Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1317/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOFA2 1.19.0 (landing page) Ricard Argelaguet
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the MOFA2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOFA2.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MOFA2 |
Version: 1.19.0 |
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA2 |
StartedAt: 2025-08-01 01:18:00 -0000 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 01:20:10 -0000 (Fri, 01 Aug 2025) |
EllapsedTime: 130.1 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/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 Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (22.0.4) Collecting pip Downloading pip-25.2-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 436.5 kB/s eta 0:00:00 Collecting wheel Using cached wheel-0.45.1-py3-none-any.whl (72 kB) Requirement already satisfied: setuptools in /home/biocbuild/.cache/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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.2 kB) Collecting scipy==1.8.1 Using cached scipy-1.8.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.2 kB) Collecting pandas==1.4.3 Using cached pandas-1.4.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (10 kB) Collecting dtw-python==1.2.2 Using cached dtw_python-1.2.2-cp310-cp310-linux_aarch64.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-1.5.1-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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (13.9 MB) Using cached scipy-1.8.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (38.9 MB) Using cached pandas-1.4.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (10.9 MB) Using cached scikit_learn-1.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (30.0 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-1.5.1-py3-none-any.whl (307 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 ╰─> [541 lines of output] /home/biocbuild/tmp/pip-build-env-ge7yl27f/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.linux-aarch64-cpython-310/h5py copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-cpython-310/h5py copying h5py/version.py -> build/lib.linux-aarch64-cpython-310/h5py copying h5py/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py copying h5py/ipy_completer.py -> build/lib.linux-aarch64-cpython-310/h5py creating build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/files.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/vds.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/dataset.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/selections2.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/attrs.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/dims.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/compat.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/base.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/filters.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/group.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/selections.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/datatype.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl creating build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_selections.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5p.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_objects.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dimension_scales.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/conftest.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_datatype.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_big_endian_file.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dtype.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dataset.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5o.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_file2.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5pl.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_filters.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_slicing.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5t.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_file.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_attrs.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_attrs_data.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_group.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_file_image.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_errors.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_completions.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5f.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_attribute_create.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_base.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/common.py -> build/lib.linux-aarch64-cpython-310/h5py/tests creating build/lib.linux-aarch64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files creating build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files running build_ext warning: h5py/defs.pxd:15:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:62:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:64:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:66:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:68:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:70:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:72:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:74:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:76:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:78:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:102:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:104:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:106:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:107:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:109:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:110:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:112:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:114:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:116:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:180:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:197:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:199:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:201:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:203:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:213:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:215:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:229:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:231:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:233:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:235:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:237:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:239:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:241:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:269:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:271:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:273:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:275:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:277:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:279:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:285:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:287:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:289:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:291:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:293:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:295:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:297:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:299:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:333:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:335:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:337:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:339:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:341:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:343:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:345:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:347:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:349:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:383:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:385:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:48:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:64:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:143:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:148:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:156:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:165:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:198:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:287:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:334:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_ext.pxd:14:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_ext.pxd:25:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_ext.pxd:52:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/_conv.pyx:161:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/_conv.pyx:422:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/h5r.pxd:17:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 Error compiling Cython file: ------------------------------------------------------------ ... # License: Standard 3-clause BSD; see "license.txt" for full license terms # and contributor agreement. from .defs cimport * from ._objects cimport class ObjectID ^ ------------------------------------------------------------ h5py/h5t.pxd:13:23: Expected an identifier Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_OBJ.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/typewrap.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/py_create.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/TypeID.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_PYTHON_OPAQUE_TAG.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... void* ptr cdef int conv_vlen2ndarray(void* ipt, void* opt, cnp.dtype elem_dtype, TypeID intype, ^ ------------------------------------------------------------ h5py/_conv.pyx:687:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef int conv_vlen2ndarray(void* ipt, void* opt, cnp.dtype elem_dtype, TypeID intype, TypeID outtype) except -1: ^ ------------------------------------------------------------ h5py/_conv.pyx:688:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... return 0 cdef int conv_ndarray2vlen(void* ipt, void* opt, TypeID intype, ^ ------------------------------------------------------------ h5py/_conv.pyx:820:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef int conv_ndarray2vlen(void* ipt, void* opt, TypeID intype, TypeID outtype) except -1: ^ ------------------------------------------------------------ h5py/_conv.pyx:821:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... :return: error-code """ cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype ^ ------------------------------------------------------------ h5py/_conv.pyx:629:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... """ cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype TypeID outtype ^ ------------------------------------------------------------ h5py/_conv.pyx:630:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... void *bkg_i, hid_t dxpl) except -1 with gil: cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype ^ ------------------------------------------------------------ h5py/_conv.pyx:752:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... hid_t dxpl) except -1 with gil: cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype TypeID outtype ^ ------------------------------------------------------------ h5py/_conv.pyx:753:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef char* ctag = NULL try: if H5Tget_class(obj) == H5T_OPAQUE: ctag = H5Tget_tag(obj) if ctag != NULL: if strcmp(ctag, H5PY_PYTHON_OPAQUE_TAG) == 0: ^ ------------------------------------------------------------ h5py/_conv.pyx:157:32: 'H5PY_PYTHON_OPAQUE_TAG' is not a constant, variable or function identifier warning: h5py/_conv.pyx:157:32: Obtaining 'const char *' from externally modifiable global Python value Error compiling Cython file: ------------------------------------------------------------ ... elif command == H5T_CONV_FREE: pass elif command == H5T_CONV_CONV: # need to pass element dtype to converter supertype = typewrap(H5Tget_super(src_id)) ^ ------------------------------------------------------------ h5py/_conv.pyx:645:20: 'typewrap' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... elif command == H5T_CONV_CONV: # need to pass element dtype to converter supertype = typewrap(H5Tget_super(src_id)) dt = supertype.dtype outtype = py_create(dt) ^ ------------------------------------------------------------ h5py/_conv.pyx:647:18: 'py_create' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... PyObject *pdata_elem char* buf = <char*>buf_i if command == H5T_CONV_INIT: cdata[0].need_bkg = H5T_BKG_NO if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN: ^ ------------------------------------------------------------ h5py/_conv.pyx:761:32: 'H5PY_OBJ' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... if command == H5T_CONV_INIT: cdata[0].need_bkg = H5T_BKG_NO if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN: return -2 supertype = typewrap(H5Tget_super(dst_id)) ^ ------------------------------------------------------------ h5py/_conv.pyx:763:20: 'typewrap' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... return -2 supertype = typewrap(H5Tget_super(dst_id)) for i in range(nl): # smells a lot memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem)) if supertype != py_create((<cnp.ndarray> pdata_elem).dtype, 1): ^ ------------------------------------------------------------ h5py/_conv.pyx:767:28: 'py_create' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... if nl == 0: return 0 # need to pass element dtype to converter pdata_elem = pdata[0] supertype = py_create((<cnp.ndarray> pdata_elem).dtype) ^ ------------------------------------------------------------ h5py/_conv.pyx:784:20: 'py_create' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... return 0 # need to pass element dtype to converter pdata_elem = pdata[0] supertype = py_create((<cnp.ndarray> pdata_elem).dtype) outtype = typewrap(H5Tget_super(dst_id)) ^ ------------------------------------------------------------ h5py/_conv.pyx:785:18: 'typewrap' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... enum = H5Tenum_create(H5T_STD_I32LE) vlentype = H5Tvlen_create(H5T_STD_I32LE) pyobj = H5PY_OBJ ^ ------------------------------------------------------------ h5py/_conv.pyx:894:12: 'H5PY_OBJ' is not a constant, variable or function identifier Loading library to get build settings and version: libhdf5.so ******************************************************************************** Summary of the h5py configuration HDF5 include dirs: [] HDF5 library dirs: [] HDF5 Version: (1, 12, 1) MPI Enabled: False ROS3 VFD Enabled: False Rebuild Required: True ******************************************************************************** Executing api_gen rebuild of defs Executing cythonize() [ 1/24] Cythonizing /home/biocbuild/tmp/pip-install-1e18_dx2/h5py_238d9b160e5842fba6f96664f4a21eee/h5py/_conv.pyx Traceback (most recent call last): File "/home/biocbuild/.cache/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module> main() File "/home/biocbuild/.cache/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main json_out["return_val"] = hook(**hook_input["kwargs"]) File "/home/biocbuild/.cache/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel return _build_backend().build_wheel( File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 435, in build_wheel return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)]) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 423, in _build return self._build_with_temp_dir( File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 404, in _build_with_temp_dir self.run_setup() File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 317, in run_setup exec(code, locals()) File "<string>", line 104, in <module> File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 115, in setup return distutils.core.setup(**attrs) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 186, in setup return run_commands(dist) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 202, in run_commands dist.run_commands() File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands self.run_command(cmd) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1102, in run_command super().run_command(command) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command cmd_obj.run() File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py", line 370, in run self.run_command("build") File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command self.distribution.run_command(command) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1102, in run_command super().run_command(command) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command cmd_obj.run() File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command self.distribution.run_command(command) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1102, in run_command super().run_command(command) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command cmd_obj.run() File "/home/biocbuild/tmp/pip-install-1e18_dx2/h5py_238d9b160e5842fba6f96664f4a21eee/setup_build.py", line 170, in run self.extensions = cythonize(self._make_extensions(config), File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize cythonize_one(*args) File "/home/biocbuild/tmp/pip-build-env-ge7yl27f/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: /home/biocbuild/tmp/pip-install-1e18_dx2/h5py_238d9b160e5842fba6f96664f4a21eee/h5py/_conv.pyx [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/rlang_error> 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 /home/biocbuild/.cache/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 /home/biocbuild/.cache/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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.2 kB) Collecting scipy==1.8.1 Using cached scipy-1.8.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.2 kB) Collecting pandas==1.4.3 Using cached pandas-1.4.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (10 kB) Collecting dtw-python==1.2.2 Using cached dtw_python-1.2.2-cp310-cp310-linux_aarch64.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-1.5.1-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-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (13.9 MB) Using cached scipy-1.8.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (38.9 MB) Using cached pandas-1.4.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (10.9 MB) Using cached scikit_learn-1.1.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (30.0 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-1.5.1-py3-none-any.whl (307 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 ╰─> [541 lines of output] /home/biocbuild/tmp/pip-build-env-tchw22lc/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.linux-aarch64-cpython-310/h5py copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-cpython-310/h5py copying h5py/version.py -> build/lib.linux-aarch64-cpython-310/h5py copying h5py/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py copying h5py/ipy_completer.py -> build/lib.linux-aarch64-cpython-310/h5py creating build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/files.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/vds.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/dataset.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/selections2.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/attrs.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/dims.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/compat.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/base.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/filters.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/group.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/selections.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl copying h5py/_hl/datatype.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl creating build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_selections.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5p.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_objects.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dimension_scales.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/conftest.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_datatype.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_big_endian_file.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dtype.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dataset.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5o.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_file2.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5pl.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_filters.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_slicing.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5t.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_file.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_attrs.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_attrs_data.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_group.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_file_image.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_errors.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_completions.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5f.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_attribute_create.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_base.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-aarch64-cpython-310/h5py/tests copying h5py/tests/common.py -> build/lib.linux-aarch64-cpython-310/h5py/tests creating build/lib.linux-aarch64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files creating build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/test_vds/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files running build_ext warning: h5py/defs.pxd:15:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:62:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:64:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:66:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:68:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:70:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:72:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:74:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:76:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:78:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:102:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:104:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:106:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:107:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:109:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:110:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:112:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:114:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:116:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:180:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:197:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:199:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:201:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:203:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:213:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:215:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:229:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:231:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:233:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:235:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:237:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:239:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:241:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:269:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:271:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:273:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:275:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:277:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:279:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:285:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:287:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:289:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:291:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:293:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:295:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:297:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:299:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:333:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:335:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:337:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:339:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:341:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:343:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:345:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:347:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:349:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:383:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/defs.pxd:385:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:48:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:64:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:143:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:148:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:156:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:165:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:198:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:287:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_hdf5.pxd:334:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_ext.pxd:14:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_ext.pxd:25:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/api_types_ext.pxd:52:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/_conv.pyx:161:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/_conv.pyx:422:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 warning: h5py/h5r.pxd:17:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 Error compiling Cython file: ------------------------------------------------------------ ... # License: Standard 3-clause BSD; see "license.txt" for full license terms # and contributor agreement. from .defs cimport * from ._objects cimport class ObjectID ^ ------------------------------------------------------------ h5py/h5t.pxd:13:23: Expected an identifier Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_OBJ.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/typewrap.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/py_create.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/TypeID.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... from logging import getLogger from .h5 import get_config from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG ^ ------------------------------------------------------------ h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_PYTHON_OPAQUE_TAG.pxd' not found Error compiling Cython file: ------------------------------------------------------------ ... void* ptr cdef int conv_vlen2ndarray(void* ipt, void* opt, cnp.dtype elem_dtype, TypeID intype, ^ ------------------------------------------------------------ h5py/_conv.pyx:687:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef int conv_vlen2ndarray(void* ipt, void* opt, cnp.dtype elem_dtype, TypeID intype, TypeID outtype) except -1: ^ ------------------------------------------------------------ h5py/_conv.pyx:688:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... return 0 cdef int conv_ndarray2vlen(void* ipt, void* opt, TypeID intype, ^ ------------------------------------------------------------ h5py/_conv.pyx:820:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef int conv_ndarray2vlen(void* ipt, void* opt, TypeID intype, TypeID outtype) except -1: ^ ------------------------------------------------------------ h5py/_conv.pyx:821:27: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... :return: error-code """ cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype ^ ------------------------------------------------------------ h5py/_conv.pyx:629:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... """ cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype TypeID outtype ^ ------------------------------------------------------------ h5py/_conv.pyx:630:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... void *bkg_i, hid_t dxpl) except -1 with gil: cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype ^ ------------------------------------------------------------ h5py/_conv.pyx:752:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... hid_t dxpl) except -1 with gil: cdef: int command = cdata[0].command size_t src_size, dst_size TypeID supertype TypeID outtype ^ ------------------------------------------------------------ h5py/_conv.pyx:753:8: 'TypeID' is not a type identifier Error compiling Cython file: ------------------------------------------------------------ ... cdef char* ctag = NULL try: if H5Tget_class(obj) == H5T_OPAQUE: ctag = H5Tget_tag(obj) if ctag != NULL: if strcmp(ctag, H5PY_PYTHON_OPAQUE_TAG) == 0: ^ ------------------------------------------------------------ h5py/_conv.pyx:157:32: 'H5PY_PYTHON_OPAQUE_TAG' is not a constant, variable or function identifier warning: h5py/_conv.pyx:157:32: Obtaining 'const char *' from externally modifiable global Python value Error compiling Cython file: ------------------------------------------------------------ ... elif command == H5T_CONV_FREE: pass elif command == H5T_CONV_CONV: # need to pass element dtype to converter supertype = typewrap(H5Tget_super(src_id)) ^ ------------------------------------------------------------ h5py/_conv.pyx:645:20: 'typewrap' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... elif command == H5T_CONV_CONV: # need to pass element dtype to converter supertype = typewrap(H5Tget_super(src_id)) dt = supertype.dtype outtype = py_create(dt) ^ ------------------------------------------------------------ h5py/_conv.pyx:647:18: 'py_create' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... PyObject *pdata_elem char* buf = <char*>buf_i if command == H5T_CONV_INIT: cdata[0].need_bkg = H5T_BKG_NO if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN: ^ ------------------------------------------------------------ h5py/_conv.pyx:761:32: 'H5PY_OBJ' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... if command == H5T_CONV_INIT: cdata[0].need_bkg = H5T_BKG_NO if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN: return -2 supertype = typewrap(H5Tget_super(dst_id)) ^ ------------------------------------------------------------ h5py/_conv.pyx:763:20: 'typewrap' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... return -2 supertype = typewrap(H5Tget_super(dst_id)) for i in range(nl): # smells a lot memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem)) if supertype != py_create((<cnp.ndarray> pdata_elem).dtype, 1): ^ ------------------------------------------------------------ h5py/_conv.pyx:767:28: 'py_create' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... if nl == 0: return 0 # need to pass element dtype to converter pdata_elem = pdata[0] supertype = py_create((<cnp.ndarray> pdata_elem).dtype) ^ ------------------------------------------------------------ h5py/_conv.pyx:784:20: 'py_create' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... return 0 # need to pass element dtype to converter pdata_elem = pdata[0] supertype = py_create((<cnp.ndarray> pdata_elem).dtype) outtype = typewrap(H5Tget_super(dst_id)) ^ ------------------------------------------------------------ h5py/_conv.pyx:785:18: 'typewrap' is not a constant, variable or function identifier Error compiling Cython file: ------------------------------------------------------------ ... enum = H5Tenum_create(H5T_STD_I32LE) vlentype = H5Tvlen_create(H5T_STD_I32LE) pyobj = H5PY_OBJ ^ ------------------------------------------------------------ h5py/_conv.pyx:894:12: 'H5PY_OBJ' is not a constant, variable or function identifier Loading library to get build settings and version: libhdf5.so ******************************************************************************** Summary of the h5py configuration HDF5 include dirs: [] HDF5 library dirs: [] HDF5 Version: (1, 12, 1) MPI Enabled: False ROS3 VFD Enabled: False Rebuild Required: True ******************************************************************************** Executing api_gen rebuild of defs Executing cythonize() [ 1/24] Cythonizing /home/biocbuild/tmp/pip-install-al8s_wfp/h5py_757662a44eb64a798d3e603e938d9a3a/h5py/_conv.pyx Traceback (most recent call last): File "/home/biocbuild/.cache/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module> main() File "/home/biocbuild/.cache/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main json_out["return_val"] = hook(**hook_input["kwargs"]) File "/home/biocbuild/.cache/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel return _build_backend().build_wheel( File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 435, in build_wheel return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)]) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 423, in _build return self._build_with_temp_dir( File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 404, in _build_with_temp_dir self.run_setup() File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 317, in run_setup exec(code, locals()) File "<string>", line 104, in <module> File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 115, in setup return distutils.core.setup(**attrs) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 186, in setup return run_commands(dist) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 202, in run_commands dist.run_commands() File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands self.run_command(cmd) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1102, in run_command super().run_command(command) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command cmd_obj.run() File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py", line 370, in run self.run_command("build") File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command self.distribution.run_command(command) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1102, in run_command super().run_command(command) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command cmd_obj.run() File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command self.distribution.run_command(command) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1102, in run_command super().run_command(command) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command cmd_obj.run() File "/home/biocbuild/tmp/pip-install-al8s_wfp/h5py_757662a44eb64a798d3e603e938d9a3a/setup_build.py", line 170, in run self.extensions = cythonize(self._make_extensions(config), File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize cythonize_one(*args) File "/home/biocbuild/tmp/pip-build-env-tchw22lc/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: /home/biocbuild/tmp/pip-install-al8s_wfp/h5py_757662a44eb64a798d3e603e938d9a3a/h5py/_conv.pyx [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/rlang_error> 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