##############################################################################
##############################################################################
###
### Running command:
###
### /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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘velociraptor.Rmd’ using rmarkdown
python-build: use openssl@3 from homebrew
python-build: use readline from homebrew
Downloading Python-3.11.9.tar.xz...
-> https://www.python.org/ftp/python/3.11.9/Python-3.11.9.tar.xz
Installing Python-3.11.9...
python-build: use tcl-tk from homebrew
python-build: use readline from homebrew
python-build: use zlib from xcode sdk
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/biocbuild/.pyenv/versions/3.11.9/lib/python3.11/tkinter/__init__.py", line 38, in <module>
import _tkinter # If this fails your Python may not be configured for Tk
^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named '_tkinter'
WARNING: The Python tkinter extension was not compiled and GUI subsystem has been detected. Missing the Tk toolkit?
Installed Python-3.11.9 to /Users/biocbuild/.pyenv/versions/3.11.9
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/velociraptor/1.17.0/env/lib/python3.11/site-packages (24.0)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.19.2/velociraptor/1.17.0/env/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 65.5.0
Uninstalling setuptools-65.5.0:
Successfully uninstalled setuptools-65.5.0
Attempting uninstall: pip
Found existing installation: pip 24.0
Uninstalling pip-24.0:
Successfully uninstalled pip-24.0
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Collecting absl-py==2.1.0
Using cached absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting anndata==0.10.9
Using cached anndata-0.10.9-py3-none-any.whl.metadata (6.9 kB)
ERROR: Could not find a version that satisfies the requirement aom==3.9.1 (from versions: none)
ERROR: No matching distribution found for aom==3.9.1
Quitting from velociraptor.Rmd:75-82 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'absl-py==2.1.0'", "'anndata==0.10.9'", "'aom==3.9.1'", "'array-api-compat==1.8'", "'asttokens==2.4.1'", "'blosc==1.21.6'", "'brotli==1.1.0'", "'brotli-bin==1.1.0'", "'brotli-python==1.1.0'", "'bzip2==1.0.8'", "'c-ares==1.33.1'", "'ca-certificates==2024.8.30'", "'cached-property==1.5.2'", "'cached_property==1.5.2'", "'certifi==2024.8.30'", "'cffi==1.17.1'", "'charset-normalizer==3.3.2'", "'chex==0.1.86'", "'click==8.1.7'", "'colorama==0.4.6'", "'comm==0.2.2'", "'contextlib2==21.6.0'", "'contourpy==1.3.0'", "'cycler==0.12.1'", "'dav1d==1.2.1'", "'decorator==5.1.1'", "'docrep==0.3.2'", "'et_xmlfile==1.1.0'", "'etils==1.9.4'", "'exceptiongroup==1.2.2'", "'executing==2.1.0'", "'filelock==3.16.0'", "'flax==0.9.0'", "'fonttools==4.53.1'", "'freetype==2.12.1'", "'fsspec==2024.9.0'", "'get-annotations==0.1.2'", "'gmp==6.3.0'", "'gmpy2==2.1.5'", "'h2==4.1.0'", "'h5py==3.11.0'", "'hdf5==1.14.3'", "'hpack==4.0.0'", "'hyperframe==6.0.1'", "'icu==75.1'", "'idna==3.8'", "'importlib-metadata==8.4.0'", "'importlib_resources==6.4.4'", "'ipython==8.27.0'", "'ipywidgets==8.1.5'", "'jax==0.4.31'", "'jaxlib==0.4.31'", "'jedi==0.19.1'", "'jinja2==3.1.4'", "'joblib==1.4.2'", "'jupyterlab_widgets==3.0.13'", "'kiwisolver==1.4.7'", "'krb5==1.21.3'", "'lcms2==2.16'", "'legacy-api-wrap==1.4'", "'lerc==4.0.0'", "'libabseil==20240116.2'", "'libaec==1.1.3'", "'libavif16==1.1.1'", "'libblas==3.9.0'", "'libbrotlicommon==1.1.0'", "'libbrotlidec==1.1.0'", "'libbrotlienc==1.1.0'", "'libcblas==3.9.0'", "'libcurl==8.9.1'", "'libcxx==18.1.8'", "'libdeflate==1.21'", "'libedit==3.1.20191231'", "'libev==4.33'", "'libexpat==2.6.3'", "'libffi==3.4.2'", "'libgfortran==5.0.0'", "'libgfortran5==13.2.0'", "'libgrpc==1.62.2'", "'libhwloc==2.11.1'", "'libiconv==1.17'", "'libjpeg-turbo==3.0.0'", "'liblapack==3.9.0'", "'libllvm14==14.0.6'", "'libnghttp2==1.58.0'", "'libopenblas==0.3.27'", "'libpng==1.6.43'", "'libprotobuf==4.25.3'", "'libre2-11==2023.09.01'", "'libsqlite==3.46.1'", "'libssh2==1.11.0'", "'libtiff==4.6.0'", "'libtorch==2.4.0'", "'libuv==1.48.0'", "'libwebp-base==1.4.0'", "'libxcb==1.16'", "'libxml2==2.12.7'", "'libzlib==1.3.1'", "'lightning==2.4.0'", "'lightning-utilities==0.11.7'", "'llvm-openmp==18.1.8'", "'llvmlite==0.43.0'", "'loompy==3.0.6'", "'lz4-c==1.9.4'", "'markdown-it-py==3.0.0'", "'markupsafe==2.1.5'", "'matplotlib-base==3.9.2'", "'matplotlib-inline==0.1.7'", "'mdurl==0.1.2'", "'ml-collections==0.1.1'", "'ml_dtypes==0.4.0'", "'mpc==1.3.1'", "'mpfr==4.2.1'", "'mpmath==1.3.0'", "'msgpack-python==1.0.8'", "'mudata==0.3.1'", "'multipledispatch==0.6.0'", "'munkres==1.1.4'", "'natsort==8.4.0'", "'ncurses==6.5'", "'nest-asyncio==1.6.0'", "'networkx==3.3'", "'nomkl==1.0'", "'numba==0.60.0'", "'numpy==1.26.4'", "'numpy_groupies==0.11.2'", "'numpyro==0.15.2'", "'openjpeg==2.5.2'", "'openpyxl==3.1.5'", "'openssl==3.3.2'", "'opt-einsum==3.3.0'", "'opt_einsum==3.3.0'", "'optax==0.2.2'", "'orbax-checkpoint==0.4.4'", "'packaging==24.1'", "'pandas==2.2.2'", "'parso==0.8.4'", "'patsy==0.5.6'", "'pexpect==4.9.0'", "'pickleshare==0.7.5'", "'pillow==10.4.0'", "'pip==24.2'", "'prompt-toolkit==3.0.47'", "'protobuf==4.25.3'", "'pthread-stubs==0.4'", "'ptyprocess==0.7.0'", "'pure_eval==0.2.3'", "'pybind11-abi==4'", "'pycparser==2.22'", "'pygments==2.18.0'", "'pynndescent==0.5.13'", "'pyparsing==3.1.4'", "'pyro-api==0.1.2'", "'pyro-ppl==1.9.1'", "'pysocks==1.7.1'", "'python==3.11.9'", "'python-dateutil==2.9.0'", "'python-tzdata==2024.1'", "'python_abi==3.11'", "'pytorch==2.4.0'", "'pytorch-lightning==2.4.0'", "'pytz==2024.1'", "'pyyaml==6.0.2'", "'qhull==2020.2'", "'rav1e==0.6.6'", "'re2==2023.09.01'", "'readline==8.2'", "'requests==2.32.3'", "'rich==13.7.1'", "'scanpy==1.10.2'", "'scikit-learn==1.1.3'", "'scipy==1.13.1'", "'scvelo==0.3.2'", "'scvi-tools==1.1.6'", "'seaborn==0.13.2'", "'seaborn-base==0.13.2'", "'session-info==1.0.0'", "'setuptools==73.0.1'", "'six==1.16.0'", "'sleef==3.6.1'", "'snappy==1.2.1'", "'sparse==0.15.4'", "'stack_data==0.6.2'", "'statsmodels==0.14.2'", "'stdlib-list==0.10.0'", "'svt-av1==2.2.1'", "'sympy==1.13.2'", "'tbb==2021.13.0'", "'tensorstore==0.1.62'", "'threadpoolctl==3.5.0'", "'tk==8.6.13'", "'toolz==0.12.1'", "'torchmetrics==1.4.0.post0'", "'tqdm==4.66.5'", "'traitlets==5.14.3'", "'typing-extensions==4.12.2'", "'typing_extensions==4.12.2'", "'tzdata==2024a'", "'umap-learn==0.5.6'", "'urllib3==2.2.2'", "'wcwidth==0.2.13'", "'wheel==0.44.0'", "'widgetsnbextension==4.0.13'", "'xarray==2024.7.0'", "'xorg-libxau==1.0.11'", "'xorg-libxdmcp==1.1.3'", "'xz==5.2.6'", "'yaml==0.2.5'", "'zipp==3.20.1'", "'zstandard==0.23.0'", "'zstd==1.5.6'"
---
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. └─basilisk::basiliskStart(...)
12. └─basilisk::obtainEnvironmentPath(env)
13. └─basilisk::setupBasiliskEnv(...)
14. └─reticulate::virtualenv_install(...)
15. └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'velociraptor.Rmd' failed with diagnostics:
Error installing package(s): "'absl-py==2.1.0'", "'anndata==0.10.9'", "'aom==3.9.1'", "'array-api-compat==1.8'", "'asttokens==2.4.1'", "'blosc==1.21.6'", "'brotli==1.1.0'", "'brotli-bin==1.1.0'", "'brotli-python==1.1.0'", "'bzip2==1.0.8'", "'c-ares==1.33.1'", "'ca-certificates==2024.8.30'", "'cached-property==1.5.2'", "'cached_property==1.5.2'", "'certifi==2024.8.30'", "'cffi==1.17.1'", "'charset-normalizer==3.3.2'", "'chex==0.1.86'", "'click==8.1.7'", "'colorama==0.4.6'", "'comm==0.2.2'", "'contextlib2==21.6.0'", "'contourpy==1.3.0'", "'cycler==0.12.1'", "'dav1d==1.2.1'", "'decorator==5.1.1'", "'docrep==0.3.2'", "'et_xmlfile==1.1.0'", "'etils==1.9.4'", "'exceptiongroup==1.2.2'", "'executing==2.1.0'", "'filelock==3.16.0'", "'flax==0.9.0'", "'fonttools==4.53.1'", "'freetype==2.12.1'", "'fsspec==2024.9.0'", "'get-annotations==0.1.2'", "'gmp==6.3.0'", "'gmpy2==2.1.5'", "'h2==4.1.0'", "'h5py==3.11.0'", "'hdf5==1.14.3'", "'hpack==4.0.0'", "'hyperframe==6.0.1'", "'icu==75.1'", "'idna==3.8'", "'importlib-metadata==8.4.0'", "'importlib_resources==6.4.4'", "'ipython==8.27.0'", "'ipywidgets==8.1.5'", "'jax==0.4.31'", "'jaxlib==0.4.31'", "'jedi==0.19.1'", "'jinja2==3.1.4'", "'joblib==1.4.2'", "'jupyterlab_widgets==3.0.13'", "'kiwisolver==1.4.7'", "'krb5==1.21.3'", "'lcms2==2.16'", "'legacy-api-wrap==1.4'", "'lerc==4.0.0'", "'libabseil==20240116.2'", "'libaec==1.1.3'", "'libavif16==1.1.1'", "'libblas==3.9.0'", "'libbrotlicommon==1.1.0'", "'libbrotlidec==1.1.0'", "'libbrotlienc==1.1.0'", "'libcblas==3.9.0'", "'libcurl==8.9.1'", "'libcxx==18.1.8'", "'libdeflate==1.21'", "'libedit==3.1.20191231'", "'libev==4.33'", "'libexpat==2.6.3'", "'libffi==3.4.2'", "'libgfortran==5.0.0'", "'libgfortran5==13.2.0'", "'libgrpc==1.62.2'", "'libhwloc==2.11.1'", "'libiconv==1.17'", "'libjpeg-turbo==3.0.0'", "'liblapack==3.9.0'", "'libllvm14==14.0.6'", "'libnghttp2==1.58.0'", "'libopenblas==0.3.27'", "'libpng==1.6.43'", "'libprotobuf==4.25.3'", "'libre2-11==2023.09.01'", "'libsqlite==3.46.1'", "'libssh2==1.11.0'", "'libtiff==4.6.0'", "'libtorch==2.4.0'", "'libuv==1.48.0'", "'libwebp-base==1.4.0'", "'libxcb==1.16'", "'libxml2==2.12.7'", "'libzlib==1.3.1'", "'lightning==2.4.0'", "'lightning-utilities==0.11.7'", "'llvm-openmp==18.1.8'", "'llvmlite==0.43.0'", "'loompy==3.0.6'", "'lz4-c==1.9.4'", "'markdown-it-py==3.0.0'", "'markupsafe==2.1.5'", "'matplotlib-base==3.9.2'", "'matplotlib-inline==0.1.7'", "'mdurl==0.1.2'", "'ml-collections==0.1.1'", "'ml_dtypes==0.4.0'", "'mpc==1.3.1'", "'mpfr==4.2.1'", "'mpmath==1.3.0'", "'msgpack-python==1.0.8'", "'mudata==0.3.1'", "'multipledispatch==0.6.0'", "'munkres==1.1.4'", "'natsort==8.4.0'", "'ncurses==6.5'", "'nest-asyncio==1.6.0'", "'networkx==3.3'", "'nomkl==1.0'", "'numba==0.60.0'", "'numpy==1.26.4'", "'numpy_groupies==0.11.2'", "'numpyro==0.15.2'", "'openjpeg==2.5.2'", "'openpyxl==3.1.5'", "'openssl==3.3.2'", "'opt-einsum==3.3.0'", "'opt_einsum==3.3.0'", "'optax==0.2.2'", "'orbax-checkpoint==0.4.4'", "'packaging==24.1'", "'pandas==2.2.2'", "'parso==0.8.4'", "'patsy==0.5.6'", "'pexpect==4.9.0'", "'pickleshare==0.7.5'", "'pillow==10.4.0'", "'pip==24.2'", "'prompt-toolkit==3.0.47'", "'protobuf==4.25.3'", "'pthread-stubs==0.4'", "'ptyprocess==0.7.0'", "'pure_eval==0.2.3'", "'pybind11-abi==4'", "'pycparser==2.22'", "'pygments==2.18.0'", "'pynndescent==0.5.13'", "'pyparsing==3.1.4'", "'pyro-api==0.1.2'", "'pyro-ppl==1.9.1'", "'pysocks==1.7.1'", "'python==3.11.9'", "'python-dateutil==2.9.0'", "'python-tzdata==2024.1'", "'python_abi==3.11'", "'pytorch==2.4.0'", "'pytorch-lightning==2.4.0'", "'pytz==2024.1'", "'pyyaml==6.0.2'", "'qhull==2020.2'", "'rav1e==0.6.6'", "'re2==2023.09.01'", "'readline==8.2'", "'requests==2.32.3'", "'rich==13.7.1'", "'scanpy==1.10.2'", "'scikit-learn==1.1.3'", "'scipy==1.13.1'", "'scvelo==0.3.2'", "'scvi-tools==1.1.6'", "'seaborn==0.13.2'", "'seaborn-base==0.13.2'", "'session-info==1.0.0'", "'setuptools==73.0.1'", "'six==1.16.0'", "'sleef==3.6.1'", "'snappy==1.2.1'", "'sparse==0.15.4'", "'stack_data==0.6.2'", "'statsmodels==0.14.2'", "'stdlib-list==0.10.0'", "'svt-av1==2.2.1'", "'sympy==1.13.2'", "'tbb==2021.13.0'", "'tensorstore==0.1.62'", "'threadpoolctl==3.5.0'", "'tk==8.6.13'", "'toolz==0.12.1'", "'torchmetrics==1.4.0.post0'", "'tqdm==4.66.5'", "'traitlets==5.14.3'", "'typing-extensions==4.12.2'", "'typing_extensions==4.12.2'", "'tzdata==2024a'", "'umap-learn==0.5.6'", "'urllib3==2.2.2'", "'wcwidth==0.2.13'", "'wheel==0.44.0'", "'widgetsnbextension==4.0.13'", "'xarray==2024.7.0'", "'xorg-libxau==1.0.11'", "'xorg-libxdmcp==1.1.3'", "'xz==5.2.6'", "'yaml==0.2.5'", "'zipp==3.20.1'", "'zstandard==0.23.0'", "'zstd==1.5.6'"
--- failed re-building ‘velociraptor.Rmd’
SUMMARY: processing the following file failed:
‘velociraptor.Rmd’
Error: Vignette re-building failed.
Execution halted