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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data velociraptor
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* checking for file ‘velociraptor/DESCRIPTION’ ... OK
* preparing ‘velociraptor’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘velociraptor.Rmd’ using rmarkdown
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/velociraptor/1.21.1/env/lib/python3.12/site-packages (25.0.1)
Collecting pip
Using cached pip-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Collecting setuptools
Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
Using cached packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.0-py3-none-any.whl (74 kB)
Installing collected packages: setuptools, pip, packaging, wheel
Attempting uninstall: pip
Found existing installation: pip 25.0.1
Uninstalling pip-25.0.1:
Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.0 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
Collecting anndata==0.11.4
Using cached anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting array-api-compat==1.12.0
Using cached array_api_compat-1.12.0-py3-none-any.whl.metadata (2.5 kB)
Collecting click==8.2.1
Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 kB)
Collecting contourpy==1.3.2
Using cached contourpy-1.3.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (5.5 kB)
Collecting cycler==0.12.1
Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools==4.58.5
Using cached fonttools-4.58.5-cp312-cp312-macosx_10_13_universal2.whl.metadata (106 kB)
Collecting h5py==3.14.0
Using cached h5py-3.14.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.7 kB)
Collecting joblib==1.5.1
Using cached joblib-1.5.1-py3-none-any.whl.metadata (5.6 kB)
Collecting kiwisolver==1.4.8
Using cached kiwisolver-1.4.8-cp312-cp312-macosx_11_0_arm64.whl.metadata (6.2 kB)
Collecting legacy-api-wrap==1.4.1
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Collecting llvmlite==0.44.0
Using cached llvmlite-0.44.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (4.8 kB)
Collecting loompy==3.0.8
Using cached loompy-3.0.8-py3-none-any.whl
Collecting matplotlib==3.10.3
Using cached matplotlib-3.10.3-cp312-cp312-macosx_11_0_arm64.whl.metadata (11 kB)
Collecting natsort==8.4.0
Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting networkx==3.5
Using cached networkx-3.5-py3-none-any.whl.metadata (6.3 kB)
Collecting numba==0.61.2
Using cached numba-0.61.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.8 kB)
Collecting numpy==2.2.6
Downloading numpy-2.2.6-cp312-cp312-macosx_14_0_arm64.whl.metadata (62 kB)
Collecting numpy-groupies==0.11.3
Using cached numpy_groupies-0.11.3-py3-none-any.whl.metadata (18 kB)
Collecting packaging==25.0
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting pandas==2.3.1
Using cached pandas-2.3.1-cp312-cp312-macosx_11_0_arm64.whl.metadata (91 kB)
Collecting patsy==1.0.1
Using cached patsy-1.0.1-py2.py3-none-any.whl.metadata (3.3 kB)
Collecting pillow==11.3.0
Using cached pillow-11.3.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (9.0 kB)
Collecting pip==25.1.1
Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting pynndescent==0.5.13
Using cached pynndescent-0.5.13-py3-none-any.whl.metadata (6.8 kB)
Collecting pyparsing==3.2.3
Using cached pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB)
Collecting python-dateutil==2.9.0.post0
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz==2025.2
Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting scanpy==1.11.3
Using cached scanpy-1.11.3-py3-none-any.whl.metadata (9.0 kB)
Collecting scikit-learn==1.7.0
Using cached scikit_learn-1.7.0-cp312-cp312-macosx_12_0_arm64.whl.metadata (31 kB)
Collecting scipy==1.15.3
Downloading scipy-1.15.3-cp312-cp312-macosx_14_0_arm64.whl.metadata (61 kB)
Collecting scvelo==0.3.3
Using cached scvelo-0.3.3-py3-none-any.whl.metadata (8.0 kB)
Collecting seaborn==0.13.2
Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting session-info2==0.1.2
Using cached session_info2-0.1.2-py3-none-any.whl.metadata (2.5 kB)
Collecting setuptools==80.9.0
Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Collecting six==1.17.0
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Collecting statsmodels==0.14.5
Using cached statsmodels-0.14.5-cp312-cp312-macosx_11_0_arm64.whl.metadata (9.5 kB)
Collecting threadpoolctl==3.6.0
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting tqdm==4.67.1
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting typing_extensions==4.14.1
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Collecting tzdata==2025.2
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Collecting umap-learn==0.5.9.post2
Using cached umap_learn-0.5.9.post2-py3-none-any.whl.metadata (25 kB)
Collecting wheel==0.45.1
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Using cached anndata-0.11.4-py3-none-any.whl (144 kB)
Using cached array_api_compat-1.12.0-py3-none-any.whl (58 kB)
Using cached click-8.2.1-py3-none-any.whl (102 kB)
Using cached contourpy-1.3.2-cp312-cp312-macosx_11_0_arm64.whl (255 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.58.5-cp312-cp312-macosx_10_13_universal2.whl (2.8 MB)
Using cached h5py-3.14.0-cp312-cp312-macosx_11_0_arm64.whl (2.8 MB)
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Using cached llvmlite-0.44.0-cp312-cp312-macosx_11_0_arm64.whl (26.2 MB)
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Using cached networkx-3.5-py3-none-any.whl (2.0 MB)
Using cached numba-0.61.2-cp312-cp312-macosx_11_0_arm64.whl (2.8 MB)
Downloading numpy-2.2.6-cp312-cp312-macosx_14_0_arm64.whl (5.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.1/5.1 MB 8.1 MB/s 0:00:00
Using cached numpy_groupies-0.11.3-py3-none-any.whl (40 kB)
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Using cached pillow-11.3.0-cp312-cp312-macosx_11_0_arm64.whl (4.7 MB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached pynndescent-0.5.13-py3-none-any.whl (56 kB)
Using cached pyparsing-3.2.3-py3-none-any.whl (111 kB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Using cached scanpy-1.11.3-py3-none-any.whl (2.1 MB)
Downloading scipy-1.15.3-cp312-cp312-macosx_14_0_arm64.whl (22.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 22.4/22.4 MB 8.5 MB/s 0:00:02
Using cached scikit_learn-1.7.0-cp312-cp312-macosx_12_0_arm64.whl (10.7 MB)
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Using cached statsmodels-0.14.5-cp312-cp312-macosx_11_0_arm64.whl (9.7 MB)
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Using cached umap_learn-0.5.9.post2-py3-none-any.whl (90 kB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Installing collected packages: pytz, wheel, tzdata, typing_extensions, tqdm, threadpoolctl, six, setuptools, session-info2, pyparsing, pip, pillow, packaging, numpy, networkx, natsort, llvmlite, legacy-api-wrap, kiwisolver, joblib, fonttools, cycler, click, array-api-compat, scipy, python-dateutil, patsy, numpy-groupies, numba, h5py, contourpy, scikit-learn, pandas, matplotlib, loompy, statsmodels, seaborn, pynndescent, anndata, umap-learn, scanpy, scvelo
Attempting uninstall: wheel
Found existing installation: wheel 0.46.3
Uninstalling wheel-0.46.3:
Successfully uninstalled wheel-0.46.3
Attempting uninstall: setuptools
Found existing installation: setuptools 82.0.1
Uninstalling setuptools-82.0.1:
Successfully uninstalled setuptools-82.0.1
Attempting uninstall: pip
Found existing installation: pip 26.0.1
Uninstalling pip-26.0.1:
Successfully uninstalled pip-26.0.1
Attempting uninstall: packaging
Found existing installation: packaging 26.0
Uninstalling packaging-26.0:
Successfully uninstalled packaging-26.0
Successfully installed anndata-0.11.4 array-api-compat-1.12.0 click-8.2.1 contourpy-1.3.2 cycler-0.12.1 fonttools-4.58.5 h5py-3.14.0 joblib-1.5.1 kiwisolver-1.4.8 legacy-api-wrap-1.4.1 llvmlite-0.44.0 loompy-3.0.8 matplotlib-3.10.3 natsort-8.4.0 networkx-3.5 numba-0.61.2 numpy-2.2.6 numpy-groupies-0.11.3 packaging-25.0 pandas-2.3.1 patsy-1.0.1 pillow-11.3.0 pip-25.1.1 pynndescent-0.5.13 pyparsing-3.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 scanpy-1.11.3 scikit-learn-1.7.0 scipy-1.15.3 scvelo-0.3.3 seaborn-0.13.2 session-info2-0.1.2 setuptools-80.9.0 six-1.17.0 statsmodels-0.14.5 threadpoolctl-3.6.0 tqdm-4.67.1 typing_extensions-4.14.1 tzdata-2025.2 umap-learn-0.5.9.post2 wheel-0.45.1
[notice] A new release of pip is available: 25.1.1 -> 26.0.1
[notice] To update, run: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.23.0/velociraptor/1.21.1/env/bin/python -m pip install --upgrade pip
Quitting from velociraptor.Rmd:75-82 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `py_module_import()`:
! OSError: Could not find/load shared object file
Run `reticulate::py_last_error()` for details.
---
Backtrace:
▆
1. ├─velociraptor::scvelo(...)
2. └─velociraptor::scvelo(...)
3. └─velociraptor (local) .local(x, ...)
4. ├─methods::callNextMethod(x, ..., sf.X = sf.X, dimred = dimred)
5. │ └─base::eval(call, callEnv)
6. │ └─base::eval(call, callEnv)
7. └─velociraptor (local) .nextMethod(x, ..., sf.X = sf.X, dimred = dimred)
8. └─velociraptor (local) .local(x, ...)
9. └─velociraptor:::.scvelo(...)
10. └─basilisk::basiliskRun(...)
11. └─velociraptor (local) fun(...)
12. └─reticulate::import("scvelo")
13. └─reticulate:::py_module_import(module, convert = convert)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'velociraptor.Rmd' failed with diagnostics:
OSError: Could not find/load shared object file
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘velociraptor.Rmd’
SUMMARY: processing the following file failed:
‘velociraptor.Rmd’
Error: Vignette re-building failed.
Execution halted
