############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data velociraptor ### ############################################################################## ############################################################################## * 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 Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/velociraptor/1.16.0/env added / updated specs: - python=3.10.14 The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h68df207_7 ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.12.14-hcefe29a_0 ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_2 libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_1 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_1 libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_1 liblzma conda-forge/linux-aarch64::liblzma-5.6.3-h86ecc28_1 liblzma-devel conda-forge/linux-aarch64::liblzma-devel-5.6.3-h86ecc28_1 libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 libsqlite conda-forge/linux-aarch64::libsqlite-3.48.0-h5eb1b54_0 libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0 libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1 libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_2 openssl conda-forge/linux-aarch64::openssl-3.4.0-hd08dc88_1 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_2 python conda-forge/linux-aarch64::python-3.10.14-hbbe8eec_0_cpython readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 setuptools conda-forge/noarch::setuptools-75.8.0-pyhff2d567_0 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 tzdata conda-forge/noarch::tzdata-2025a-h78e105d_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 xz conda-forge/linux-aarch64::xz-5.6.3-h2dbfc1b_1 xz-gpl-tools conda-forge/linux-aarch64::xz-gpl-tools-5.6.3-h2dbfc1b_1 xz-tools conda-forge/linux-aarch64::xz-tools-5.6.3-h86ecc28_1 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.11.3 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.11.3 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /home/biocbuild/.cache/R/basilisk/1.18.0/velociraptor/1.16.0/env added / updated specs: - ipywidgets=8.1.2 - libtiff=4.5.1 - pillow=10.0.0 - python=3.10.14 - scipy=1.13.1 - scvelo=0.3.2 - tqdm=4.66.5 The following packages will be downloaded: package | build ---------------------------|----------------- comm-0.2.2 | pyhd8ed1ab_1 12 KB conda-forge decorator-5.1.1 | pyhd8ed1ab_1 14 KB conda-forge docrep-0.3.2 | pyh44b312d_0 19 KB conda-forge et_xmlfile-2.0.0 | pyhd8ed1ab_1 21 KB conda-forge filelock-3.16.1 | pyhd8ed1ab_1 17 KB conda-forge importlib-metadata-8.6.1 | pyha770c72_0 28 KB conda-forge importlib_metadata-8.6.1 | hd8ed1ab_0 9 KB conda-forge libuv-1.50.0 | h86ecc28_0 606 KB conda-forge markupsafe-3.0.2 | py310h66848f9_1 23 KB conda-forge matplotlib-inline-0.1.7 | pyhd8ed1ab_1 14 KB conda-forge mdurl-0.1.2 | pyhd8ed1ab_1 14 KB conda-forge mpfr-4.2.1 | h2305555_3 1.8 MB conda-forge multipledispatch-0.6.0 | pyhd8ed1ab_1 17 KB conda-forge nomkl-1.0 | h5ca1d4c_0 4 KB conda-forge pickleshare-0.7.5 | pyhd8ed1ab_1004 11 KB conda-forge pillow-10.0.0 | py310hd04a61c_0 44.0 MB conda-forge ptyprocess-0.7.0 | pyhd8ed1ab_1 19 KB conda-forge pure_eval-0.2.3 | pyhd8ed1ab_1 16 KB conda-forge pyro-api-0.1.2 | pyhd8ed1ab_0 15 KB conda-forge pytorch-2.0.0 |cpu_generic_py310hb4d244f_1 46.8 MB conda-forge sparse-0.15.5 | pyh72ffeb9_0 96 KB conda-forge stack_data-0.6.3 | pyhd8ed1ab_1 26 KB conda-forge stdlib-list-0.11.0 | pyhd8ed1ab_1 26 KB conda-forge typing-extensions-4.12.2 | hd8ed1ab_1 10 KB conda-forge xorg-libxau-1.0.12 | h86ecc28_0 16 KB conda-forge zipp-3.21.0 | pyhd8ed1ab_1 21 KB conda-forge ------------------------------------------------------------ Total: 93.6 MB The following NEW packages will be INSTALLED: absl-py conda-forge/noarch::absl-py-2.1.0-pyhd8ed1ab_1 anndata conda-forge/noarch::anndata-0.11.3-pyhd8ed1ab_0 array-api-compat conda-forge/noarch::array-api-compat-1.10.0-pyhd8ed1ab_0 asttokens conda-forge/noarch::asttokens-3.0.0-pyhd8ed1ab_1 brotli conda-forge/linux-aarch64::brotli-1.1.0-h86ecc28_2 brotli-bin conda-forge/linux-aarch64::brotli-bin-1.1.0-h86ecc28_2 brotli-python conda-forge/linux-aarch64::brotli-python-1.1.0-py310he30c3ed_2 c-ares conda-forge/linux-aarch64::c-ares-1.34.4-h86ecc28_0 cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 certifi conda-forge/noarch::certifi-2024.12.14-pyhd8ed1ab_0 cffi conda-forge/linux-aarch64::cffi-1.17.1-py310h1451162_0 charset-normalizer conda-forge/noarch::charset-normalizer-3.4.1-pyhd8ed1ab_0 chex conda-forge/noarch::chex-0.1.83-pyhd8ed1ab_0 click conda-forge/noarch::click-8.1.8-pyh707e725_0 colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_1 comm conda-forge/noarch::comm-0.2.2-pyhd8ed1ab_1 contourpy conda-forge/linux-aarch64::contourpy-1.3.1-py310hf54e67a_0 cycler conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_1 decorator conda-forge/noarch::decorator-5.1.1-pyhd8ed1ab_1 dm-tree conda-forge/linux-aarch64::dm-tree-0.1.8-py310h188d666_0 docrep conda-forge/noarch::docrep-0.3.2-pyh44b312d_0 et_xmlfile conda-forge/noarch::et_xmlfile-2.0.0-pyhd8ed1ab_1 exceptiongroup conda-forge/noarch::exceptiongroup-1.2.2-pyhd8ed1ab_1 executing conda-forge/noarch::executing-2.1.0-pyhd8ed1ab_1 filelock conda-forge/noarch::filelock-3.16.1-pyhd8ed1ab_1 flax conda-forge/noarch::flax-0.6.1-pyhd8ed1ab_1 fonttools conda-forge/linux-aarch64::fonttools-4.55.3-py310heeae437_1 freetype conda-forge/linux-aarch64::freetype-2.12.1-hf0a5ef3_2 fsspec conda-forge/noarch::fsspec-2024.12.0-pyhd8ed1ab_0 gmp conda-forge/linux-aarch64::gmp-6.3.0-h0a1ffab_2 gmpy2 conda-forge/linux-aarch64::gmpy2-2.1.5-py310h615e639_3 grpcio conda-forge/linux-aarch64::grpcio-1.56.2-py310h20b6881_1 h2 conda-forge/noarch::h2-4.1.0-pyhd8ed1ab_1 h5py conda-forge/linux-aarch64::h5py-3.12.1-nompi_py310hfd945c4_103 hdf5 conda-forge/linux-aarch64::hdf5-1.14.4-nompi_h6ed7ac7_105 hpack conda-forge/noarch::hpack-4.0.0-pyhd8ed1ab_1 hyperframe conda-forge/noarch::hyperframe-6.0.1-pyhd8ed1ab_1 icu conda-forge/linux-aarch64::icu-75.1-hf9b3779_0 idna conda-forge/noarch::idna-3.10-pyhd8ed1ab_1 importlib-metadata conda-forge/noarch::importlib-metadata-8.6.1-pyha770c72_0 importlib_metadata conda-forge/noarch::importlib_metadata-8.6.1-hd8ed1ab_0 ipython conda-forge/noarch::ipython-8.31.0-pyh707e725_0 ipywidgets conda-forge/noarch::ipywidgets-8.1.2-pyhd8ed1ab_1 jax conda-forge/noarch::jax-0.4.13-pyhd8ed1ab_0 jaxlib conda-forge/linux-aarch64::jaxlib-0.4.12-cpu_py310h539dc2b_1 jedi conda-forge/noarch::jedi-0.19.2-pyhd8ed1ab_1 jinja2 conda-forge/noarch::jinja2-3.1.5-pyhd8ed1ab_0 joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_1 jupyterlab_widgets conda-forge/noarch::jupyterlab_widgets-3.0.13-pyhd8ed1ab_1 keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_0 kiwisolver conda-forge/linux-aarch64::kiwisolver-1.4.7-py310h5d7f10c_0 krb5 conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0 lcms2 conda-forge/linux-aarch64::lcms2-2.15-h3e0bdec_1 legacy-api-wrap conda-forge/noarch::legacy-api-wrap-1.4.1-pyhd8ed1ab_0 lerc conda-forge/linux-aarch64::lerc-4.0.0-h4de3ea5_0 libabseil conda-forge/linux-aarch64::libabseil-20230125.3-cxx17_h2f0025b_0 libaec conda-forge/linux-aarch64::libaec-1.1.3-h2f0025b_0 libblas conda-forge/linux-aarch64::libblas-3.9.0-26_linuxaarch64_openblas libbrotlicommon conda-forge/linux-aarch64::libbrotlicommon-1.1.0-h86ecc28_2 libbrotlidec conda-forge/linux-aarch64::libbrotlidec-1.1.0-h86ecc28_2 libbrotlienc conda-forge/linux-aarch64::libbrotlienc-1.1.0-h86ecc28_2 libcblas conda-forge/linux-aarch64::libcblas-3.9.0-26_linuxaarch64_openblas libcurl conda-forge/linux-aarch64::libcurl-8.11.1-h6702fde_0 libdeflate conda-forge/linux-aarch64::libdeflate-1.18-hb4cce97_0 libedit conda-forge/linux-aarch64::libedit-3.1.20240808-pl5321h976ea20_0 libev conda-forge/linux-aarch64::libev-4.33-h31becfc_2 libgfortran conda-forge/linux-aarch64::libgfortran-14.2.0-he9431aa_1 libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-14.2.0-he9431aa_1 libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.2.0-hb6113d0_1 libgrpc conda-forge/linux-aarch64::libgrpc-1.56.2-h097270e_1 libhwloc conda-forge/linux-aarch64::libhwloc-2.11.2-default_h2c612a5_1001 libiconv conda-forge/linux-aarch64::libiconv-1.17-h31becfc_2 libjpeg-turbo conda-forge/linux-aarch64::libjpeg-turbo-2.1.5.1-h31becfc_1 liblapack conda-forge/linux-aarch64::liblapack-3.9.0-26_linuxaarch64_openblas libllvm14 conda-forge/linux-aarch64::libllvm14-14.0.6-h966f666_4 libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.64.0-hc8609a4_0 libopenblas conda-forge/linux-aarch64::libopenblas-0.3.28-pthreads_h9d3fd7e_1 libpng conda-forge/linux-aarch64::libpng-1.6.45-hec79eb8_0 libprotobuf conda-forge/linux-aarch64::libprotobuf-4.23.3-h6b51aa4_1 libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-ha41c0db_0 libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_1 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_1 libtiff conda-forge/linux-aarch64::libtiff-4.5.1-h360e80f_1 libuv conda-forge/linux-aarch64::libuv-1.50.0-h86ecc28_0 libwebp-base conda-forge/linux-aarch64::libwebp-base-1.5.0-h0886dbf_0 libxcb conda-forge/linux-aarch64::libxcb-1.15-h2a766a3_0 libxml2 conda-forge/linux-aarch64::libxml2-2.13.5-h2e0c361_1 lightning conda-forge/noarch::lightning-2.3.3-pyhd8ed1ab_0 lightning-utiliti~ conda-forge/noarch::lightning-utilities-0.11.9-pyhd8ed1ab_1 llvmlite conda-forge/linux-aarch64::llvmlite-0.43.0-py310h59bf934_1 loompy conda-forge/noarch::loompy-3.0.6-py_0 markdown conda-forge/noarch::markdown-3.6-pyhd8ed1ab_0 markdown-it-py conda-forge/noarch::markdown-it-py-3.0.0-pyhd8ed1ab_1 markupsafe conda-forge/linux-aarch64::markupsafe-3.0.2-py310h66848f9_1 matplotlib-base conda-forge/linux-aarch64::matplotlib-base-3.10.0-py310h2cc5e2d_0 matplotlib-inline conda-forge/noarch::matplotlib-inline-0.1.7-pyhd8ed1ab_1 mdurl conda-forge/noarch::mdurl-0.1.2-pyhd8ed1ab_1 ml-collections conda-forge/noarch::ml-collections-1.0.0-pyh29332c3_0 ml_dtypes conda-forge/linux-aarch64::ml_dtypes-0.5.1-py310hce852f7_0 mpc conda-forge/linux-aarch64::mpc-1.3.1-h783934e_1 mpfr conda-forge/linux-aarch64::mpfr-4.2.1-h2305555_3 mpmath conda-forge/noarch::mpmath-1.3.0-pyhd8ed1ab_1 msgpack-python conda-forge/linux-aarch64::msgpack-python-1.1.0-py310hf54e67a_0 mudata conda-forge/noarch::mudata-0.3.1-pyhd8ed1ab_1 multipledispatch conda-forge/noarch::multipledispatch-0.6.0-pyhd8ed1ab_1 munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0 natsort conda-forge/noarch::natsort-8.4.0-pyh29332c3_1 networkx conda-forge/noarch::networkx-3.4.2-pyh267e887_2 nomkl conda-forge/noarch::nomkl-1.0-h5ca1d4c_0 numba conda-forge/linux-aarch64::numba-0.60.0-py310hbfe28cf_0 numpy conda-forge/linux-aarch64::numpy-1.26.4-py310hcbab775_0 numpy_groupies conda-forge/noarch::numpy_groupies-0.11.2-pyhd8ed1ab_1 numpyro conda-forge/noarch::numpyro-0.13.2-pyhd8ed1ab_0 openjpeg conda-forge/linux-aarch64::openjpeg-2.5.0-h9508984_2 openpyxl conda-forge/linux-aarch64::openpyxl-3.1.5-py310hbb13f8e_1 opt_einsum conda-forge/noarch::opt_einsum-3.4.0-pyhd8ed1ab_1 optax conda-forge/noarch::optax-0.2.2-pyhd8ed1ab_0 packaging conda-forge/noarch::packaging-24.2-pyhd8ed1ab_2 pandas conda-forge/linux-aarch64::pandas-2.2.3-py310hce852f7_2 parso conda-forge/noarch::parso-0.8.4-pyhd8ed1ab_1 patsy conda-forge/noarch::patsy-1.0.1-pyhd8ed1ab_1 pexpect conda-forge/noarch::pexpect-4.9.0-pyhd8ed1ab_1 pickleshare conda-forge/noarch::pickleshare-0.7.5-pyhd8ed1ab_1004 pillow conda-forge/linux-aarch64::pillow-10.0.0-py310hd04a61c_0 prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.48-pyha770c72_1 protobuf conda-forge/linux-aarch64::protobuf-4.23.3-py310h188d666_0 pthread-stubs conda-forge/linux-aarch64::pthread-stubs-0.4-h86ecc28_1002 ptyprocess conda-forge/noarch::ptyprocess-0.7.0-pyhd8ed1ab_1 pure_eval conda-forge/noarch::pure_eval-0.2.3-pyhd8ed1ab_1 pycparser conda-forge/noarch::pycparser-2.22-pyh29332c3_1 pygments conda-forge/noarch::pygments-2.19.1-pyhd8ed1ab_0 pynndescent conda-forge/noarch::pynndescent-0.5.13-pyhd8ed1ab_1 pyparsing conda-forge/noarch::pyparsing-3.2.1-pyhd8ed1ab_0 pyro-api conda-forge/noarch::pyro-api-0.1.2-pyhd8ed1ab_0 pyro-ppl conda-forge/noarch::pyro-ppl-1.9.1-pyhd8ed1ab_1 pysocks conda-forge/noarch::pysocks-1.7.1-pyha55dd90_7 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 python-tzdata conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_1 python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310 pytorch conda-forge/linux-aarch64::pytorch-2.0.0-cpu_generic_py310hb4d244f_1 pytorch-lightning conda-forge/noarch::pytorch-lightning-2.3.3-pyhd8ed1ab_0 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 pyyaml conda-forge/linux-aarch64::pyyaml-6.0.2-py310ha766c32_1 qhull conda-forge/linux-aarch64::qhull-2020.2-h70be974_5 re2 conda-forge/linux-aarch64::re2-2023.03.02-hdc0ed08_0 requests conda-forge/noarch::requests-2.32.3-pyhd8ed1ab_1 rich conda-forge/noarch::rich-13.9.4-pyhd8ed1ab_1 scanpy conda-forge/noarch::scanpy-1.10.4-pyhd8ed1ab_0 scikit-learn conda-forge/linux-aarch64::scikit-learn-1.1.3-py310ha66c8a9_1 scipy conda-forge/linux-aarch64::scipy-1.13.1-py310h70fbbe5_0 scvelo conda-forge/noarch::scvelo-0.3.2-pyhd8ed1ab_1 scvi-tools conda-forge/noarch::scvi-tools-1.2.2.post2-pyhd8ed1ab_2 seaborn conda-forge/noarch::seaborn-0.13.2-hd8ed1ab_3 seaborn-base conda-forge/noarch::seaborn-base-0.13.2-pyhd8ed1ab_3 session-info conda-forge/noarch::session-info-1.0.0-pyhd8ed1ab_0 six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 sleef conda-forge/linux-aarch64::sleef-3.7-h8fb0607_2 sparse conda-forge/noarch::sparse-0.15.5-pyh72ffeb9_0 stack_data conda-forge/noarch::stack_data-0.6.3-pyhd8ed1ab_1 statsmodels conda-forge/linux-aarch64::statsmodels-0.14.4-py310h3a805a6_0 stdlib-list conda-forge/noarch::stdlib-list-0.11.0-pyhd8ed1ab_1 sympy conda-forge/noarch::sympy-1.13.3-pypyh2585a3b_103 tbb conda-forge/linux-aarch64::tbb-2022.0.0-h243be18_0 tensorboard conda-forge/noarch::tensorboard-2.18.0-pyhd8ed1ab_1 tensorboard-data-~ conda-forge/linux-aarch64::tensorboard-data-server-0.7.0-py310he4218bc_2 threadpoolctl conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0 toolz conda-forge/noarch::toolz-1.0.0-pyhd8ed1ab_1 torchmetrics conda-forge/noarch::torchmetrics-1.6.1-pyhd8ed1ab_0 tqdm conda-forge/noarch::tqdm-4.66.5-pyhd8ed1ab_0 traitlets conda-forge/noarch::traitlets-5.14.3-pyhd8ed1ab_1 typing-extensions conda-forge/noarch::typing-extensions-4.12.2-hd8ed1ab_1 typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_1 umap-learn conda-forge/linux-aarch64::umap-learn-0.5.7-py310h4c7bcd0_0 unicodedata2 conda-forge/linux-aarch64::unicodedata2-16.0.0-py310ha766c32_0 urllib3 conda-forge/noarch::urllib3-2.3.0-pyhd8ed1ab_0 wcwidth conda-forge/noarch::wcwidth-0.2.13-pyhd8ed1ab_1 werkzeug conda-forge/noarch::werkzeug-3.1.3-pyhd8ed1ab_1 widgetsnbextension conda-forge/noarch::widgetsnbextension-4.0.13-pyhd8ed1ab_1 xarray conda-forge/noarch::xarray-2025.1.1-pyhd8ed1ab_0 xorg-libxau conda-forge/linux-aarch64::xorg-libxau-1.0.12-h86ecc28_0 xorg-libxdmcp conda-forge/linux-aarch64::xorg-libxdmcp-1.1.5-h57736b2_0 yaml conda-forge/linux-aarch64::yaml-0.2.5-hf897c2e_2 zipp conda-forge/noarch::zipp-3.21.0-pyhd8ed1ab_1 zstandard conda-forge/linux-aarch64::zstandard-0.23.0-py310h6a57b22_1 zstd conda-forge/linux-aarch64::zstd-1.5.6-h02f22dd_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Quitting from lines 76-82 [unnamed-chunk-5] (velociraptor.Rmd) Error: processing vignette 'velociraptor.Rmd' failed with diagnostics: AttributeError: module 'scipy.linalg' has no attribute 'tril' 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