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).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1317/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA2 1.19.0  (landing page)
Ricard Argelaguet
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 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)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for MOFA2 on taishan

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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
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Collecting scipy==1.8.1
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  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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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)
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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-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