############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA2 ### ############################################################################## ############################################################################## * checking for file ‘MOFA2/DESCRIPTION’ ... OK * preparing ‘MOFA2’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘MEFISTO_temporal.Rmd’ using rmarkdown 2025-10-19 17:02:47.181 R[61118:494952877] XType: Using static font registry. Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (22.0.4) Collecting pip Using cached pip-25.2-py3-none-any.whl (1.8 MB) Collecting wheel Using cached wheel-0.45.1-py3-none-any.whl (72 kB) Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (58.1.0) Collecting setuptools Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB) Installing collected packages: wheel, setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 58.1.0 Uninstalling setuptools-58.1.0: Successfully uninstalled setuptools-58.1.0 Attempting uninstall: pip Found existing installation: pip 22.0.4 Uninstalling pip-22.0.4: Successfully uninstalled pip-22.0.4 Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1 Collecting numpy==1.23.1 Using cached numpy-1.23.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (2.2 kB) Collecting scipy==1.8.1 Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (2.2 kB) Collecting pandas==1.4.3 Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (12 kB) Collecting h5py==3.6.0 Using cached h5py-3.6.0.tar.gz (384 kB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting scikit-learn==1.1.1 Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (10 kB) Collecting dtw-python==1.2.2 Using cached dtw_python-1.2.2-cp310-cp310-macosx_11_0_arm64.whl Collecting mofapy2==0.7.0 Using cached mofapy2-0.7.0-py3-none-any.whl.metadata (1.7 kB) Collecting python-dateutil>=2.8.1 (from pandas==1.4.3) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting pytz>=2020.1 (from pandas==1.4.3) Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) Collecting joblib>=1.0.0 (from scikit-learn==1.1.1) Using cached joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB) Collecting threadpoolctl>=2.0.0 (from scikit-learn==1.1.1) Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB) Collecting anndata<0.9,>=0.8 (from mofapy2==0.7.0) Using cached anndata-0.8.0-py3-none-any.whl.metadata (4.6 kB) Collecting natsort (from anndata<0.9,>=0.8->mofapy2==0.7.0) Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting packaging>=20 (from anndata<0.9,>=0.8->mofapy2==0.7.0) Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB) Collecting six>=1.5 (from python-dateutil>=2.8.1->pandas==1.4.3) Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Using cached numpy-1.23.1-cp310-cp310-macosx_11_0_arm64.whl (13.3 MB) Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl (28.7 MB) Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl (10.4 MB) Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB) Using cached mofapy2-0.7.0-py3-none-any.whl (1.0 MB) Using cached anndata-0.8.0-py3-none-any.whl (96 kB) Using cached joblib-1.5.2-py3-none-any.whl (308 kB) Using cached packaging-25.0-py3-none-any.whl (66 kB) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB) Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB) Using cached natsort-8.4.0-py3-none-any.whl (38 kB) Building wheels for collected packages: h5py Building wheel for h5py (pyproject.toml): started Building wheel for h5py (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error × Building wheel for h5py (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [82 lines of output] /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-build-env-e3h6x8tf/overlay/lib/python3.10/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/h5py_warnings.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/version.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/ipy_completer.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py creating build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/files.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/compat.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/selections2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/dims.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_attribute_create.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_file_image.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/conftest.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5f.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_errors.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_slicing.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5pl.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_attrs_data.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5t.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_big_endian_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5p.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5o.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/common.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dtype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_file2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_completions.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_objects.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files running build_ext Loading library to get build settings and version: libhdf5.dylib error: Unable to load dependency HDF5, make sure HDF5 is installed properly error: dlopen(libhdf5.dylib, 0x0006): tried: 'libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache), 'libhdf5.dylib' (no such file), '/usr/local/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache) [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for h5py Failed to build h5py error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> h5py Quitting from MEFISTO_temporal.Rmd:95-98 [unnamed-chunk-7] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! Error installing package(s): "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'" --- Backtrace: ▆ 1. └─MOFA2::run_mofa(sm, outfile, use_basilisk = TRUE) 2. └─basilisk::basiliskStart(mofa_env) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─reticulate::virtualenv_create(...) 6. └─reticulate:::pip_install(python, packages) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'MEFISTO_temporal.Rmd' failed with diagnostics: Error installing package(s): "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'" --- failed re-building ‘MEFISTO_temporal.Rmd’ --- re-building ‘downstream_analysis.Rmd’ using rmarkdown --- finished re-building ‘downstream_analysis.Rmd’ --- re-building ‘getting_started_R.Rmd’ using rmarkdown Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (22.0.4) Collecting pip Using cached pip-25.2-py3-none-any.whl (1.8 MB) Collecting wheel Using cached wheel-0.45.1-py3-none-any.whl (72 kB) Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (58.1.0) Collecting setuptools Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB) Installing collected packages: wheel, setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 58.1.0 Uninstalling setuptools-58.1.0: Successfully uninstalled setuptools-58.1.0 Attempting uninstall: pip Found existing installation: pip 22.0.4 Uninstalling pip-22.0.4: Successfully uninstalled pip-22.0.4 Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1 Collecting numpy==1.23.1 Using cached numpy-1.23.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (2.2 kB) Collecting scipy==1.8.1 Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (2.2 kB) Collecting pandas==1.4.3 Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (12 kB) Collecting h5py==3.6.0 Using cached h5py-3.6.0.tar.gz (384 kB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting scikit-learn==1.1.1 Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (10 kB) Collecting dtw-python==1.2.2 Using cached dtw_python-1.2.2-cp310-cp310-macosx_11_0_arm64.whl Collecting mofapy2==0.7.0 Using cached mofapy2-0.7.0-py3-none-any.whl.metadata (1.7 kB) Collecting python-dateutil>=2.8.1 (from pandas==1.4.3) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) Collecting pytz>=2020.1 (from pandas==1.4.3) Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) Collecting joblib>=1.0.0 (from scikit-learn==1.1.1) Using cached joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB) Collecting threadpoolctl>=2.0.0 (from scikit-learn==1.1.1) Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB) Collecting anndata<0.9,>=0.8 (from mofapy2==0.7.0) Using cached anndata-0.8.0-py3-none-any.whl.metadata (4.6 kB) Collecting natsort (from anndata<0.9,>=0.8->mofapy2==0.7.0) Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting packaging>=20 (from anndata<0.9,>=0.8->mofapy2==0.7.0) Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB) Collecting six>=1.5 (from python-dateutil>=2.8.1->pandas==1.4.3) Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Using cached numpy-1.23.1-cp310-cp310-macosx_11_0_arm64.whl (13.3 MB) Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl (28.7 MB) Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl (10.4 MB) Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB) Using cached mofapy2-0.7.0-py3-none-any.whl (1.0 MB) Using cached anndata-0.8.0-py3-none-any.whl (96 kB) Using cached joblib-1.5.2-py3-none-any.whl (308 kB) Using cached packaging-25.0-py3-none-any.whl (66 kB) Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB) Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB) Using cached natsort-8.4.0-py3-none-any.whl (38 kB) Building wheels for collected packages: h5py Building wheel for h5py (pyproject.toml): started Building wheel for h5py (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error × Building wheel for h5py (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [82 lines of output] /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-build-env-_tbezcex/overlay/lib/python3.10/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/h5py_warnings.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/version.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py copying h5py/ipy_completer.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py creating build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/files.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/compat.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/selections2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/dims.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl copying h5py/_hl/filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_attribute_create.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_file_image.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/conftest.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5f.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_errors.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_slicing.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5pl.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_attrs_data.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5t.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_big_endian_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5p.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5o.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/common.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_dtype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_h5.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_file2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_completions.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests copying h5py/tests/test_objects.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files running build_ext Loading library to get build settings and version: libhdf5.dylib error: Unable to load dependency HDF5, make sure HDF5 is installed properly error: dlopen(libhdf5.dylib, 0x0006): tried: 'libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache), 'libhdf5.dylib' (no such file), '/usr/local/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache) [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for h5py Failed to build h5py error: failed-wheel-build-for-install × Failed to build installable wheels for some pyproject.toml based projects ╰─> h5py Quitting from getting_started_R.Rmd:212-215 [unnamed-chunk-14] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! Error installing package(s): "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'" --- Backtrace: ▆ 1. └─MOFA2::run_mofa(MOFAobject, outfile, use_basilisk = TRUE) 2. └─basilisk::basiliskStart(mofa_env) 3. └─basilisk::obtainEnvironmentPath(env) 4. └─basilisk::setupBasiliskEnv(...) 5. └─reticulate::virtualenv_create(...) 6. └─reticulate:::pip_install(python, packages) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'getting_started_R.Rmd' failed with diagnostics: Error installing package(s): "'numpy==1.23.1'", "'scipy==1.8.1'", "'pandas==1.4.3'", "'h5py==3.6.0'", "'scikit-learn==1.1.1'", "'dtw-python==1.2.2'", "'mofapy2==0.7.0'" --- failed re-building ‘getting_started_R.Rmd’ SUMMARY: processing the following files failed: ‘MEFISTO_temporal.Rmd’ ‘getting_started_R.Rmd’ Error: Vignette re-building failed. Execution halted