from anndata>=0.9->squidpy==1.6.2) Using cached legacy_api_wrap-1.5-py3-none-any.whl.metadata (2.2 kB) Collecting natsort (from anndata>=0.9->squidpy==1.6.2) Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting scipy>=1.12 (from anndata>=0.9->squidpy==1.6.2) Using cached scipy-1.16.3-cp311-cp311-macosx_12_0_arm64.whl.metadata (62 kB) Collecting python-dateutil>=2.8.2 (from pandas>=2.1.0->squidpy==1.6.2) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting pytz>=2020.1 (from pandas>=2.1.0->squidpy==1.6.2) Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) Collecting tzdata>=2022.7 (from pandas>=2.1.0->squidpy==1.6.2) Using cached tzdata-2025.3-py2.py3-none-any.whl.metadata (1.4 kB) Collecting pims>=0.4.1 (from dask-image>=0.5.0->squidpy==1.6.2) Using cached pims-0.7-py3-none-any.whl Collecting dask-expr<1.2,>=1.1 (from dask[array,dataframe]>=2024.4.1->dask-image>=0.5.0->squidpy==1.6.2) Using cached dask_expr-1.1.21-py3-none-any.whl.metadata (2.6 kB) Collecting pyarrow>=14.0.1 (from dask-expr<1.2,>=1.1->dask[array,dataframe]>=2024.4.1->dask-image>=0.5.0->squidpy==1.6.2) Using cached pyarrow-22.0.0-cp311-cp311-macosx_12_0_arm64.whl.metadata (3.1 kB) Collecting six (from docrep>=0.3.1->squidpy==1.6.2) Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Collecting zipp>=3.20 (from importlib_metadata>=4.13.0->Dask==2024.12.1) Using cached zipp-3.23.0-py3-none-any.whl.metadata (3.6 kB) Collecting igraph<2.0,>=1.0.0 (from leidenalg>=0.8.2->squidpy==1.6.2) Using cached igraph-1.0.0-cp39-abi3-macosx_11_0_arm64.whl.metadata (4.4 kB) Collecting texttable>=1.6.2 (from igraph<2.0,>=1.0.0->leidenalg>=0.8.2->squidpy==1.6.2) Using cached texttable-1.7.0-py2.py3-none-any.whl.metadata (9.8 kB) Collecting contourpy>=1.0.1 (from matplotlib>=3.3->squidpy==1.6.2) Using cached contourpy-1.3.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.5 kB) Collecting fonttools>=4.22.0 (from matplotlib>=3.3->squidpy==1.6.2) Using cached fonttools-4.61.1-cp311-cp311-macosx_10_9_universal2.whl.metadata (114 kB) Collecting kiwisolver>=1.3.1 (from matplotlib>=3.3->squidpy==1.6.2) Using cached kiwisolver-1.4.9-cp311-cp311-macosx_11_0_arm64.whl.metadata (6.3 kB) Collecting pyparsing>=3 (from matplotlib>=3.3->squidpy==1.6.2) Using cached pyparsing-3.2.5-py3-none-any.whl.metadata (5.0 kB) Requirement already satisfied: llvmlite<0.47,>=0.46.0dev0 in /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/lib/python3.11/site-packages (from numba>=0.56.4->squidpy==1.6.2) (0.46.0) Collecting inflect>=4.1.0 (from omnipath>=1.0.7->squidpy==1.6.2) Using cached inflect-7.5.0-py3-none-any.whl.metadata (24 kB) Collecting requests>=2.24.0 (from omnipath>=1.0.7->squidpy==1.6.2) Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB) 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charset_normalizer<4,>=2 (from requests>=2.24.0->omnipath>=1.0.7->squidpy==1.6.2) Using cached charset_normalizer-3.4.4-cp311-cp311-macosx_10_9_universal2.whl.metadata (37 kB) Requirement already satisfied: certifi>=2017.4.17 in /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/lib/python3.11/site-packages (from requests>=2.24.0->omnipath>=1.0.7->squidpy==1.6.2) (2025.11.12) Collecting joblib (from scanpy>=1.9.3->squidpy==1.6.2) Using cached joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB) Collecting patsy!=1.0.0 (from scanpy>=1.9.3->squidpy==1.6.2) Using cached patsy-1.0.2-py2.py3-none-any.whl.metadata (3.6 kB) Collecting pynndescent>=0.5.13 (from scanpy>=1.9.3->squidpy==1.6.2) Using cached pynndescent-0.5.13-py3-none-any.whl.metadata (6.8 kB) Collecting seaborn>=0.13.2 (from scanpy>=1.9.3->squidpy==1.6.2) Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting session-info2 (from scanpy>=1.9.3->squidpy==1.6.2) Using cached 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(348 kB) Using cached umap_learn-0.5.9.post2-py3-none-any.whl (90 kB) Using cached validators-0.35.0-py3-none-any.whl (44 kB) Using cached xarray_dataclasses-1.9.1-py3-none-any.whl (14 kB) Using cached xarray_datatree-0.0.15-py3-none-any.whl (64 kB) Using cached xarray-2024.7.0-py3-none-any.whl (1.2 MB) Downloading xarray_spatial-0.5.1-py3-none-any.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 2.7 MB/s 0:00:00 Using cached datashader-0.18.2-py3-none-any.whl (18.3 MB) Using cached zipp-3.23.0-py3-none-any.whl (10 kB) Using cached colorcet-3.1.0-py3-none-any.whl (260 kB) Using cached deprecated-1.3.1-py2.py3-none-any.whl (11 kB) Using cached fasteners-0.20-py3-none-any.whl (18 kB) Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB) Using cached multipledispatch-1.0.0-py3-none-any.whl (12 kB) Using cached natsort-8.4.0-py3-none-any.whl (38 kB) Using cached param-2.3.1-py3-none-any.whl (139 kB) Using cached pooch-1.8.2-py3-none-any.whl (64 kB) Using cached platformdirs-4.5.1-py3-none-any.whl (18 kB) Using cached pyct-0.6.0-py3-none-any.whl (16 kB) Using cached rich-14.2.0-py3-none-any.whl (243 kB) Using cached pygments-2.19.2-py3-none-any.whl (1.2 MB) Using cached markdown_it_py-4.0.0-py3-none-any.whl (87 kB) Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB) Using cached s3fs-2023.6.0-py3-none-any.whl (28 kB) Using cached aiobotocore-2.5.4-py3-none-any.whl (73 kB) Using cached aioitertools-0.13.0-py3-none-any.whl (24 kB) Using cached botocore-1.31.17-py3-none-any.whl (11.1 MB) Using cached jmespath-1.0.1-py3-none-any.whl (20 kB) Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) Using cached wrapt-1.17.3-cp311-cp311-macosx_11_0_arm64.whl (38 kB) Using cached session_info2-0.2.3-py3-none-any.whl (16 kB) Using cached xarray_schema-0.0.3-py3-none-any.whl (10 kB) Installing collected packages: texttable, slicerator, pytz, multipledispatch, asciitree, zipp, wrapt, validators, urllib3, tzdata, typing-extensions, tqdm, toolz, tifffile, threadpoolctl, six, shapely, session-info2, scipy, pyyaml, pyparsing, pygments, pyarrow, propcache, platformdirs, pillow, patsy, param, packaging, networkx, natsort, multidict, more_itertools, mdurl, locket, legacy-api-wrap, kiwisolver, joblib, jmespath, igraph, idna, h5py, fsspec, frozenlist, fonttools, fasteners, cycler, contourpy, colorcet, cloudpickle, click, charset_normalizer, attrs, array-api-compat, aioitertools, aiohappyeyeballs, yarl, typeguard, scikit-learn, requests, python-dateutil, pyogrio, pyct, partd, markdown-it-py, leidenalg, lazy-loader, importlib_metadata, imageio, docrep, deprecated, aiosignal, scikit-image, rich, pynndescent, pooch, pims, pandas, numcodecs, matplotlib, inflect, Dask, botocore, aiohttp, zarr, xarray, umap-learn, statsmodels, seaborn, omnipath, matplotlib-scalebar, geopandas, dask-expr, aiobotocore, xarray-schema, xarray-datatree, xarray-dataclasses, s3fs, datashader, anndata, xarray-spatial, spatial-image, scanpy, dask-image, ome-zarr, multiscale-spatial-image, spatialdata, squidpy Successfully installed Dask-2024.12.1 aiobotocore-2.5.4 aiohappyeyeballs-2.6.1 aiohttp-3.13.2 aioitertools-0.13.0 aiosignal-1.4.0 anndata-0.12.7 array-api-compat-1.12.0 asciitree-0.3.3 attrs-25.4.0 botocore-1.31.17 charset_normalizer-3.4.4 click-8.3.1 cloudpickle-3.1.2 colorcet-3.1.0 contourpy-1.3.3 cycler-0.12.1 dask-expr-1.1.21 dask-image-2025.11.0 datashader-0.18.2 deprecated-1.3.1 docrep-0.3.2 fasteners-0.20 fonttools-4.61.1 frozenlist-1.8.0 fsspec-2023.6.0 geopandas-1.1.1 h5py-3.15.1 idna-3.11 igraph-1.0.0 imageio-2.37.2 importlib_metadata-8.7.0 inflect-7.5.0 jmespath-1.0.1 joblib-1.5.3 kiwisolver-1.4.9 lazy-loader-0.4 legacy-api-wrap-1.5 leidenalg-0.11.0 locket-1.0.0 markdown-it-py-4.0.0 matplotlib-3.10.8 matplotlib-scalebar-0.9.0 mdurl-0.1.2 more_itertools-10.8.0 multidict-6.7.0 multipledispatch-1.0.0 multiscale-spatial-image-1.0.1 natsort-8.4.0 networkx-3.6.1 numcodecs-0.15.1 ome-zarr-0.11.1 omnipath-1.0.12 packaging-25.0 pandas-2.3.3 param-2.3.1 partd-1.4.2 patsy-1.0.2 pillow-12.0.0 pims-0.7 platformdirs-4.5.1 pooch-1.8.2 propcache-0.4.1 pyarrow-22.0.0 pyct-0.6.0 pygments-2.19.2 pynndescent-0.5.13 pyogrio-0.12.1 pyparsing-3.2.5 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.3 requests-2.32.5 rich-14.2.0 s3fs-2023.6.0 scanpy-1.11.5 scikit-image-0.25.2 scikit-learn-1.8.0 scipy-1.16.3 seaborn-0.13.2 session-info2-0.2.3 shapely-2.1.2 six-1.17.0 slicerator-1.1.0 spatial-image-1.1.0 spatialdata-0.2.5.post0 squidpy-1.6.2 statsmodels-0.14.6 texttable-1.7.0 threadpoolctl-3.6.0 tifffile-2025.12.12 toolz-1.1.0 tqdm-4.67.1 typeguard-4.4.4 typing-extensions-4.15.0 tzdata-2025.3 umap-learn-0.5.9.post2 urllib3-1.26.20 validators-0.35.0 wrapt-1.17.3 xarray-2024.7.0 xarray-dataclasses-1.9.1 xarray-datatree-0.0.15 xarray-schema-0.0.3 xarray-spatial-0.5.1 yarl-1.22.0 zarr-2.18.7 zipp-3.23.0 17/51 18/51 [python-reticulate] 19/51 20/51 [load-sce] 21/51 22/51 [uniq-celltype] 23/51 24/51 [anndata2sce] sys:1: FutureWarning: Use varm (e.g. `k in adata.varm` or `adata.varm.keys() | {'u'}`) instead of AnnData.varm_keys, AnnData.varm_keys is deprecated and will be removed in the future. sys:1: FutureWarning: Use obsm (e.g. `k in adata.obsm` or `adata.obsm.keys() | {'u'}`) instead of AnnData.obsm_keys, AnnData.obsm_keys is deprecated and will be removed in the future. 25/51 26/51 [sce2anndata] 27/51 28/51 [load-spe] 29/51 30/51 [scalefactors] 31/51 32/51 [spe2anndata] 33/51 34/51 [coords] 35/51 36/51 [uns] 37/51 38/51 [writeh5ad] 39/51 40/51 [modules] 41/51 42/51 [spatial-scatter] 43/51 44/51 [unnamed-chunk-2] 45/51 46/51 [env] 47/51 48/51 [load-sce-basilisk] 49/51 50/51 [unnamed-chunk-3] 51/51 output file: bkg-python-interoperability.knit.md Registered S3 method overwritten by 'zellkonverter': method from py_to_r.pandas.core.arrays.categorical.Categorical reticulate Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [ 9/43] pages/seq-introduction.qmd  processing file: seq-introduction.qmd 1/7 2/7 [unnamed-chunk-1] 3/7 4/7 [unnamed-chunk-2] 5/7 6/7 [unnamed-chunk-3] 7/7 output file: seq-introduction.knit.md  [10/43] pages/seq-reads-to-counts.qmd  processing file: seq-reads-to-counts.qmd 1/5 2/5 [unnamed-chunk-1] 3/5 4/5 [unnamed-chunk-2] 5/5 output file: seq-reads-to-counts.knit.md  [11/43] pages/seq-quality-control.qmd  processing file: seq-quality-control.qmd 1/61 2/61 [unnamed-chunk-1] 3/61 4/61 [load-libs] 5/61 6/61 [load-data] 7/61 8/61 [unnamed-chunk-2] 9/61 10/61 [unnamed-chunk-3] 11/61 12/61 [unnamed-chunk-4] 13/61 14/61 [unnamed-chunk-5] 2025-12-17 06:53:17.489 R[16672:429952136] XType: Using static font registry. 15/61 16/61 [unnamed-chunk-6] 17/61 18/61 [unnamed-chunk-7] 19/61 20/61 [unnamed-chunk-8] 21/61 22/61 [unnamed-chunk-9] 23/61 24/61 [unnamed-chunk-10] 25/61 26/61 [unnamed-chunk-11] 27/61 28/61 [unnamed-chunk-12] 29/61 30/61 [unnamed-chunk-13] 31/61 32/61 [unnamed-chunk-14] 33/61 34/61 [unnamed-chunk-15] 35/61 36/61 [unnamed-chunk-16] 37/61 38/61 [unnamed-chunk-17] 39/61 40/61 [unnamed-chunk-18] 41/61 42/61 [unnamed-chunk-19] 43/61 44/61 [unnamed-chunk-20] 45/61 46/61 [unnamed-chunk-21] 47/61 48/61 [unnamed-chunk-22] 49/61 50/61 [unnamed-chunk-23] 51/61 52/61 [unnamed-chunk-24] 53/61 54/61 [unnamed-chunk-25] 55/61 56/61 [unnamed-chunk-26] 57/61 58/61 [unnamed-chunk-27] 59/61 60/61 [unnamed-chunk-28] 61/61 output file: seq-quality-control.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [12/43] pages/seq-intermediate-processing.qmd  processing file: seq-intermediate-processing.qmd 1/35 2/35 [unnamed-chunk-1] 3/35 4/35 [load-libs] Error: package or namespace load failed for 'BayesSpace' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace 'xgboost' 3.1.2.1 is being loaded, but < 2.0.0 is required  Quitting from seq-intermediate-processing.qmd:34-42 [load-libs] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! package or namespace load failed for 'BayesSpace' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace 'xgboost' 3.1.2.1 is being loaded, but < 2.0.0 is required --- Backtrace: ▆ 1. └─base::library(BayesSpace) 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted make: *** [render] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted