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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 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-2025.11.12-hbd8a1cb_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.45-default_hbd61a6d_104
libexpat conda-forge/linux-64::libexpat-2.7.3-hecca717_0
libffi conda-forge/linux-64::libffi-3.5.2-h9ec8514_0
libgcc conda-forge/linux-64::libgcc-15.2.0-he0feb66_16
libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_16
libgomp conda-forge/linux-64::libgomp-15.2.0-he0feb66_16
liblzma conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2
libnsl conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1
libsqlite conda-forge/linux-64::libsqlite-3.51.1-h0c1763c_0
libuuid conda-forge/linux-64::libuuid-2.41.2-h5347b49_1
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-3.6.0-h26f9b46_0
pip conda-forge/noarch::pip-25.3-pyh8b19718_0
python conda-forge/linux-64::python-3.11.14-hd63d673_2_cpython
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
tk conda-forge/linux-64::tk-8.6.13-noxft_ha0e22de_103
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
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
---------------------------|-----------------
libcurl-8.17.0 | h4e3cde8_1 449 KB conda-forge
numba-0.63.1 | py311h3c884d5_0 5.6 MB conda-forge
------------------------------------------------------------
Total: 6.0 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-2025.11.12-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-3.11.0-4_h4a7cf45_openblas
libcblas conda-forge/linux-64::libcblas-3.11.0-4_h0358290_openblas
libcurl conda-forge/linux-64::libcurl-8.17.0-h4e3cde8_1
libcxx conda-forge/linux-64::libcxx-21.1.7-ha0f52bf_0
libcxxabi conda-forge/linux-64::libcxxabi-21.1.7-h9fd08b6_0
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_16
libgfortran5 conda-forge/linux-64::libgfortran5-15.2.0-h68bc16d_16
libjpeg-turbo conda-forge/linux-64::libjpeg-turbo-3.1.2-hb03c661_0
liblapack conda-forge/linux-64::liblapack-3.11.0-4_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 conda-forge/linux-64::libstdcxx-15.2.0-h934c35e_16
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-15.2.0-hdf11a46_16
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-21.1.7-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_0
proj conda-forge/linux-64::proj-9.7.1-h99ae125_0
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-3.51.1-hbc0de68_0
Downloading and Extracting Packages: ...working...
numba-0.63.1 | 5.6 MB | | 0%
libcurl-8.17.0 | 449 KB | | 0% [A
libcurl-8.17.0 | 449 KB | 3 | 4% [A
numba-0.63.1 | 5.6 MB | | 0%
libcurl-8.17.0 | 449 KB | ######4 | 64% [A
libcurl-8.17.0 | 449 KB | ########## | 100% [A
libcurl-8.17.0 | 449 KB | ########## | 100% [A
numba-0.63.1 | 5.6 MB | 3 | 4%
numba-0.63.1 | 5.6 MB | ##8 | 29%
numba-0.63.1 | 5.6 MB | ########## | 100%
numba-0.63.1 | 5.6 MB | ########## | 100%
numba-0.63.1 | 5.6 MB | ########## | 100%
[A done
Preparing transaction: - \ | / done
Verifying transaction: \ | / - \ | / - \ | / done
Executing transaction: \ | / - \ | / - \ | / - \ done
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+ . /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)
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Collecting click>=8.1 (from Dask==2024.12.1)
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Collecting cloudpickle>=3.0.0 (from Dask==2024.12.1)
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Collecting cycler>=0.11.0 (from squidpy==1.6.2)
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Collecting docrep>=0.3.1 (from squidpy==1.6.2)
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Using cached matplotlib_scalebar-0.9.0-py3-none-any.whl.metadata (18 kB)
Collecting matplotlib>=3.3 (from squidpy==1.6.2)
Downloading 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)
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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 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-image>=0.20 (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 spatialdata>=0.2.5 (from squidpy==1.6.2)
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Collecting statsmodels>=0.12.0 (from squidpy==1.6.2)
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Collecting tifffile!=2022.4.22 (from squidpy==1.6.2)
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Collecting tqdm>=4.50.2 (from squidpy==1.6.2)
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Collecting aiohappyeyeballs>=2.5.0 (from aiohttp>=3.8.1->squidpy==1.6.2)
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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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Collecting propcache>=0.2.0 (from aiohttp>=3.8.1->squidpy==1.6.2)
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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)
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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, 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-0.12.6 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-4.61.0 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-1.5.2 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-2025.10.16 toolz-1.1.0 tqdm-4.67.1 typeguard-4.4.4 typing-extensions-4.15.0 tzdata-2025.2 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-0.4.0 yarl-1.22.0 zarr-2.18.7 zipp-3.23.0
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[39m[31msys: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.
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[31moutput file: bkg-python-interoperability.knit.md
[39m[31mRegistered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
[39m[31mWarning: stack imbalance in 'vapply', 24 then 26
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[31mError: 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
[39m[31m
Quitting from seq-intermediate-processing.qmd:34-42 [load-libs]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[39m[31mExecution halted
[39mmake: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted