############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-books/R/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 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] 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: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done # All requested packages already installed. 9/51 10/51 [conda-create] Channels: - conda-forge - bioconda Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/.local/share/r-miniconda/envs/py-interop added / updated specs: - python=3.11 The following packages will be downloaded: package | build ---------------------------|----------------- ld_impl_linux-64-2.45.1 |default_hbd61a6d_101 709 KB conda-forge libgcc-15.2.0 | he0feb66_17 1016 KB conda-forge libgcc-ng-15.2.0 | h69a702a_17 27 KB conda-forge libgomp-15.2.0 | he0feb66_17 589 KB conda-forge libstdcxx-15.2.0 | h934c35e_17 5.6 MB conda-forge pip-26.0.1 | pyh8b19718_0 1.1 MB conda-forge ------------------------------------------------------------ Total: 9.0 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_8 ca-certificates conda-forge/noarch::ca-certificates-2026.1.4-hbd8a1cb_0 icu conda-forge/linux-64::icu-78.2-h33c6efd_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.45.1-default_hbd61a6d_101 libexpat conda-forge/linux-64::libexpat-2.7.3-hecca717_0 libffi conda-forge/linux-64::libffi-3.5.2-h3435931_0 libgcc conda-forge/linux-64::libgcc-15.2.0-he0feb66_17 libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_17 libgomp conda-forge/linux-64::libgomp-15.2.0-he0feb66_17 liblzma conda-forge/linux-64::liblzma-5.8.2-hb03c661_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1 libsqlite conda-forge/linux-64::libsqlite-3.51.2-hf4e2dac_0 libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_17 libuuid conda-forge/linux-64::libuuid-2.41.3-h5347b49_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3 openssl conda-forge/linux-64::openssl-3.6.1-h35e630c_1 packaging conda-forge/noarch::packaging-26.0-pyhcf101f3_0 pip conda-forge/noarch::pip-26.0.1-pyh8b19718_0 python conda-forge/linux-64::python-3.11.14-hd63d673_3_cpython readline conda-forge/linux-64::readline-8.3-h853b02a_0 setuptools conda-forge/noarch::setuptools-80.10.2-pyh332efcf_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h366c992_103 tzdata conda-forge/noarch::tzdata-2025c-hc9c84f9_1 wheel conda-forge/noarch::wheel-0.46.3-pyhd8ed1ab_0 zstd conda-forge/linux-64::zstd-1.5.7-hb78ec9c_6 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: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/.local/share/r-miniconda/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 ---------------------------|----------------- libcxx-21.1.8 | ha0f52bf_2 2.2 MB conda-forge libcxxabi-21.1.8 | h9fd08b6_2 167 KB conda-forge libgfortran-15.2.0 | h69a702a_17 27 KB conda-forge libgfortran5-15.2.0 | h68bc16d_17 2.4 MB conda-forge libstdcxx-ng-15.2.0 | hdf11a46_17 27 KB conda-forge ------------------------------------------------------------ Total: 4.8 MB The following NEW packages will be INSTALLED: c-ares conda-forge/linux-64::c-ares-1.34.6-hb03c661_0 certifi conda-forge/noarch::certifi-2026.1.4-pyhd8ed1ab_0 keyutils conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0 krb5 conda-forge/linux-64::krb5-1.21.3-h659f571_0 lerc conda-forge/linux-64::lerc-4.0.0-h0aef613_1 libblas conda-forge/linux-64::libblas-3.11.0-5_h4a7cf45_openblas libcblas conda-forge/linux-64::libcblas-3.11.0-5_h0358290_openblas libcurl conda-forge/linux-64::libcurl-8.18.0-h4e3cde8_0 libcxx conda-forge/linux-64::libcxx-21.1.8-ha0f52bf_2 libcxxabi conda-forge/linux-64::libcxxabi-21.1.8-h9fd08b6_2 libdeflate conda-forge/linux-64::libdeflate-1.25-h17f619e_0 libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 libev conda-forge/linux-64::libev-4.33-hd590300_2 libgfortran conda-forge/linux-64::libgfortran-15.2.0-h69a702a_17 libgfortran5 conda-forge/linux-64::libgfortran5-15.2.0-h68bc16d_17 libjpeg-turbo conda-forge/linux-64::libjpeg-turbo-3.1.2-hb03c661_0 liblapack conda-forge/linux-64::liblapack-3.11.0-5_h47877c9_openblas libnghttp2 conda-forge/linux-64::libnghttp2-1.67.0-had1ee68_0 libopenblas conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_4 libssh2 conda-forge/linux-64::libssh2-1.11.1-hcf80075_0 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-15.2.0-hdf11a46_17 libtiff conda-forge/linux-64::libtiff-4.7.1-h9d88235_1 libwebp-base conda-forge/linux-64::libwebp-base-1.6.0-hd42ef1d_0 llvm-openmp conda-forge/linux-64::llvm-openmp-21.1.8-h4922eb0_0 llvmlite conda-forge/linux-64::llvmlite-0.46.0-py311h41a00d4_0 numba conda-forge/linux-64::numba-0.63.1-py311h3c884d5_0 numpy conda-forge/linux-64::numpy-2.3.5-py311h2e04523_1 proj conda-forge/linux-64::proj-9.7.1-he0df7b0_2 pyproj conda-forge/linux-64::pyproj-3.7.2-py311h4e6619b_2 python_abi conda-forge/noarch::python_abi-3.11-8_cp311 sqlite conda-forge/linux-64::sqlite-3.51.2-h04a0ce9_0 Downloading and Extracting Packages: ...working... libgfortran5-15.2.0 | 2.4 MB | | 0% libcxx-21.1.8 | 2.2 MB | | 0%  libcxxabi-21.1.8 | 167 KB | | 0%  libstdcxx-ng-15.2.0 | 27 KB | | 0%  libgfortran-15.2.0 | 27 KB | | 0%  libgfortran-15.2.0 | 27 KB | #####9 | 60%  libgfortran-15.2.0 | 27 KB | ########## | 100%  libgfortran5-15.2.0 | 2.4 MB | | 1% libstdcxx-ng-15.2.0 | 27 KB | #####9 | 59%  libstdcxx-ng-15.2.0 | 27 KB | ########## | 100%  libcxxabi-21.1.8 | 167 KB | 9 | 10%  libcxx-21.1.8 | 2.2 MB | | 1%  libgfortran-15.2.0 | 27 KB | ########## | 100%  libcxxabi-21.1.8 | 167 KB | ########## | 100%  libstdcxx-ng-15.2.0 | 27 KB | ########## | 100%  libcxxabi-21.1.8 | 167 KB | ########## | 100%  libcxx-21.1.8 | 2.2 MB | ########## | 100%  libgfortran5-15.2.0 | 2.4 MB | ########## | 100% libgfortran5-15.2.0 | 2.4 MB | ########## | 100% libcxx-21.1.8 | 2.2 MB | ########## | 100%  libcxx-21.1.8 | 2.2 MB | ########## | 100%  libgfortran5-15.2.0 | 2.4 MB | ########## | 100%     done Preparing transaction: - \ done Verifying transaction: / - \ | / - done Executing transaction: | / - \ | / - \ | / - \ | done 15/51 16/51 [deps-pypi] + . /home/biocbuild/.local/share/r-miniconda/bin/activate + conda activate 'py-interop' + '/home/biocbuild/.local/share/r-miniconda/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) Downloading fsspec-2026.2.0-py3-none-any.whl.metadata (10 kB) Requirement already satisfied: packaging>=20.0 in /home/biocbuild/.local/share/r-miniconda/envs/py-interop/lib/python3.11/site-packages (from Dask==2024.12.1) (26.0) 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-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.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-8.7.1-py3-none-any.whl.metadata (4.7 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 /home/biocbuild/.local/share/r-miniconda/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-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB) Collecting aiohttp>=3.8.1 (from squidpy==1.6.2) Using cached aiohttp-3.13.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB) Collecting anndata>=0.9 (from squidpy==1.6.2) Using cached anndata-0.12.9-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-manylinux_2_27_x86_64.manylinux_2_28_x86_64.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-manylinux2014_x86_64.manylinux_2_17_x86_64.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 /home/biocbuild/.local/share/r-miniconda/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-3.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB) Collecting pillow>=8.0.0 (from squidpy==1.6.2) Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.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-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB) Collecting scikit-learn>=0.24.0 (from squidpy==1.6.2) Using cached scikit_learn-1.8.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (11 kB) Collecting spatialdata>=0.2.5 (from squidpy==1.6.2) Using cached spatialdata-0.7.1.post1-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-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (9.5 kB) Collecting tifffile!=2022.4.22 (from squidpy==1.6.2) Using cached tifffile-2026.1.28-py3-none-any.whl.metadata (30 kB) Collecting tqdm>=4.50.2 (from squidpy==1.6.2) Using cached tqdm-4.67.3-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-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (20 kB) Collecting multidict<7.0,>=4.5 (from aiohttp>=3.8.1->squidpy==1.6.2) Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.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-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.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-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.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-1.13.0-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-manylinux_2_27_x86_64.manylinux_2_28_x86_64.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 pandas>=2.1.0 (from squidpy==1.6.2) Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB) Collecting scipy!=1.17.0,>=1.12 (from anndata>=0.9->squidpy==1.6.2) Using cached scipy-1.16.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.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-23.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.0 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-manylinux_2_28_x86_64.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 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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) Collecting urllib3>=1.26.0 (from omnipath>=1.0.7->squidpy==1.6.2) Using cached urllib3-2.6.3-py3-none-any.whl.metadata (6.9 kB) Collecting wrapt>=1.12.0 (from omnipath>=1.0.7->squidpy==1.6.2) Using cached wrapt-2.1.1-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (7.4 kB) Collecting more_itertools>=8.5.0 (from inflect>=4.1.0->omnipath>=1.0.7->squidpy==1.6.2) Using cached more_itertools-10.8.0-py3-none-any.whl.metadata (39 kB) Collecting typeguard>=4.0.1 (from inflect>=4.1.0->omnipath>=1.0.7->squidpy==1.6.2) Using cached typeguard-4.4.4-py3-none-any.whl.metadata (3.3 kB) Collecting locket (from partd>=1.4.0->Dask==2024.12.1) Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB) Collecting imageio (from pims>=0.4.1->dask-image>=0.5.0->squidpy==1.6.2) Using cached imageio-2.37.2-py3-none-any.whl.metadata (9.7 kB) 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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-1.1.0-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-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (82 kB) Using cached session_info2-0.3-py3-none-any.whl (17 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, pyogrio, pygments, pyarrow, propcache, platformdirs, pillow, patsy, param, networkx, natsort, multidict, more_itertools, mdurl, locket, legacy-api-wrap, lazy-loader, 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, pyct, partd, markdown-it-py, leidenalg, 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-3.13.3 aioitertools-0.13.0 aiosignal-1.4.0 anndata-0.12.9 array-api-compat-1.13.0 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-1.1.2 h5py-3.15.1 idna-3.11 igraph-1.0.0 imageio-2.37.2 importlib_metadata-8.7.1 inflect-7.5.0 jmespath-1.1.0 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-6.7.1 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 pandas-2.3.3 param-2.3.1 partd-1.4.2 patsy-1.0.2 pillow-12.1.0 pims-0.7 platformdirs-4.5.1 pooch-1.9.0 propcache-0.4.1 pyarrow-23.0.0 pyct-0.6.0 pygments-2.19.2 pynndescent-0.6.0 pyogrio-0.12.1 pyparsing-3.3.2 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.3 requests-2.32.5 rich-14.3.2 s3fs-2023.6.0 scanpy-1.11.5 scikit-image-0.26.0 scikit-learn-1.8.0 scipy-1.16.3 seaborn-0.13.2 session-info2-0.3 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-2026.1.28 toolz-1.1.0 tqdm-4.67.3 typeguard-4.4.4 typing-extensions-4.15.0 tzdata-2025.3 umap-learn-0.5.11 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-0.5.2 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] 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] 5/35 6/35 [unnamed-chunk-2] 7/35 8/35 [load-data] 9/35 10/35 [logcounts] 11/35 12/35 [mt] 13/35 14/35 [hvgs] 15/35 16/35 [pca] 17/35 18/35 [umap] 19/35 20/35 [clu] 21/35 22/35 [plt-xy-clu] 23/35 24/35 [plot-xy-pcs] 25/35 26/35 [mgs] 27/35 28/35 [plt-mgs-hm] 29/35 30/35 [plt-mgs-xy] 31/35 32/35 [save-data] 33/35 34/35 [unnamed-chunk-3] 35/35 output file: seq-intermediate-processing.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [13/43] pages/seq-deconvolution.qmd  processing file: seq-deconvolution.qmd 1/57 2/57 [unnamed-chunk-1] 3/57 4/57 [unnamed-chunk-2] 5/57 6/57 [deps] 7/57 8/57 [load-vis] 9/57 10/57 [plt-hne] 11/57 12/57 [qcvis] 13/57 14/57 [plt-xy-qc] 15/57 16/57 [vis-filter] 17/57 18/57 [visanno] 19/57 20/57 [deconvis] 21/57 22/57 [qcchrom_vis] 23/57 24/57 [dec] 25/57 26/57 [dec-res] 27/57 28/57 [unnamed-chunk-3] 29/57 30/57 [card-dec] 31/57 32/57 [pltxy] 33/57 34/57 [plt-dec-xy-rctd] 35/57 36/57 [plt-dec-xy-card] 37/57 38/57 [heatmap] 39/57 40/57 [dec-clu] 41/57 42/57 [plt-clu-xy] 43/57 44/57 [plt-clu-fq] 45/57 46/57 [dec-clu-nostroma] 47/57 48/57 [pca] 49/57 50/57 [pcr] 51/57 52/57 [pcr-plot] 53/57 54/57 [plt-pcs-xy] 55/57 56/57 [unnamed-chunk-4] 57/57 output file: seq-deconvolution.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [14/43] pages/seq-workflow-dlpfc.qmd  processing file: seq-workflow-dlpfc.qmd 1/83 2/83 [unnamed-chunk-1] 3/83 4/83 [unnamed-chunk-2] 5/83 6/83 [load-data] 7/83 8/83 [plt-xy] 9/83 10/83 [in-tissue] 11/83 12/83 [is-mito] 13/83 14/83 [qc] 15/83 16/83 [plt-qc] 17/83 18/83 [qc-thresholds] 19/83 20/83 [plt-ex] 21/83 22/83 [unnamed-chunk-3] 23/83 24/83 [unnamed-chunk-4] 25/83 26/83 [unnamed-chunk-5] 27/83 28/83 [unnamed-chunk-6] 29/83 30/83 [unnamed-chunk-7] 31/83 32/83 [hvgs] 33/83 34/83 [unnamed-chunk-8] 35/83 36/83 [unnamed-chunk-9] 37/83 38/83 [unnamed-chunk-10] 39/83 40/83 [unnamed-chunk-11] 41/83 42/83 [unnamed-chunk-12] 43/83 44/83 [unnamed-chunk-13] 45/83 46/83 [unnamed-chunk-14] 47/83 48/83 [unnamed-chunk-15] 49/83 50/83 [unnamed-chunk-16] 51/83 52/83 [spatiallibd-markers] 53/83 54/83 [spatialLIBD_basic_info] 55/83 56/83 [spatialLIBD_gene_annotation] 57/83 58/83 [spatialLIBD_gene_annotation-hide] 59/83 60/83 [spatialLIBD_gene_annotation-cont] 61/83 62/83 [spatialLIBD_gene_search] 63/83 64/83 [spatialLIBD_final_touches] 65/83 66/83 [spatialLIBD_check] 67/83 68/83 [spatialLIBD_vis_gene] 69/83 70/83 [spatialLIBD_interactive] 71/83 72/83 [unnamed-chunk-17] 73/83 74/83 [spatialLIBD_object_size] 75/83 76/83 [spatialLIBD_app_file] 77/83 78/83 [unnamed-chunk-18] 79/83 80/83 [spatialLIBD_deploy_file] 81/83 82/83 [unnamed-chunk-19] 83/83 output file: seq-workflow-dlpfc.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [15/43] pages/seq-workflow-visium-crc.qmd  processing file: seq-workflow-visium-crc.qmd 1/61 2/61 [unnamed-chunk-1] 3/61 4/61 [load-libs] 5/61 6/61 [load-spe] 7/61 8/61 [spe] 9/61 10/61 [plt-hne] 11/61 12/61 [add-qc] 13/61 14/61 [plt-xy-qc] 15/61 16/61 [ol] 17/61 18/61 [plt-ol-xy] 19/61 20/61 [pro] 21/61 22/61 [clu] 23/61 24/61 [load-sce] 25/61 26/61 [sce] 27/61 28/61 [dec] 29/61 30/61 [dec-res] 31/61 32/61 [dec-clu] 33/61 34/61 [unnamed-chunk-2] 35/61 36/61 [plt-dec-xy] 37/61 38/61 [plt-clu-xy] 39/61 40/61 [plt-clu-fq] 41/61 42/61 [plt-pcs-xy] 43/61 44/61 [plt-clu-qc] 45/61 46/61 [MSigDB] 47/61 48/61 [AUCell] 49/61 50/61 [top] 51/61 52/61 [plt-auc-xy] 53/61 54/61 [plt-auc-hm] 55/61 56/61 [cor-auc-dec] 57/61 58/61 [plt-cor] 59/61 60/61 [unnamed-chunk-3] 61/61 output file: seq-workflow-visium-crc.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [16/43] pages/seq-workflow-visium-hd-bin.qmd  processing file: seq-workflow-visium-hd-bin.qmd 1/89 2/89 [unnamed-chunk-1] 3/89 4/89 [deps] 5/89 6/89 [load-vhd8] adding: LICENSE.txt (deflated 37%) adding: barcode_mappings.parquet (deflated 56%) adding: binned_outputs/ (stored 0%) adding: binned_outputs/square_008um/ (stored 0%) adding: binned_outputs/square_008um/spatial/ (stored 0%) adding: binned_outputs/square_008um/spatial/scalefactors_json.json (deflated 42%) adding: binned_outputs/square_008um/spatial/tissue_positions.parquet (deflated 2%) adding: binned_outputs/square_008um/spatial/tissue_lowres_image.png (deflated 0%) adding: binned_outputs/square_008um/filtered_feature_bc_matrix.h5 (deflated 1%) adding: binned_outputs/square_008um/deconvolution.csv.gz (deflated 15%) adding: binned_outputs/square_008um/clustering.csv.gz (deflated 0%) adding: binned_outputs/square_016um/ (stored 0%) adding: binned_outputs/square_016um/spatial/ (stored 0%) adding: binned_outputs/square_016um/spatial/scalefactors_json.json (deflated 42%) adding: binned_outputs/square_016um/spatial/tissue_positions.parquet (deflated 2%) adding: binned_outputs/square_016um/spatial/tissue_lowres_image.png (deflated 0%) adding: binned_outputs/square_016um/filtered_feature_bc_matrix.h5 (deflated 1%) adding: binned_outputs/square_016um/clustering.csv.gz (deflated 0%) adding: segmented_outputs/ (stored 0%) adding: segmented_outputs/spatial/ (stored 0%) adding: segmented_outputs/spatial/scalefactors_json.json (deflated 38%) adding: segmented_outputs/spatial/tissue_lowres_image.png (deflated 0%) adding: segmented_outputs/spatial/tissue_hires_image.png (deflated 0%) adding: segmented_outputs/nucleus_segmentations.geojson (deflated 81%) adding: segmented_outputs/filtered_feature_cell_matrix.h5 (deflated 2%) adding: segmented_outputs/cell_segmentations.geojson (deflated 78%) 7/89 8/89 [load-anno] 9/89 10/89 [plt-lab-xy] 11/89 12/89 [load-vhd16] 13/89 14/89 [vhd16-libsize] 15/89 16/89 [vhd16-empvis] 17/89 18/89 [load-clus] 19/89 20/89 [clusvis] 21/89 22/89 [plt-xy-box] 23/89 24/89 [vhd16-sub] 25/89 26/89 [qc-vhd16-local] 27/89 28/89 [plt-xy-qc] 29/89 30/89 [qc-vis] 31/89 32/89 [vhd16-qc-subset] 33/89 34/89 [vhd16-hvg] 35/89 36/89 [Banksy] 37/89 38/89 [mgs] 39/89 40/89 [plt-mgs-hm] 41/89 42/89 [plt-mgs-xy] 43/89 44/89 [load-sce] 45/89 46/89 [sce-heatmap-level12] 47/89 48/89 [sce-level1addprolifimmune] 49/89 50/89 [diff-labs-lvl2] 51/89 52/89 [vhd8-lv1] 53/89 54/89 [vhd8-singlets] 55/89 56/89 [vhd8-doublets] 57/89 58/89 [vhd8-subset-zoom] 59/89 60/89 [RCTD] 61/89 62/89 [dec-res] 63/89 64/89 [plt-dec-est] 65/89 66/89 [dec-lab] 67/89 68/89 [dec-816] 69/89 70/89 [plt-dec-lab] 71/89 72/89 [plt-dec-clu-xy] 73/89 74/89 [plt-dec-clu-hm] 75/89 76/89 [Statial] 77/89 78/89 [Statial-df] 79/89 80/89 [Statial-fd] 81/89 82/89 [Statial-plt] 83/89 84/89 [vhd8-getdis] 85/89 86/89 [vhd8-ccm] 87/89 88/89 [unnamed-chunk-2] 89/89 output file: seq-workflow-visium-hd-bin.knit.md Warning message: In in_dir(input_dir(), expr) : You changed the working directory to /tmp/RtmpLAztoM/file280120681ea2dd (probably via setwd()). It will be restored to /tmp/RtmpzmwpSm/Rbuild25e69d3b04c7a0/OSTA/inst/pages. See the Note section in ?knitr::knit Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [17/43] pages/seq-workflow-visium-hd-seg.qmd  processing file: seq-workflow-visium-hd-seg.qmd 1/57 2/57 [unnamed-chunk-1] 3/57 4/57 [fig-10x-vhdseg] 5/57 6/57 [load-deps] 7/57 8/57 [unnamed-chunk-2] 9/57 10/57 [load-data] 11/57 12/57 [add-mapping] 13/57 14/57 [unnamed-chunk-3] 15/57 16/57 [sub] 17/57 18/57 [plt-spe-vs-sub-xy] 19/57 20/57 [unnamed-chunk-4] 21/57 22/57 [unnamed-chunk-5] 23/57 24/57 [sfe] 25/57 26/57 [plt-seg] 27/57 28/57 [um2] 29/57 30/57 [bin-vs-cell] 31/57 32/57 [qc-scuttle] 33/57 34/57 [unnamed-chunk-6] 35/57 36/57 [qc-SpotSweeper] 37/57 38/57 [plt-ex] 39/57 40/57 [fil] 41/57 42/57 [load-sce] 43/57 44/57 [down-sce] 45/57 46/57 [lab-lv1] 47/57 48/57 [lab-lv0] 49/57 50/57 [plt-lab-roi] 51/57 52/57 [plt-lab-all] 53/57 54/57 [unnamed-chunk-7] 55/57 56/57 [unnamed-chunk-8] 57/57 output file: seq-workflow-visium-hd-seg.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [18/43] pages/img-introduction.qmd  processing file: img-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: img-introduction.knit.md  [19/43] pages/img-segmentation.qmd  processing file: img-segmentation.qmd 1/9 2/9 [unnamed-chunk-1] 3/9 4/9 [fig-10xsegmentation] 5/9 6/9 [fig-SSAM] 7/9 8/9 [unnamed-chunk-2] 9/9 output file: img-segmentation.knit.md  [20/43] pages/img-quality-control.qmd  processing file: img-quality-control.qmd 1/61 2/61 [unnamed-chunk-1] 3/61 4/61 [deps] 5/61 6/61 [load-data-xen] 7/61 8/61 [load-data-cos] 9/61 10/61 [plot-xy] 11/61 12/61 [scuttle-qc] 13/61 14/61 [gc-1] 15/61 16/61 [plot-cos-xy-dapi] 17/61 18/61 [gc-2] 19/61 20/61 [SpaceTrooper-qc] 21/61 22/61 [gc-3] 23/61 24/61 [plot-qc-1d] 25/61 26/61 [plot-qc-xy] 27/61 28/61 [plot-qc-2d-one] 29/61 30/61 [plot-cos-fov] 31/61 32/61 [cos-plot-ns] 33/61 34/61 [cos-plot-qc] 35/61 36/61 [cos-est-rad] 37/61 38/61 [cos-plot-ds] 39/61 40/61 [cos-plot-ex] 41/61 42/61 [SpaceTrooper-ol-cos] 43/61 44/61 [SpaceTrooper-calc-score] 45/61 46/61 [SpaceTrooper-plot-score] 47/61 48/61 [xen-ol] 49/61 50/61 [xen-plot-ol] 51/61 52/61 [xen-ex] 53/61 54/61 [cos-ex] 55/61 56/61 [plot-ex] 57/61 58/61 [save-data] 59/61 60/61 [unnamed-chunk-2] 61/61 output file: img-quality-control.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [21/43] pages/img-intermediate-processing.qmd  processing file: img-intermediate-processing.qmd 1/23 2/23 [unnamed-chunk-1] 3/23 4/23 [load-libs] 5/23 6/23 [load-anno] 7/23 8/23 [log] 9/23 10/23 [dr-tx] 11/23 12/23 [dr-sp] 13/23 14/23 [dr-nm] 15/23 16/23 [clu] 17/23 18/23 [plt-clu-xy] 19/23 20/23 [save-data] 21/23 22/23 [unnamed-chunk-2] 23/23 output file: img-intermediate-processing.knit.md Warning: stack imbalance in 'vapply', 24 then 26 Warning: stack imbalance in 'vapply', 10 then 12  [22/43] pages/img-neighborhood-analysis.qmd  processing file: img-neighborhood-analysis.qmd 1/53 2/53 [unnamed-chunk-1] 3/53 4/53 [deps] 5/53 6/53 [unnamed-chunk-2] 7/53 8/53 [unnamed-chunk-3] 9/53 10/53 [nns-calc] 11/53 12/53 [nns-plot] 13/53 14/53 [nns-note-test] 15/53 16/53 [nns-note-real] 17/53 18/53 [imcRtools-calc] 19/53 20/53 [imcRtools-show] 21/53 22/53 [imcRtools-plot] 23/53 24/53 [hoodscanR-calc] 25/53 26/53 [hoodscanR-plot-corr] 27/53 28/53 [hoodscanR-calc-mets] 29/53 30/53 [hoodscanR-plot-mets-xy] Error in `mutate()`: ℹ In argument: `value = case_when(abs(value) > 2 ~ sign(value) * 2, TRUE ~ value)`. Caused by error in `case_when()`: ! `..1 (left)` must be a logical vector, not a logical matrix. Backtrace: ▆ 1. ├─dplyr::mutate(...) 2. ├─dplyr:::mutate.data.frame(...) 3. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 4. │ ├─base::withCallingHandlers(...) 5. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 6. │ └─mask$eval_all_mutate(quo) 7. │ └─dplyr (local) eval() 8. ├─dplyr::case_when(abs(value) > 2 ~ sign(value) * 2, TRUE ~ value) 9. │ └─vctrs::vec_case_when(...) 10. └─rlang::abort(message = message, call = call) Warning message: Duplicated chunk option(s) 'message' in both chunk header and pipe comments of the chunk 'scider-load-package-and-data'.  Quitting from img-neighborhood-analysis.qmd:226-239 [hoodscanR-plot-mets-xy] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `mutate()`: ℹ In argument: `value = case_when(abs(value) > 2 ~ sign(value) * 2, TRUE ~ value)`. Caused by error in `case_when()`: ! `..1 (left)` must be a logical vector, not a logical matrix. --- Backtrace: ▆ 1. ├─dplyr::mutate(...) 2. ├─dplyr:::mutate.data.frame(...) 3. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) 4. │ ├─base::withCallingHandlers(...) 5. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) 6. │ └─mask$eval_all_mutate(quo) 7. │ └─dplyr (local) eval() 8. └─dplyr::case_when(abs(value) > 2 ~ sign(value) * 2, TRUE ~ value) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Execution halted make: *** [Makefile:4: render] Error 1 Error in tools::buildVignettes(dir = ".", tangle = TRUE) : running 'make' failed Execution halted