Ricard Argelaguet
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/MOFA2 |
| git_branch: devel |
| git_last_commit: b2755a0 |
| git_last_commit_date: 2025-04-15 12:12:13 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:07 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1341/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MOFA2 1.19.0 (landing page) Ricard Argelaguet
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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: 2025-10-21 01:23:28 -0000 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 01:25:38 -0000 (Tue, 21 Oct 2025) |
| EllapsedTime: 130.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /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
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
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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)
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Collecting python-dateutil>=2.8.1 (from pandas==1.4.3)
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Collecting pytz>=2020.1 (from pandas==1.4.3)
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Collecting joblib>=1.0.0 (from scikit-learn==1.1.1)
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Collecting threadpoolctl>=2.0.0 (from scikit-learn==1.1.1)
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Collecting anndata<0.9,>=0.8 (from mofapy2==0.7.0)
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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)
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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-rgti8nbt/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-r__qqr7y/h5py_69aefc9f365348d7bf96e519cfbb746b/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/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-rgti8nbt/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
cmd_obj.run()
File "/home/biocbuild/tmp/pip-install-r__qqr7y/h5py_69aefc9f365348d7bf96e519cfbb746b/setup_build.py", line 170, in run
self.extensions = cythonize(self._make_extensions(config),
File "/home/biocbuild/tmp/pip-build-env-rgti8nbt/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1159, in cythonize
cythonize_one(*args)
File "/home/biocbuild/tmp/pip-build-env-rgti8nbt/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1303, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /home/biocbuild/tmp/pip-install-r__qqr7y/h5py_69aefc9f365348d7bf96e519cfbb746b/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-1.5.2-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-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-1.5.2-py3-none-any.whl (308 kB)
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Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
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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-qk9jdxgz/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-qk2alvm8/h5py_a6cf2dfd6ffa424e8af959b81b45233b/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/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-qk9jdxgz/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
cmd_obj.run()
File "/home/biocbuild/tmp/pip-install-qk2alvm8/h5py_a6cf2dfd6ffa424e8af959b81b45233b/setup_build.py", line 170, in run
self.extensions = cythonize(self._make_extensions(config),
File "/home/biocbuild/tmp/pip-build-env-qk9jdxgz/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1159, in cythonize
cythonize_one(*args)
File "/home/biocbuild/tmp/pip-build-env-qk9jdxgz/overlay/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1303, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /home/biocbuild/tmp/pip-install-qk2alvm8/h5py_a6cf2dfd6ffa424e8af959b81b45233b/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