############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data basilisk ### ############################################################################## ############################################################################## * checking for file ‘basilisk/DESCRIPTION’ ... OK * preparing ‘basilisk’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘motivation.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/tmp/RtmpDf8QGq/Rbuild29890c76ce7ce5/basilisk/vignettes/basilisk-vignette-test/1.19.0 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-3.47.2-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-hcccb83c_1 openssl conda-forge/linux-aarch64::openssl-3.4.0-h86ecc28_0 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-75.6.0-pyhff2d567_1 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_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: 24.11.2 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: 24.11.2 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /home/biocbuild/tmp/RtmpDf8QGq/Rbuild29890c76ce7ce5/basilisk/vignettes/basilisk-vignette-test/1.19.0 added / updated specs: - numpy=1.22.1 - python=3.10.14 - scikit-learn=1.1.1 The following NEW packages will be INSTALLED: brotli-python conda-forge/linux-aarch64::brotli-python-1.1.0-py310he30c3ed_2 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-3.4.0-pyhd8ed1ab_1 h2 conda-forge/noarch::h2-4.1.0-pyhd8ed1ab_1 hpack conda-forge/noarch::hpack-4.0.0-pyhd8ed1ab_1 hyperframe conda-forge/noarch::hyperframe-6.0.1-pyhd8ed1ab_1 idna conda-forge/noarch::idna-3.10-pyhd8ed1ab_1 joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_1 libblas conda-forge/linux-aarch64::libblas-3.9.0-20_linuxaarch64_openblas libcblas conda-forge/linux-aarch64::libcblas-3.9.0-20_linuxaarch64_openblas 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 liblapack conda-forge/linux-aarch64::liblapack-3.9.0-20_linuxaarch64_openblas libopenblas conda-forge/linux-aarch64::libopenblas-0.3.25-pthreads_h5a5ec62_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 numpy conda-forge/linux-aarch64::numpy-1.22.1-py310ha311ffb_0 packaging conda-forge/noarch::packaging-24.2-pyhd8ed1ab_2 platformdirs conda-forge/noarch::platformdirs-4.3.6-pyhd8ed1ab_1 pooch conda-forge/noarch::pooch-1.8.2-pyhd8ed1ab_1 pycparser conda-forge/noarch::pycparser-2.22-pyh29332c3_1 pysocks conda-forge/noarch::pysocks-1.7.1-pyha55dd90_7 python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310 requests conda-forge/noarch::requests-2.32.3-pyhd8ed1ab_1 scikit-learn conda-forge/linux-aarch64::scikit-learn-1.1.1-py310h960e1e0_0 scipy conda-forge/linux-aarch64::scipy-1.11.2-py310h7f380f4_0 threadpoolctl conda-forge/noarch::threadpoolctl-3.5.0-pyhc1e730c_0 urllib3 conda-forge/noarch::urllib3-2.3.0-pyhd8ed1ab_0 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 Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/tmp/RtmpDf8QGq/Rbuild29890c76ce7ce5/basilisk/vignettes/basilisk-vignette-test2 added / updated specs: - python=3.10 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 libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 libsqlite conda-forge/linux-aarch64::libsqlite-3.47.2-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-hcccb83c_1 openssl conda-forge/linux-aarch64::openssl-3.4.0-h86ecc28_0 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_2 python conda-forge/linux-aarch64::python-3.10.16-h57b00e1_1_cpython readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 setuptools conda-forge/noarch::setuptools-75.6.0-pyhff2d567_1 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_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: 24.11.2 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: 24.11.2 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /home/biocbuild/tmp/RtmpDf8QGq/Rbuild29890c76ce7ce5/basilisk/vignettes/basilisk-vignette-test2 added / updated specs: - python=3.10 - scipy==1.9.1 The following NEW packages will be INSTALLED: libblas conda-forge/linux-aarch64::libblas-3.9.0-20_linuxaarch64_openblas libcblas conda-forge/linux-aarch64::libcblas-3.9.0-20_linuxaarch64_openblas 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 liblapack conda-forge/linux-aarch64::liblapack-3.9.0-20_linuxaarch64_openblas libopenblas conda-forge/linux-aarch64::libopenblas-0.3.25-pthreads_h5a5ec62_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 numpy conda-forge/linux-aarch64::numpy-1.26.4-py310hcbab775_0 python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310 scipy conda-forge/linux-aarch64::scipy-1.9.1-py310hdd6f644_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Quitting from lines 303-331 [unnamed-chunk-6] (motivation.Rmd) Error: processing vignette 'motivation.Rmd' failed with diagnostics: internet routines cannot be loaded --- failed re-building ‘motivation.Rmd’ SUMMARY: processing the following file failed: ‘motivation.Rmd’ Error: Vignette re-building failed. Execution halted