| Back to Books build report for BioC 3.22 |
This page was generated on 2025-10-24 14:30 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 10/11 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| OSTA 0.99.31 (landing page) Lukas M. Weber
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the OSTA package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OSTA |
| Version: 0.99.31 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA |
| StartedAt: 2025-10-24 06:51:31 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 06:54:53 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 202.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### 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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’
quarto render ../inst/
[1m[34m
[ 1/40] index.qmd[39m[22m
[31m
processing file: index.qmd
[39m1/4 [unnamed-chunk-1]
2/4
3/4 [carousel]
4/4
[31moutput file: index.knit.md
[39m[1m[34m
[ 2/40] pages/bkg-introduction.qmd[39m[22m
[1m[34m
[ 3/40] pages/bkg-spatial-omics.qmd[39m[22m
[1m[34m
[ 4/40] pages/bkg-infrastructure.qmd[39m[22m
[31m
processing file: bkg-infrastructure.qmd
[39m1/5
2/5 [fig-spatialexperiment]
3/5
4/5 [fig-spatialdata]
5/5
[31moutput file: bkg-infrastructure.knit.md
[39m[1m[34m
[ 5/40] pages/bkg-ecosystem.qmd[39m[22m
[31m
processing file: bkg-ecosystem.qmd
[39m1/19
2/19 [unnamed-chunk-1]
3/19
4/19 [unnamed-chunk-2]
5/19
6/19 [unnamed-chunk-3]
7/19
8/19 [unnamed-chunk-4]
9/19
10/19 [unnamed-chunk-5]
[31m2025-10-24 06:53:30.215 R[80166:538684978] XType: Using static font registry.
[39m11/19
12/19 [unnamed-chunk-6]
13/19
14/19 [unnamed-chunk-7]
15/19
16/19 [unnamed-chunk-8]
17/19
18/19 [unnamed-chunk-9]
19/19
[31moutput file: bkg-ecosystem.knit.md
[39m[1m[34m
[ 6/40] pages/bkg-importing-data.qmd[39m[22m
[31m
processing file: bkg-importing-data.qmd
[39m1/9
2/9 [unnamed-chunk-1]
3/9
4/9 [unnamed-chunk-2]
5/9
6/9 [unnamed-chunk-3]
7/9
8/9 [unnamed-chunk-4]
9/9
[31moutput file: bkg-importing-data.knit.md
[39m[1m[34m
[ 7/40] pages/bkg-example-datasets.qmd[39m[22m
[31m
processing file: bkg-example-datasets.qmd
[39m1/5
2/5 [list-data]
3/5
4/5 [list-stexampledata]
5/5
[31moutput file: bkg-example-datasets.knit.md
[39m[1m[34m
[ 8/40] pages/bkg-python-interoperability.qmd[39m[22m
[31m
processing file: bkg-python-interoperability.qmd
[39m1/45
2/45 [libraries]
3/45
4/45 [install-miniconda]
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
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2025.10.5 | pyhd8ed1ab_0 156 KB conda-forge
conda-24.11.3 | py310hbe9552e_0 908 KB conda-forge
frozendict-2.4.6 | py310h7bdd564_1 48 KB conda-forge
------------------------------------------------------------
Total: 1.1 MB
The following NEW packages will be INSTALLED:
frozendict conda-forge/osx-arm64::frozendict-2.4.6-py310h7bdd564_1
The following packages will be UPDATED:
ca-certificates conda-forge/osx-arm64::ca-certificate~ --> conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0
certifi 2024.2.2-pyhd8ed1ab_0 --> 2025.10.5-pyhd8ed1ab_0
conda 24.3.0-py310hbe9552e_0 --> 24.11.3-py310hbe9552e_0
openssl 3.2.1-h0d3ecfb_1 --> 3.5.4-h5503f6c_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
5/45
6/45 [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
---------------------------|-----------------
libffi-3.5.2 | he5f378a_0 39 KB conda-forge
python-3.11.14 |h18782d2_2_cpython 14.1 MB conda-forge
------------------------------------------------------------
Total: 14.1 MB
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-2025.10.5-hbd8a1cb_0
icu conda-forge/osx-arm64::icu-75.1-hfee45f7_0
libexpat conda-forge/osx-arm64::libexpat-2.7.1-hec049ff_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-3.50.4-h4237e3c_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-3.5.4-h5503f6c_0
pip conda-forge/noarch::pip-25.2-pyh8b19718_0
python conda-forge/osx-arm64::python-3.11.14-h18782d2_2_cpython
readline conda-forge/osx-arm64::readline-8.2-h1d1bf99_2
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
tk conda-forge/osx-arm64::tk-8.6.13-h892fb3f_2
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
7/45
8/45 [conda-list]
9/45
10/45 [deps-conda-forge]
Channels:
- conda-forge
- bioconda
Platform: osx-arm64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
[31m
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.9.1
Please update conda by running
$ conda update -n base -c conda-forge conda
[39m
## Package Plan ##
environment location: /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop
added / updated specs:
- libcxx
- llvm-openmp
- llvmlite
- numba
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.9.0 |37_h51639a9_openblas 17 KB conda-forge
libcblas-3.9.0 |37_hb0561ab_openblas 17 KB conda-forge
libcxx-21.1.4 | hf598326_0 555 KB conda-forge
libgfortran-15.2.0 | hfcf01ff_1 131 KB conda-forge
libgfortran5-15.2.0 | h742603c_1 746 KB conda-forge
liblapack-3.9.0 |37_hd9741b5_openblas 17 KB conda-forge
libopenblas-0.3.30 |openmp_ha158390_2 4.1 MB conda-forge
llvm-openmp-21.1.4 | h4a912ad_0 279 KB conda-forge
llvmlite-0.45.1 | py311h27de090_0 23.2 MB conda-forge
numba-0.62.1 | py311h922685c_0 5.6 MB conda-forge
numpy-2.3.4 | py311h8685306_0 6.9 MB conda-forge
python_abi-3.11 | 8_cp311 7 KB conda-forge
------------------------------------------------------------
Total: 41.5 MB
The following NEW packages will be INSTALLED:
libblas conda-forge/osx-arm64::libblas-3.9.0-37_h51639a9_openblas
libcblas conda-forge/osx-arm64::libcblas-3.9.0-37_hb0561ab_openblas
libcxx conda-forge/osx-arm64::libcxx-21.1.4-hf598326_0
libgfortran conda-forge/osx-arm64::libgfortran-15.2.0-hfcf01ff_1
libgfortran5 conda-forge/osx-arm64::libgfortran5-15.2.0-h742603c_1
liblapack conda-forge/osx-arm64::liblapack-3.9.0-37_hd9741b5_openblas
libopenblas conda-forge/osx-arm64::libopenblas-0.3.30-openmp_ha158390_2
llvm-openmp conda-forge/osx-arm64::llvm-openmp-21.1.4-h4a912ad_0
llvmlite conda-forge/osx-arm64::llvmlite-0.45.1-py311h27de090_0
numba conda-forge/osx-arm64::numba-0.62.1-py311h922685c_0
numpy conda-forge/osx-arm64::numpy-2.3.4-py311h8685306_0
python_abi conda-forge/noarch::python_abi-3.11-8_cp311
zstd conda-forge/osx-arm64::zstd-1.5.7-h6491c7d_2
Downloading and Extracting Packages: ...working...
llvmlite-0.45.1 | 23.2 MB | | 0%
numpy-2.3.4 | 6.9 MB | | 0% [A
numba-0.62.1 | 5.6 MB | | 0% [A[A
libopenblas-0.3.30 | 4.1 MB | | 0% [A[A[A
libgfortran5-15.2.0 | 746 KB | | 0% [A[A[A[A
libcxx-21.1.4 | 555 KB | | 0% [A[A[A[A[A
llvm-openmp-21.1.4 | 279 KB | | 0% [A[A[A[A[A[A
libgfortran-15.2.0 | 131 KB | | 0% [A[A[A[A[A[A[A
libblas-3.9.0 | 17 KB | | 0% [A[A[A[A[A[A[A[A
libcblas-3.9.0 | 17 KB | | 0% [A[A[A[A[A[A[A[A[A
liblapack-3.9.0 | 17 KB | | 0% [A[A[A[A[A[A[A[A[A[A
python_abi-3.11 | 7 KB | | 0% [A[A[A[A[A[A[A[A[A[A[A
numba-0.62.1 | 5.6 MB | | 0% [A[A
llvmlite-0.45.1 | 23.2 MB | | 0%
libgfortran5-15.2.0 | 746 KB | 2 | 2% [A[A[A[A
libopenblas-0.3.30 | 4.1 MB | | 0% [A[A[A
numpy-2.3.4 | 6.9 MB | | 0% [A
libgfortran5-15.2.0 | 746 KB | ########## | 100% [A[A[A[A
libgfortran5-15.2.0 | 746 KB | ########## | 100% [A[A[A[A
numba-0.62.1 | 5.6 MB | #####1 | 51% [A[A
llvmlite-0.45.1 | 23.2 MB | 3 | 4%
libopenblas-0.3.30 | 4.1 MB | #######4 | 74% [A[A[A
numpy-2.3.4 | 6.9 MB | ###2 | 32% [A
libopenblas-0.3.30 | 4.1 MB | ########## | 100% [A[A[A
libcxx-21.1.4 | 555 KB | 2 | 3% [A[A[A[A[A
numba-0.62.1 | 5.6 MB | ########## | 100% [A[A
libopenblas-0.3.30 | 4.1 MB | ########## | 100% [A[A[A
llvmlite-0.45.1 | 23.2 MB | #1 | 12%
libcxx-21.1.4 | 555 KB | ########## | 100% [A[A[A[A[A
numpy-2.3.4 | 6.9 MB | ########## | 100% [A
numpy-2.3.4 | 6.9 MB | ########## | 100% [A
llvm-openmp-21.1.4 | 279 KB | 5 | 6% [A[A[A[A[A[A
libgfortran-15.2.0 | 131 KB | #2 | 12% [A[A[A[A[A[A[A
libcxx-21.1.4 | 555 KB | ########## | 100% [A[A[A[A[A
llvm-openmp-21.1.4 | 279 KB | ########## | 100% [A[A[A[A[A[A
libgfortran-15.2.0 | 131 KB | ########## | 100% [A[A[A[A[A[A[A
libblas-3.9.0 | 17 KB | #########2 | 93% [A[A[A[A[A[A[A[A
libblas-3.9.0 | 17 KB | ########## | 100% [A[A[A[A[A[A[A[A
llvmlite-0.45.1 | 23.2 MB | #####8 | 58%
llvm-openmp-21.1.4 | 279 KB | ########## | 100% [A[A[A[A[A[A
libcblas-3.9.0 | 17 KB | #########2 | 93% [A[A[A[A[A[A[A[A[A
libcblas-3.9.0 | 17 KB | ########## | 100% [A[A[A[A[A[A[A[A[A
libgfortran-15.2.0 | 131 KB | ########## | 100% [A[A[A[A[A[A[A
libblas-3.9.0 | 17 KB | ########## | 100% [A[A[A[A[A[A[A[A
python_abi-3.11 | 7 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A[A
python_abi-3.11 | 7 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A[A
liblapack-3.9.0 | 17 KB | #########2 | 93% [A[A[A[A[A[A[A[A[A[A
liblapack-3.9.0 | 17 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A
libcblas-3.9.0 | 17 KB | ########## | 100% [A[A[A[A[A[A[A[A[A
python_abi-3.11 | 7 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A[A
liblapack-3.9.0 | 17 KB | ########## | 100% [A[A[A[A[A[A[A[A[A[A
llvmlite-0.45.1 | 23.2 MB | ########## | 100%
llvmlite-0.45.1 | 23.2 MB | ########## | 100%
llvmlite-0.45.1 | 23.2 MB | ########## | 100%
numba-0.62.1 | 5.6 MB | ########## | 100% [A[A
numba-0.62.1 | 5.6 MB | ########## | 100% [A[A
numpy-2.3.4 | 6.9 MB | ########## | 100% [A
[A
[A[A
[A[A[A
[A[A[A[A
[A[A[A[A[A
[A[A[A[A[A[A
[A[A[A[A[A[A[A
[A[A[A[A[A[A[A[A
[A[A[A[A[A[A[A[A[A
[A[A[A[A[A[A[A[A[A[A
[A[A[A[A[A[A[A[A[A[A[A done
Preparing transaction: - done
Verifying transaction: | / - \ | / - done
Executing transaction: | / - \ | / - \ | / done
11/45
12/45 [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
Downloading dask-2024.12.1-py3-none-any.whl.metadata (3.7 kB)
Collecting zarr==2.18.7
Downloading zarr-2.18.7-py3-none-any.whl.metadata (5.8 kB)
Collecting squidpy==1.6.2
Downloading squidpy-1.6.2-py3-none-any.whl.metadata (8.8 kB)
Collecting click>=8.1 (from Dask==2024.12.1)
Using cached click-8.3.0-py3-none-any.whl.metadata (2.6 kB)
Collecting cloudpickle>=3.0.0 (from Dask==2024.12.1)
Downloading cloudpickle-3.1.1-py3-none-any.whl.metadata (7.1 kB)
Collecting fsspec>=2021.09.0 (from Dask==2024.12.1)
Using cached fsspec-2025.9.0-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)
Downloading partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
Collecting pyyaml>=5.3.1 (from Dask==2024.12.1)
Downloading 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)
Downloading 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)
Downloading asciitree-0.3.3.tar.gz (4.0 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
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) (2.3.4)
Collecting fasteners (from zarr==2.18.7)
Downloading 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)
Downloading 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)
Downloading aiohttp-3.13.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (8.1 kB)
Collecting anndata>=0.9 (from squidpy==1.6.2)
Downloading anndata-0.12.3-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)
Downloading dask_image-2024.5.3-py3-none-any.whl.metadata (2.8 kB)
Collecting docrep>=0.3.1 (from squidpy==1.6.2)
Using cached docrep-0.3.2.tar.gz (33 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting leidenalg>=0.8.2 (from squidpy==1.6.2)
Using cached leidenalg-0.10.2-cp38-abi3-macosx_11_0_arm64.whl.metadata (10 kB)
Collecting matplotlib-scalebar>=0.8.0 (from squidpy==1.6.2)
Downloading matplotlib_scalebar-0.9.0-py3-none-any.whl.metadata (18 kB)
Collecting matplotlib>=3.3 (from squidpy==1.6.2)
Downloading matplotlib-3.10.7-cp311-cp311-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting networkx>=2.6.0 (from squidpy==1.6.2)
Using cached networkx-3.5-py3-none-any.whl.metadata (6.3 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) (0.62.1)
Collecting omnipath>=1.0.7 (from squidpy==1.6.2)
Downloading omnipath-1.0.12-py3-none-any.whl.metadata (7.0 kB)
Collecting pandas>=2.1.0 (from squidpy==1.6.2)
Downloading pandas-2.3.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB)
Collecting pillow>=8.0.0 (from squidpy==1.6.2)
Downloading 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)
Downloading scanpy-1.11.5-py3-none-any.whl.metadata (9.3 kB)
Collecting scikit-image>=0.20 (from squidpy==1.6.2)
Downloading 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)
Downloading scikit_learn-1.7.2-cp311-cp311-macosx_12_0_arm64.whl.metadata (11 kB)
Collecting spatialdata>=0.2.5 (from squidpy==1.6.2)
Downloading spatialdata-0.5.0-py3-none-any.whl.metadata (10 kB)
Collecting statsmodels>=0.12.0 (from squidpy==1.6.2)
Downloading statsmodels-0.14.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (9.5 kB)
Collecting tifffile!=2022.4.22 (from squidpy==1.6.2)
Downloading tifffile-2025.10.16-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)
Downloading 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)
Downloading 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-1.2.18-py2.py3-none-any.whl.metadata (5.7 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)
Downloading 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)
Downloading 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)
Downloading 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)
Downloading 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)
Downloading 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)
Downloading 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-1.4.1-py3-none-any.whl.metadata (2.1 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)
Downloading scipy-1.16.2-cp311-cp311-macosx_12_0_arm64.whl.metadata (62 kB)
Collecting pims>=0.4.1 (from dask-image>=0.5.0->squidpy==1.6.2)
Downloading pims-0.7.tar.gz (87 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting dask-expr<1.2,>=1.1 (from dask[array,dataframe]>=2024.4.1->dask-image>=0.5.0->squidpy==1.6.2)
Downloading 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)
Downloading 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<0.12,>=0.10.0 (from leidenalg>=0.8.2->squidpy==1.6.2)
Downloading igraph-0.11.9-cp39-abi3-macosx_11_0_arm64.whl.metadata (4.4 kB)
Collecting texttable>=1.6.2 (from igraph<0.12,>=0.10.0->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)
Downloading fonttools-4.60.1-cp311-cp311-macosx_10_9_universal2.whl.metadata (112 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)
Collecting python-dateutil>=2.7 (from matplotlib>=3.3->squidpy==1.6.2)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Requirement already satisfied: llvmlite<0.46,>=0.45.0dev0 in /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/lib/python3.11/site-packages (from numba>=0.56.4->squidpy==1.6.2) (0.45.1)
Collecting inflect>=4.1.0 (from omnipath>=1.0.7->squidpy==1.6.2)
Downloading 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)
Collecting urllib3>=1.26.0 (from omnipath>=1.0.7->squidpy==1.6.2)
Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
Collecting wrapt>=1.12.0 (from omnipath>=1.0.7->squidpy==1.6.2)
Downloading wrapt-2.0.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (8.8 kB)
Collecting more_itertools>=8.5.0 (from inflect>=4.1.0->omnipath>=1.0.7->squidpy==1.6.2)
Downloading 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)
Downloading typeguard-4.4.4-py3-none-any.whl.metadata (3.3 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-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting locket (from partd>=1.4.0->Dask==2024.12.1)
Downloading 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)
Downloading imageio-2.37.0-py3-none-any.whl.metadata (5.2 kB)
Collecting slicerator>=0.9.8 (from pims>=0.4.1->dask-image>=0.5.0->squidpy==1.6.2)
Downloading slicerator-1.1.0-py3-none-any.whl.metadata (1.9 kB)
Collecting charset_normalizer<4,>=2 (from requests>=2.24.0->omnipath>=1.0.7->squidpy==1.6.2)
Downloading charset_normalizer-3.4.4-cp311-cp311-macosx_10_9_universal2.whl.metadata (37 kB)
Collecting certifi>=2017.4.17 (from requests>=2.24.0->omnipath>=1.0.7->squidpy==1.6.2)
Using cached certifi-2025.10.5-py3-none-any.whl.metadata (2.5 kB)
Collecting joblib (from scanpy>=1.9.3->squidpy==1.6.2)
Using cached joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB)
Collecting patsy!=1.0.0 (from scanpy>=1.9.3->squidpy==1.6.2)
Downloading 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)
Downloading session_info2-0.2.3-py3-none-any.whl.metadata (3.4 kB)
Collecting umap-learn>=0.5.6 (from scanpy>=1.9.3->squidpy==1.6.2)
Using cached umap_learn-0.5.9.post2-py3-none-any.whl.metadata (25 kB)
Collecting lazy-loader>=0.4 (from scikit-image>=0.20->squidpy==1.6.2)
Downloading lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn>=0.24.0->squidpy==1.6.2)
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
INFO: pip is looking at multiple versions of spatialdata to determine which version is compatible with other requirements. This could take a while.
Collecting spatialdata>=0.2.5 (from squidpy==1.6.2)
Downloading spatialdata-0.4.0-py3-none-any.whl.metadata (10 kB)
Downloading spatialdata-0.3.0-py3-none-any.whl.metadata (9.8 kB)
Downloading spatialdata-0.2.6-py3-none-any.whl.metadata (9.6 kB)
Collecting fsspec>=2021.09.0 (from Dask==2024.12.1)
Downloading fsspec-2023.6.0-py3-none-any.whl.metadata (6.7 kB)
Collecting geopandas>=0.14 (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading geopandas-1.1.1-py3-none-any.whl.metadata (2.3 kB)
Collecting multiscale-spatial-image>=2.0.2 (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading multiscale_spatial_image-2.0.3-py3-none-any.whl.metadata (25 kB)
Collecting ome-zarr>=0.8.4 (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading ome_zarr-0.12.2-py3-none-any.whl.metadata (2.9 kB)
Collecting pooch (from spatialdata>=0.2.5->squidpy==1.6.2)
Using cached pooch-1.8.2-py3-none-any.whl.metadata (10 kB)
Collecting rich (from spatialdata>=0.2.5->squidpy==1.6.2)
Using cached rich-14.2.0-py3-none-any.whl.metadata (18 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/r-miniconda-arm64/envs/py-interop/lib/python3.11/site-packages (from spatialdata>=0.2.5->squidpy==1.6.2) (80.9.0)
Collecting shapely>=2.0.1 (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading shapely-2.1.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (6.8 kB)
Collecting spatial-image>=1.1.0 (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading spatial_image-1.2.3-py3-none-any.whl.metadata (7.0 kB)
Collecting xarray-schema (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading xarray_schema-0.0.3-py3-none-any.whl.metadata (4.3 kB)
Collecting xarray-spatial>=0.3.5 (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading xarray_spatial-0.4.0-py3-none-any.whl.metadata (16 kB)
Collecting spatialdata>=0.2.5 (from squidpy==1.6.2)
Downloading spatialdata-0.2.5.post0-py3-none-any.whl.metadata (9.6 kB)
Collecting multiscale-spatial-image<2.0.0,>=1.0.0 (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading multiscale_spatial_image-1.0.1-py3-none-any.whl.metadata (22 kB)
Collecting xarray-datatree (from spatialdata>=0.2.5->squidpy==1.6.2)
Downloading xarray_datatree-0.0.15-py3-none-any.whl.metadata (7.6 kB)
Collecting pyogrio>=0.7.2 (from geopandas>=0.14->spatialdata>=0.2.5->squidpy==1.6.2)
Downloading pyogrio-0.11.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (5.3 kB)
Collecting pyproj>=3.5.0 (from geopandas>=0.14->spatialdata>=0.2.5->squidpy==1.6.2)
Downloading pyproj-3.7.2.tar.gz (226 kB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'
[31m error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [1 lines of output]
ERROR: Minimum supported PROJ version is 9.4.0, installed version is 9.1.0. For more information see: https://pyproj4.github.io/pyproj/stable/installation.html
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
[39m[31merror: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
[39m[31mError: Error installing package(s): "'Dask==2024.12.1'", "'zarr==2.18.7'", "'squidpy==1.6.2'"
[39m[31m
Quitting from bkg-python-interoperability.qmd:90-97 [deps-pypi]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'Dask==2024.12.1'", "'zarr==2.18.7'", "'squidpy==1.6.2'"
---
Backtrace:
▆
1. └─reticulate::conda_install(...)
2. └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[39m[31mExecution halted
[39mmake: *** [render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted