Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-08 12:10 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 1317/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA2 1.19.0  (landing page)
Ricard Argelaguet
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 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

BUILD results for MOFA2 on kjohnson3

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.

raw results


Summary

Package: MOFA2
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA2
StartedAt: 2025-08-07 16:59:46 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 17:00:37 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 50.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MOFA2
###
##############################################################################
##############################################################################


* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* preparing ‘MOFA2’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MEFISTO_temporal.Rmd’ using rmarkdown
2025-08-07 16:59:59.424 R[17419:478287395] XType: Using static font registry.
Requirement already satisfied: pip in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (22.0.4)
Collecting pip
  Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (58.1.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.1.0
    Uninstalling setuptools-58.1.0:
      Successfully uninstalled setuptools-58.1.0
  Attempting uninstall: pip
    Found existing installation: pip 22.0.4
    Uninstalling pip-22.0.4:
      Successfully uninstalled pip-22.0.4
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Collecting numpy==1.23.1
  Using cached numpy-1.23.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (2.2 kB)
Collecting scipy==1.8.1
  Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (2.2 kB)
Collecting pandas==1.4.3
  Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (12 kB)
Collecting h5py==3.6.0
  Using cached h5py-3.6.0.tar.gz (384 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting scikit-learn==1.1.1
  Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (10 kB)
Collecting dtw-python==1.2.2
  Using cached dtw_python-1.2.2-cp310-cp310-macosx_11_0_arm64.whl
Collecting mofapy2==0.7.0
  Using cached mofapy2-0.7.0-py3-none-any.whl.metadata (1.7 kB)
Collecting python-dateutil>=2.8.1 (from pandas==1.4.3)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==1.4.3)
  Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting joblib>=1.0.0 (from scikit-learn==1.1.1)
  Using cached joblib-1.5.1-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-macosx_11_0_arm64.whl (13.3 MB)
Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl (28.7 MB)
Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl (10.4 MB)
Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB)
Using cached mofapy2-0.7.0-py3-none-any.whl (1.0 MB)
Using cached anndata-0.8.0-py3-none-any.whl (96 kB)
Using cached joblib-1.5.1-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
  ╰─> [82 lines of output]
      /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-build-env-7g8oe3gb/overlay/lib/python3.10/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!
      
              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:
      
              License :: OSI Approved :: BSD License
      
              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************
      
      !!
        self._finalize_license_expression()
      running bdist_wheel
      running build
      running build_py
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/h5py_warnings.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/version.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/ipy_completer.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/files.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/compat.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/selections2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/dims.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_attribute_create.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_file_image.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/conftest.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5f.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_errors.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_slicing.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5pl.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_attrs_data.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5t.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_big_endian_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5p.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5o.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/common.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dtype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_file2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_completions.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_objects.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      running build_ext
      Loading library to get build settings and version: libhdf5.dylib
      error: Unable to load dependency HDF5, make sure HDF5 is installed properly
      error: dlopen(libhdf5.dylib, 0x0006): tried: 'libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache), 'libhdf5.dylib' (no such file), '/usr/local/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache)
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for h5py
Failed to build h5py
error: failed-wheel-build-for-install

× Failed to build installable wheels for some pyproject.toml based projects
╰─> h5py

Quitting from MEFISTO_temporal.Rmd:95-98 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/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 /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (22.0.4)
Collecting pip
  Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.21.5/MOFA2/1.19.0/mofa_env/lib/python3.10/site-packages (58.1.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.1.0
    Uninstalling setuptools-58.1.0:
      Successfully uninstalled setuptools-58.1.0
  Attempting uninstall: pip
    Found existing installation: pip 22.0.4
    Uninstalling pip-22.0.4:
      Successfully uninstalled pip-22.0.4
Successfully installed pip-25.2 setuptools-80.9.0 wheel-0.45.1
Collecting numpy==1.23.1
  Using cached numpy-1.23.1-cp310-cp310-macosx_11_0_arm64.whl.metadata (2.2 kB)
Collecting scipy==1.8.1
  Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (2.2 kB)
Collecting pandas==1.4.3
  Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (12 kB)
Collecting h5py==3.6.0
  Using cached h5py-3.6.0.tar.gz (384 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting scikit-learn==1.1.1
  Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (10 kB)
Collecting dtw-python==1.2.2
  Using cached dtw_python-1.2.2-cp310-cp310-macosx_11_0_arm64.whl
Collecting mofapy2==0.7.0
  Using cached mofapy2-0.7.0-py3-none-any.whl.metadata (1.7 kB)
Collecting python-dateutil>=2.8.1 (from pandas==1.4.3)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==1.4.3)
  Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting joblib>=1.0.0 (from scikit-learn==1.1.1)
  Using cached joblib-1.5.1-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-macosx_11_0_arm64.whl (13.3 MB)
Using cached scipy-1.8.1-cp310-cp310-macosx_12_0_arm64.whl (28.7 MB)
Using cached pandas-1.4.3-cp310-cp310-macosx_11_0_arm64.whl (10.4 MB)
Using cached scikit_learn-1.1.1-cp310-cp310-macosx_12_0_arm64.whl (7.7 MB)
Using cached mofapy2-0.7.0-py3-none-any.whl (1.0 MB)
Using cached anndata-0.8.0-py3-none-any.whl (96 kB)
Using cached joblib-1.5.1-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
  ╰─> [82 lines of output]
      /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/pip-build-env-j_eb7iw3/overlay/lib/python3.10/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
      !!
      
              ********************************************************************************
              Please consider removing the following classifiers in favor of a SPDX license expression:
      
              License :: OSI Approved :: BSD License
      
              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************
      
      !!
        self._finalize_license_expression()
      running bdist_wheel
      running build
      running build_py
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/h5py_warnings.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/version.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      copying h5py/ipy_completer.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/files.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/compat.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/selections2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/dims.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      copying h5py/_hl/filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/_hl
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dimension_scales.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_attribute_create.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_file_image.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/conftest.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5f.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset_getitem.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_group.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_errors.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset_swmr.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_slicing.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5pl.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_attrs.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_attrs_data.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5t.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_big_endian_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5p.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5o.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_datatype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/common.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dataset.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_file.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_selections.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_dtype.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_h5.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_file2.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_completions.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_filters.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_base.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      copying h5py/tests/test_objects.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      creating build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/__init__.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/test_vds
      copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.macosx-11.0-arm64-cpython-310/h5py/tests/data_files
      running build_ext
      Loading library to get build settings and version: libhdf5.dylib
      error: Unable to load dependency HDF5, make sure HDF5 is installed properly
      error: dlopen(libhdf5.dylib, 0x0006): tried: 'libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/biocbuild/.pyenv/versions/3.10.5/lib/libhdf5.dylib' (no such file), '/opt/homebrew/lib/libhdf5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache), 'libhdf5.dylib' (no such file), '/usr/local/lib/libhdf5.dylib' (no such file), '/usr/lib/libhdf5.dylib' (no such file, not in dyld cache)
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for h5py
Failed to build h5py
error: failed-wheel-build-for-install

× Failed to build installable wheels for some pyproject.toml based projects
╰─> h5py

Quitting from getting_started_R.Rmd:212-215 [unnamed-chunk-14]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/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