Multiple platform build/check report for BioC 3.23 - BUILD results for BiocSklearn on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4957
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4686
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4627
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*

BUILD results for BiocSklearn on kunpeng2

To the developers/maintainers of the BiocSklearn package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocSklearn.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: BiocSklearn

Version: 1.33.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocSklearn

StartedAt: 2026-04-16 22:35:07 -0000 (Thu, 16 Apr 2026)

EndedAt: 2026-04-16 22:36:07 -0000 (Thu, 16 Apr 2026)

EllapsedTime: 60.0 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 BiocSklearn
###
##############################################################################
##############################################################################


* checking for file ‘BiocSklearn/DESCRIPTION’ ... OK
* preparing ‘BiocSklearn’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BiocSklearn.Rmd’ using rmarkdown
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.23.0/BiocSklearn/1.33.0/bsklenv/lib/python3.12/site-packages (25.0.1)
Collecting pip
  Using cached pip-26.0.1-py3-none-any.whl.metadata (4.7 kB)
Collecting wheel
  Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
Collecting setuptools
  Using cached setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting packaging>=24.0 (from wheel)
  Using cached packaging-26.1-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-26.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
Using cached setuptools-82.0.1-py3-none-any.whl (1.0 MB)
Using cached packaging-26.1-py3-none-any.whl (95 kB)
Installing collected packages: setuptools, pip, packaging, wheel
  Attempting uninstall: pip
    Found existing installation: pip 25.0.1
    Uninstalling pip-25.0.1:
      Successfully uninstalled pip-25.0.1
Successfully installed packaging-26.1 pip-26.0.1 setuptools-82.0.1 wheel-0.46.3
Collecting numpy==1.26.3
  Using cached numpy-1.26.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (62 kB)
Collecting scikit-learn==1.5.0
  Using cached scikit_learn-1.5.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB)
Collecting h5py==3.11.0
  Using cached h5py-3.11.0.tar.gz (406 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 pandas==2.2.2
  Using cached pandas-2.2.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (19 kB)
Collecting joblib==1.3.2
  Using cached joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting scipy==1.13.1
  Using cached scipy-1.13.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (113 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.5.0)
  Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Collecting python-dateutil>=2.8.2 (from pandas==2.2.2)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas==2.2.2)
  Using cached pytz-2026.1.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas==2.2.2)
  Using cached tzdata-2026.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas==2.2.2)
  Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached numpy-1.26.3-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (13.9 MB)
Using cached scikit_learn-1.5.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (12.1 MB)
Using cached pandas-2.2.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (15.2 MB)
Using cached joblib-1.3.2-py3-none-any.whl (302 kB)
Using cached scipy-1.13.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (33.4 MB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached pytz-2026.1.post1-py2.py3-none-any.whl (510 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 tzdata-2026.1-py2.py3-none-any.whl (348 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
  ╰─> [113 lines of output]
      /home/biocbuild/tmp/pip-build-env-dwk12te5/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
      !!
      
              ********************************************************************************
              Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).
      
              By 2027-Feb-18, you need to update your project and remove deprecated calls
              or your builds will no longer be supported.
      
              See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
              ********************************************************************************
      
      !!
        corresp(dist, value, root_dir)
      /home/biocbuild/tmp/pip-build-env-dwk12te5/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: 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.
              ********************************************************************************
      
      !!
        dist._finalize_license_expression()
      /home/biocbuild/tmp/pip-build-env-dwk12te5/overlay/lib/python3.12/site-packages/setuptools/dist.py:765: 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-312/h5py
      copying h5py/ipy_completer.py -> build/lib.linux-aarch64-cpython-312/h5py
      copying h5py/version.py -> build/lib.linux-aarch64-cpython-312/h5py
      copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-cpython-312/h5py
      copying h5py/__init__.py -> build/lib.linux-aarch64-cpython-312/h5py
      creating build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/dataset.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/base.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/datatype.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/attrs.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/compat.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/vds.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/__init__.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/filters.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/files.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/group.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/selections.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/selections2.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      copying h5py/_hl/dims.py -> build/lib.linux-aarch64-cpython-312/h5py/_hl
      creating build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_ros3.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_file2.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/conftest.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5f.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/common.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_base.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_file_alignment.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_filters.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_file_image.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_datatype.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_attrs.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_dtype.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5pl.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_errors.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_slicing.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5z.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/__init__.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_attrs_data.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_dataset.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5p.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5o.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_dimension_scales.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_big_endian_file.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_file.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_attribute_create.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_completions.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_group.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_h5t.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_objects.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      copying h5py/tests/test_selections.py -> build/lib.linux-aarch64-cpython-312/h5py/tests
      creating build/lib.linux-aarch64-cpython-312/h5py/tests/data_files
      copying h5py/tests/data_files/__init__.py -> build/lib.linux-aarch64-cpython-312/h5py/tests/data_files
      creating build/lib.linux-aarch64-cpython-312/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-aarch64-cpython-312/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-aarch64-cpython-312/h5py/tests/test_vds
      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-aarch64-cpython-312/h5py/tests/test_vds
      copying h5py/tests/test_vds/__init__.py -> build/lib.linux-aarch64-cpython-312/h5py/tests/test_vds
      copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.linux-aarch64-cpython-312/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.linux-aarch64-cpython-312/h5py/tests/data_files
      copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.linux-aarch64-cpython-312/h5py/tests/data_files
      running build_ext
      Loading library to get build settings and version: libhdf5.so
      error: Unable to load dependency HDF5, make sure HDF5 is installed properly
      Library dirs checked: []
      error: libhdf5.so: cannot open shared object file: No such file or directory
      [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 BiocSklearn.Rmd:33-39 [dsetup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'numpy==1.26.3'", "'scikit-learn==1.5.0'", "'h5py==3.11.0'", "'pandas==2.2.2'", "'joblib==1.3.2'", "'scipy==1.13.1'"
---
Backtrace:
    ▆
 1. └─BiocSklearn::skPCA(data.matrix(iris[, 1:4])) at tmp/RtmpEoJikI/Rex385b631782b645:11:1
 2.   └─basilisk::basiliskStart(bsklenv, testload = "scipy")
 3.     └─basilisk::obtainEnvironmentPath(env)
 4.       └─basilisk::setupBasiliskEnv(...)
 5.         └─reticulate::virtualenv_create(...)
 6.           └─reticulate:::pip_install(python, packages)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BiocSklearn.Rmd' failed with diagnostics:
Error installing package(s): "'numpy==1.26.3'", "'scikit-learn==1.5.0'", "'h5py==3.11.0'", "'pandas==2.2.2'", "'joblib==1.3.2'", "'scipy==1.13.1'"
--- failed re-building ‘BiocSklearn.Rmd’

SUMMARY: processing the following file failed:
  ‘BiocSklearn.Rmd’

Error: Vignette re-building failed.
Execution halted