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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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Retrieving notices: - [31m/home/biocbuild/.local/share/r-miniconda/lib/python3.12/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'anaconda.mgb.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
warnings.warn(
[39m[31m/home/biocbuild/.local/share/r-miniconda/lib/python3.12/site-packages/urllib3/connectionpool.py:1099: InsecureRequestWarning: Unverified HTTPS request is being made to host 'anaconda.mgb.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings
warnings.warn(
[39m\ done
Channels:
- conda-forge
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
# All requested packages already installed.
7/49
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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-2025.10.5-hbd8a1cb_0
icu conda-forge/linux-64::icu-75.1-he02047a_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.44-h1aa0949_4
libexpat conda-forge/linux-64::libexpat-2.7.1-hecca717_0
libffi conda-forge/linux-64::libffi-3.5.2-h9ec8514_0
libgcc conda-forge/linux-64::libgcc-15.2.0-h767d61c_7
libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7
libgomp conda-forge/linux-64::libgomp-15.2.0-h767d61c_7
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-3.51.0-hee844dc_0
libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7
libuuid conda-forge/linux-64::libuuid-2.41.2-he9a06e4_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-3.5.4-h26f9b46_0
pip conda-forge/noarch::pip-25.2-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_hd72426e_102
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-hb8e6e7a_2
Preparing transaction: ...working... done
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Executing transaction: ...working... done
9/49
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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
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-64::libblas-3.9.0-38_h4a7cf45_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-38_h0358290_openblas
libcxx conda-forge/linux-64::libcxx-21.1.5-ha0f52bf_0
libcxxabi conda-forge/linux-64::libcxxabi-21.1.5-h9fd08b6_0
libgfortran conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7
libgfortran5 conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7
liblapack conda-forge/linux-64::liblapack-3.9.0-38_h47877c9_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_3
llvm-openmp conda-forge/linux-64::llvm-openmp-21.1.5-h4922eb0_0
llvmlite conda-forge/linux-64::llvmlite-0.45.1-py311h41a00d4_0
numba conda-forge/linux-64::numba-0.62.1-py311h6220fa4_0
numpy conda-forge/linux-64::numpy-2.3.4-py311h2e04523_0
python_abi conda-forge/noarch::python_abi-3.11-8_cp311
Downloading and Extracting Packages: ...working... 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'
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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, certifi, attrs, array-api-compat, aioitertools, aiohappyeyeballs, yarl, typeguard, scikit-learn, requests, python-dateutil, pyproj, 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 certifi-2025.10.5 charset_normalizer-3.4.4 click-8.3.0 cloudpickle-3.1.2 colorcet-3.1.0 contourpy-1.3.3 cycler-0.12.1 dask-expr-1.1.21 dask-image-2024.5.3 datashader-0.18.2 deprecated-1.3.1 docrep-0.3.2 fasteners-0.20 fonttools-4.60.1 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-1.5.2 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-3.10.7 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-3.5 numcodecs-0.15.1 ome-zarr-0.11.1 omnipath-1.0.12 packaging-25.0 pandas-2.3.3 param-2.2.1 partd-1.4.2 patsy-1.0.2 pillow-12.0.0 pims-0.7 platformdirs-4.5.0 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-0.11.1 pyparsing-3.2.5 pyproj-3.7.2 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-1.7.2 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-0.14.5 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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[31moutput file: ind-spatial-statistics.knit.md
[39m[31mWarning message:
In readLines(input) :
incomplete final line found on 'ind-spatial-statistics.qmd'
[39m[1m[34m
[32/41] pages/ind-image-analysis.qmd[39m[22m
[31m
processing file: ind-image-analysis.qmd
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[31moutput file: ind-image-analysis.knit.md
[39m[31mWarning message:
In readLines(input) :
incomplete final line found on 'ind-image-analysis.qmd'
[39m[1m[34m
[33/41] pages/mult-diff-spatial-patterns.qmd[39m[22m
[31m
processing file: mult-diff-spatial-patterns.qmd
[39m1/23
2/23 [unnamed-chunk-1]
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5/23
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18/23 [plt-xy]
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21/23
22/23 [unnamed-chunk-2]
23/23
[31moutput file: mult-diff-spatial-patterns.knit.md
[39m[31mWarning message:
In readLines(input) :
incomplete final line found on 'mult-diff-spatial-patterns.qmd'
[39m[1m[34m
[34/41] pages/mult-diff-colocalization.qmd[39m[22m
[31m
processing file: mult-diff-colocalization.qmd
[39m1/41
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8/41 [load-data]
[31mError in curl::curl_fetch_disk(x$url$url, x$disk, handle = x$url$handle) :
Timeout was reached [storage.googleapis.com]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
Calls: .main ... <Anonymous> -> crul_fetch -> <Anonymous> -> raise_libcurl_error
[39m[31m
Quitting from mult-diff-colocalization.qmd:60-73 [load-data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_disk()`:
! Timeout was reached [storage.googleapis.com]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
---
Backtrace:
▆
1. ├─osfr::osf_download(osf_files, path = td)
2. ├─osfr:::osf_download.osf_tbl_file(osf_files, path = td)
3. │ └─base::Map(...)
4. │ └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
5. │ └─osfr (local) `<fn>`(...)
6. │ └─osfr:::.wb_download(...)
7. │ └─osfr:::.wb_request("get", api_path, query, disk = path, progress = progress)
8. │ └─cli$retry(...)
9. │ └─crul (local) verb_func(...)
10. │ └─private$make_request(rr, mock)
11. │ └─crul:::crul_fetch(opts)
12. │ └─curl::curl_fetch_disk(x$url$url, x$disk, handle = x$url$handle)
13. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[39m[31mExecution halted
[39mmake: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted