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### Running command:
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### /home/biocbuild/bbs-3.22-books/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
###
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* 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/
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[31moutput file: bkg-example-datasets.knit.md
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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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
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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
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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% [A
libcxxabi-21.1.8 | 167 KB | | 0% [A[A
libstdcxx-ng-15.2.0 | 27 KB | | 0% [A[A[A
libgfortran-15.2.0 | 27 KB | | 0% [A[A[A[A
libgfortran-15.2.0 | 27 KB | #####9 | 60% [A[A[A[A
libgfortran-15.2.0 | 27 KB | ########## | 100% [A[A[A[A
libgfortran5-15.2.0 | 2.4 MB | | 1%
libstdcxx-ng-15.2.0 | 27 KB | #####9 | 59% [A[A[A
libstdcxx-ng-15.2.0 | 27 KB | ########## | 100% [A[A[A
libcxxabi-21.1.8 | 167 KB | 9 | 10% [A[A
libcxx-21.1.8 | 2.2 MB | | 1% [A
libgfortran-15.2.0 | 27 KB | ########## | 100% [A[A[A[A
libcxxabi-21.1.8 | 167 KB | ########## | 100% [A[A
libstdcxx-ng-15.2.0 | 27 KB | ########## | 100% [A[A[A
libcxxabi-21.1.8 | 167 KB | ########## | 100% [A[A
libcxx-21.1.8 | 2.2 MB | ########## | 100% [A
libgfortran5-15.2.0 | 2.4 MB | ########## | 100%
libgfortran5-15.2.0 | 2.4 MB | ########## | 100%
libcxx-21.1.8 | 2.2 MB | ########## | 100% [A
libcxx-21.1.8 | 2.2 MB | ########## | 100% [A
libgfortran5-15.2.0 | 2.4 MB | ########## | 100%
[A
[A[A
[A[A[A
[A[A[A[A done
Preparing transaction: - \ done
Verifying transaction: / - \ | / - done
Executing transaction: | / - \ | / - \ | / - \ | done
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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)
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Downloading fsspec-2026.2.0-py3-none-any.whl.metadata (10 kB)
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Using cached asciitree-0.3.3-py3-none-any.whl
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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)
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Collecting matplotlib-scalebar>=0.8.0 (from squidpy==1.6.2)
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Collecting matplotlib>=3.3 (from squidpy==1.6.2)
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Collecting networkx>=2.6.0 (from squidpy==1.6.2)
Using cached networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
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Collecting omnipath>=1.0.7 (from squidpy==1.6.2)
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Collecting pandas>=2.1.0 (from squidpy==1.6.2)
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Collecting pillow>=8.0.0 (from squidpy==1.6.2)
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Collecting scanpy>=1.9.3 (from squidpy==1.6.2)
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Collecting scikit-learn>=0.24.0 (from squidpy==1.6.2)
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Collecting statsmodels>=0.12.0 (from squidpy==1.6.2)
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Collecting tqdm>=4.50.2 (from squidpy==1.6.2)
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Collecting validators>=0.18.2 (from squidpy==1.6.2)
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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)
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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)
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Collecting frozenlist>=1.1.1 (from aiohttp>=3.8.1->squidpy==1.6.2)
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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)
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Collecting yarl<2.0,>=1.17.0 (from aiohttp>=3.8.1->squidpy==1.6.2)
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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
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[31moutput file: bkg-python-interoperability.knit.md
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[31moutput file: seq-workflow-visium-hd-bin.knit.md
[39m[31mWarning message:
In in_dir(input_dir(), expr) :[39m[31m
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
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[31mError 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$eval_all_mutate(quo)
7. │ └─dplyr (local) eval()
8. ├─dplyr::case_when(abs(value) > 2 ~ sign(value) * 2, TRUE ~ value)
9. │ └─vctrs::vec_case_when(...)
10. └─rlang::abort(message = message, call = call)
[39m[31mWarning message:
Duplicated chunk option(s) 'message' in both chunk header and pipe comments of the chunk 'scider-load-package-and-data'.
[39m[31m
Quitting from img-neighborhood-analysis.qmd:226-239 [hoodscanR-plot-mets-xy]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/dplyr:::mutate_error>
Error in `mutate()`:
ℹ In argument: `value = case_when(abs(value) > 2 ~ sign(value) * 2,
TRUE ~ value)`.
Caused by error in `case_when()`:
! `..1 (left)` must be a logical vector, not a logical matrix.
---
Backtrace:
▆
1. ├─dplyr::mutate(...)
2. ├─dplyr:::mutate.data.frame(...)
3. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
4. │ ├─base::withCallingHandlers(...)
5. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
6. │ └─mask$eval_all_mutate(quo)
7. │ └─dplyr (local) eval()
8. └─dplyr::case_when(abs(value) > 2 ~ sign(value) * 2, TRUE ~ value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[39m[31mExecution halted
[39mmake: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted