############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Pirat ### ############################################################################## ############################################################################## * checking for file ‘Pirat/DESCRIPTION’ ... OK * preparing ‘Pirat’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Pirat.Rmd’ using rmarkdown Channels: - conda-forge - pytorch - torch Platform: osx-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/Pirat/1.0.2/envPirat added / updated specs: - python=3.9.5 The following NEW packages will be INSTALLED: ca-certificates conda-forge/osx-64::ca-certificates-2024.12.14-h8857fd0_0 libcxx conda-forge/osx-64::libcxx-19.1.7-hf95d169_0 libffi conda-forge/osx-64::libffi-3.3-h046ec9c_2 liblzma conda-forge/osx-64::liblzma-5.6.3-hd471939_1 liblzma-devel conda-forge/osx-64::liblzma-devel-5.6.3-hd471939_1 libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0 libzlib conda-forge/osx-64::libzlib-1.2.13-h87427d6_6 ncurses conda-forge/osx-64::ncurses-6.5-h0622a9a_2 openssl conda-forge/osx-64::openssl-1.1.1w-h8a1eda9_0 pip conda-forge/noarch::pip-25.0-pyh8b19718_0 python conda-forge/osx-64::python-3.9.5-hd187cdc_0_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-75.8.0-pyhff2d567_0 sqlite conda-forge/osx-64::sqlite-3.46.0-h28673e1_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 tzdata conda-forge/noarch::tzdata-2025a-h78e105d_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 xz conda-forge/osx-64::xz-5.6.3-h357f2ed_1 xz-gpl-tools conda-forge/osx-64::xz-gpl-tools-5.6.3-h357f2ed_1 xz-tools conda-forge/osx-64::xz-tools-5.6.3-hd471939_1 zlib conda-forge/osx-64::zlib-1.2.13-h87427d6_6 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge - pytorch - torch Platform: osx-64 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: 25.1.0 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge - pytorch - torch Platform: osx-64 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: 25.1.0 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/Pirat/1.0.2/envPirat added / updated specs: - numpy=1.20.2 - python[version='3.9.5.*,3.9.5.*'] - pytorch=1.10.0 The following packages will be downloaded: package | build ---------------------------|----------------- future-1.0.0 | pyhd8ed1ab_1 356 KB conda-forge tbb-2021.13.0 | hb890de9_1 154 KB conda-forge typing_extensions-4.12.2 | pyha770c72_1 39 KB conda-forge ------------------------------------------------------------ Total: 549 KB The following NEW packages will be INSTALLED: cffi conda-forge/osx-64::cffi-1.14.6-py39hb71fe58_0 future conda-forge/noarch::future-1.0.0-pyhd8ed1ab_1 icu conda-forge/osx-64::icu-73.2-hf5e326d_0 libblas conda-forge/osx-64::libblas-3.9.0-12_osx64_mkl libcblas conda-forge/osx-64::libcblas-3.9.0-12_osx64_mkl libhwloc conda-forge/osx-64::libhwloc-2.11.2-default_hb6fbd3b_1000 libiconv conda-forge/osx-64::libiconv-1.17-hd75f5a5_2 liblapack conda-forge/osx-64::liblapack-3.9.0-12_osx64_mkl libprotobuf conda-forge/osx-64::libprotobuf-3.19.6-hbc0c0cd_0 libxml2 conda-forge/osx-64::libxml2-2.12.7-h3e169fe_1 llvm-openmp conda-forge/osx-64::llvm-openmp-19.1.7-ha54dae1_0 mkl conda-forge/osx-64::mkl-2021.4.0-h89fa619_689 ninja conda-forge/osx-64::ninja-1.12.1-h3c5361c_0 numpy conda-forge/osx-64::numpy-1.20.2-py39h7eed0ac_0 pycparser conda-forge/noarch::pycparser-2.22-pyh29332c3_1 python_abi conda-forge/osx-64::python_abi-3.9-5_cp39 pytorch conda-forge/osx-64::pytorch-1.10.0-cpu_py39he6bcdb8_1 sleef conda-forge/osx-64::sleef-3.7-hfe0d17b_2 tbb conda-forge/osx-64::tbb-2021.13.0-hb890de9_1 typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_1 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Processing /private/tmp/RtmpVM47ve/Rinsta19a2bf7a960/Pirat/myModules Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Building wheels for collected packages: PyPirat Building wheel for PyPirat (setup.py): started Building wheel for PyPirat (setup.py): finished with status 'done' Created wheel for PyPirat: filename=PyPirat-0.1-py3-none-any.whl size=16151 sha256=67a8de5617d7e15935773da482d83ae5851953f6bc10fd53adacb417ccd24cff Stored in directory: /private/tmp/pip-ephem-wheel-cache-0u1l88fv/wheels/89/59/69/9ce33430cbcc888ceb6404db399ecc34c01f2ff5a3efa89cbe Successfully built PyPirat Installing collected packages: PyPirat Successfully installed PyPirat-0.1 Intel MKL FATAL ERROR: Cannot load libmkl_intel_thread.1.dylib.