[Debian-med-packaging] Bug#997377: python-biom-format: FTBFS: AttributeError: 'Sphinx' object has no attribute 'add_javascript'

Lucas Nussbaum lucas at debian.org
Sat Oct 23 20:50:31 BST 2021 

Source: python-biom-format
Version: 2.1.10-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # arch
> USE_CYTHON=true dh_auto_build
> 	pybuild --build --test-pytest -i python{version} -p 3.9
> I: pybuild base:232: /usr/bin/python3 setup.py build 
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/err.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/exception.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests
> copying biom/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests
> copying biom/tests/test_util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests
> copying biom/tests/long_lines.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests
> copying biom/tests/test_err.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests
> copying biom/tests/test_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests
> copying biom/tests/test_parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/table_validator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/table_subsetter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/table_normalizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/table_ids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/uc_processor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/table_summarizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/metadata_exporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/table_head.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/metadata_adder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/table_converter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> copying biom/cli/installation_informer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/cli
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_show_install_info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_normalizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_converter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_add_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_subset_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_uc_processor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_summarize_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_validate_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli
> running egg_info
> creating biom_format.egg-info
> writing biom_format.egg-info/PKG-INFO
> writing dependency_links to biom_format.egg-info/dependency_links.txt
> writing entry points to biom_format.egg-info/entry_points.txt
> writing requirements to biom_format.egg-info/requires.txt
> writing top-level names to biom_format.egg-info/top_level.txt
> writing manifest file 'biom_format.egg-info/SOURCES.txt'
> reading manifest file 'biom_format.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no directories found matching 'support_files'
> warning: no directories found matching 'tests/test_data'
> no previously-included directories found matching 'docs/_build'
> warning: no previously-included files matching '*.pyc' found anywhere in distribution
> warning: no previously-included files matching '*.pyo' found anywhere in distribution
> warning: no previously-included files matching '.git' found anywhere in distribution
> warning: no previously-included files matching '*.so' found anywhere in distribution
> warning: no previously-included files matching '.*.swp' found anywhere in distribution
> adding license file 'COPYING.txt'
> writing manifest file 'biom_format.egg-info/SOURCES.txt'
> copying biom/_filter.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/_subsample.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> copying biom/_transform.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/assets
> copying biom/assets/exercise_api.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/assets
> copying biom/assets/exercise_cli.sh -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/assets
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/bench_tables
> copying biom/tests/test_data/bad_table.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/bad_table.txt.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/empty.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/no-contents.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.json.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/tests/test_cli/test_data
> running build_ext
> building 'biom._filter' extension
> creating build
> creating build/temp.linux-x86_64-3.9
> creating build/temp.linux-x86_64-3.9/biom
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c biom/_filter.c -o build/temp.linux-x86_64-3.9/biom/_filter.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
>                  from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
>                  from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from biom/_filter.c:639:
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
>    17 | #warning "Using deprecated NumPy API, disable it with " \
>       |  ^~~~~~~
> x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/biom/_filter.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/_filter.cpython-39-x86_64-linux-gnu.so
> building 'biom._transform' extension
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c biom/_transform.c -o build/temp.linux-x86_64-3.9/biom/_transform.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
>                  from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
>                  from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from biom/_transform.c:639:
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
>    17 | #warning "Using deprecated NumPy API, disable it with " \
>       |  ^~~~~~~
> x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/biom/_transform.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/_transform.cpython-39-x86_64-linux-gnu.so
> building 'biom._subsample' extension
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.9 -c biom/_subsample.c -o build/temp.linux-x86_64-3.9/biom/_subsample.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
>                  from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
>                  from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
>                  from biom/_subsample.c:639:
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
>    17 | #warning "Using deprecated NumPy API, disable it with " \
>       |  ^~~~~~~
> x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/biom/_subsample.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_biom-format/build/biom/_subsample.cpython-39-x86_64-linux-gnu.so
> # indep:
> PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
> Running Sphinx v4.2.0
> making output directory... done
> 
> Exception occurred:
>   File "/<<PKGBUILDDIR>>/doc/conf.py", line 238, in setup
>     app.add_javascript('copybutton.js')
> AttributeError: 'Sphinx' object has no attribute 'add_javascript'
> The full traceback has been saved in /tmp/sphinx-err-fvip4rcz.log, if you want to report the issue to the developers.
> Please also report this if it was a user error, so that a better error message can be provided next time.
> A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
> make[1]: *** [debian/rules:25: override_dh_auto_build] Error 2


The full build log is available from:
http://qa-logs.debian.net/2021/10/23/python-biom-format_2.1.10-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.

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