############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/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 Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/tmp/RtmppLLYpW/Rbuild28fc141f6222cd/basilisk/vignettes/basilisk-vignette-test/1.14.0 added / updated specs: - python=3.9.12 The following packages will be downloaded: package | build ---------------------------|----------------- sqlite-3.44.0 | h3b3482f_0 1004 KB conda-forge ------------------------------------------------------------ Total: 1004 KB 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-hf897c2e_4 ca-certificates conda-forge/linux-aarch64::ca-certificates-2023.7.22-hcefe29a_0 ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0 libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-hf8544c7_2 libgomp conda-forge/linux-aarch64::libgomp-13.2.0-hf8544c7_2 libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 libsqlite conda-forge/linux-aarch64::libsqlite-3.44.0-h194ca79_0 libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0 libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5 ncurses conda-forge/linux-aarch64::ncurses-6.4-h0425590_2 openssl conda-forge/linux-aarch64::openssl-3.1.4-h31becfc_0 pip conda-forge/noarch::pip-23.3.1-pyhd8ed1ab_0 python conda-forge/linux-aarch64::python-3.9.12-h5016f1d_1_cpython readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0 sqlite conda-forge/linux-aarch64::sqlite-3.44.0-h3b3482f_0 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0 wheel conda-forge/noarch::wheel-0.41.3-pyhd8ed1ab_0 xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 23.9.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/tmp/RtmppLLYpW/Rbuild28fc141f6222cd/basilisk/vignettes/basilisk-vignette-test/1.14.0 added / updated specs: - python=3.9.12 The following packages will be UPDATED: ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hd43f75c_0 The following packages will be SUPERSEDED by a higher-priority channel: openssl conda-forge::openssl-3.1.4-h31becfc_0 --> pkgs/main::openssl-3.0.11-h2f4d8fa_2 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 23.9.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/biocbuild/tmp/RtmppLLYpW/Rbuild28fc141f6222cd/basilisk/vignettes/basilisk-vignette-test/1.14.0 added / updated specs: - numpy=1.22.1 - python=3.9.12 - scikit-learn=1.1.1 The following packages will be downloaded: package | build ---------------------------|----------------- charset-normalizer-3.3.2 | pyhd8ed1ab_0 46 KB conda-forge ------------------------------------------------------------ Total: 46 KB The following NEW packages will be INSTALLED: brotli-python conda-forge/linux-aarch64::brotli-python-1.1.0-py39h387a81e_1 certifi conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0 charset-normalizer conda-forge/noarch::charset-normalizer-3.3.2-pyhd8ed1ab_0 idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0 joblib conda-forge/noarch::joblib-1.3.2-pyhd8ed1ab_0 libblas conda-forge/linux-aarch64::libblas-3.9.0-19_linuxaarch64_openblas libcblas conda-forge/linux-aarch64::libcblas-3.9.0-19_linuxaarch64_openblas libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.2.0-he9431aa_2 libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.2.0-h582850c_2 liblapack conda-forge/linux-aarch64::liblapack-3.9.0-19_linuxaarch64_openblas libopenblas conda-forge/linux-aarch64::libopenblas-0.3.24-pthreads_h5a5ec62_0 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h9a76618_2 numpy conda-forge/linux-aarch64::numpy-1.22.1-py39h8a86e7d_0 packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0 platformdirs conda-forge/noarch::platformdirs-3.11.0-pyhd8ed1ab_0 pooch conda-forge/noarch::pooch-1.8.0-pyhd8ed1ab_0 pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6 python_abi conda-forge/linux-aarch64::python_abi-3.9-4_cp39 requests conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0 scikit-learn conda-forge/linux-aarch64::scikit-learn-1.1.1-py39hd7c7e1b_0 scipy conda-forge/linux-aarch64::scipy-1.11.2-py39hf88902c_0 threadpoolctl conda-forge/noarch::threadpoolctl-3.2.0-pyha21a80b_0 typing-extensions conda-forge/noarch::typing-extensions-4.8.0-hd8ed1ab_0 typing_extensions conda-forge/noarch::typing_extensions-4.8.0-pyha770c72_0 urllib3 conda-forge/noarch::urllib3-2.0.7-pyhd8ed1ab_0 The following packages will be UPDATED: openssl pkgs/main::openssl-3.0.11-h2f4d8fa_2 --> conda-forge::openssl-3.1.4-h31becfc_0 The following packages will be SUPERSEDED by a higher-priority channel: ca-certificates pkgs/main::ca-certificates-2023.08.22~ --> conda-forge::ca-certificates-2023.7.22-hcefe29a_0 Downloading and Extracting Packages charset-normalizer-3 | 46 KB | | 0% charset-normalizer-3 | 46 KB | ########## | 100% charset-normalizer-3 | 46 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done WARNING: ignoring environment value of R_HOME Quitting from lines 280-287 [unnamed-chunk-5] (motivation.Rmd) Error: processing vignette 'motivation.Rmd' failed with diagnostics: one node produced an error: Package ‘reticulate’ version 1.34.0 cannot be unloaded: Error in unloadNamespace(package) : namespace ‘reticulate’ is imported by ‘basilisk’ so cannot be unloaded --- failed re-building ‘motivation.Rmd’ SUMMARY: processing the following file failed: ‘motivation.Rmd’ Error: Vignette re-building failed. Execution halted