[Debian-med-packaging] Bug#955662: python-biom-format: FTBFS: ERROR: Failure: ModuleNotFoundError (No module named 'matplotlib')
Lucas Nussbaum
lucas at debian.org
Fri Apr 3 20:42:24 BST 2020
Source: python-biom-format
Version: 2.1.8+dfsg-1
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200402 ftbfs-bullseye
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-nose -i python{version} -p "3.7 3.8"
> I: pybuild base:217: /usr/bin/python3.7 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/err.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/exception.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests
> copying biom/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests
> copying biom/tests/test_util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests
> copying biom/tests/long_lines.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests
> copying biom/tests/test_err.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests
> copying biom/tests/test_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests
> copying biom/tests/test_parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/table_validator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/table_subsetter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/table_normalizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/table_ids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/uc_processor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/table_summarizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/metadata_exporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/table_head.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/metadata_adder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/table_converter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> copying biom/cli/installation_informer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/cli
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_show_install_info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_normalizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_converter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_add_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_subset_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_uc_processor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_summarize_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_validate_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_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
> writing manifest file 'biom_format.egg-info/SOURCES.txt'
> copying biom/_filter.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/_filter.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/_subsample.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/_subsample.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/_transform.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> copying biom/_transform.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/assets
> copying biom/assets/exercise_api.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/assets
> copying biom/assets/exercise_cli.sh -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/assets
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/bench_tables
> copying biom/tests/test_data/bad_table.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/bad_table.txt.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/empty.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/no-contents.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.json.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/tests/test_cli/test_data
> running build_ext
> building 'biom._filter' extension
> creating build
> creating build/temp.linux-x86_64-3.7
> creating build/temp.linux-x86_64-3.7/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 -fdebug-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/python3.7m -c biom/_filter.c -o build/temp.linux-x86_64-3.7/biom/_filter.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
> 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:617:
> /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 -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/biom/_filter.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/_filter.cpython-37m-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 -fdebug-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/python3.7m -c biom/_transform.c -o build/temp.linux-x86_64-3.7/biom/_transform.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
> 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:617:
> /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 -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/biom/_transform.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/_transform.cpython-37m-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 -fdebug-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/python3.7m -c biom/_subsample.c -o build/temp.linux-x86_64-3.7/biom/_subsample.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
> 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:617:
> /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 -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.7/biom/_subsample.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/_subsample.cpython-37m-x86_64-linux-gnu.so
> I: pybuild base:217: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/err.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/exception.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests
> copying biom/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests
> copying biom/tests/test_util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests
> copying biom/tests/long_lines.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests
> copying biom/tests/test_err.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests
> copying biom/tests/test_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests
> copying biom/tests/test_parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/table_validator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/table_subsetter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/table_normalizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/table_ids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/uc_processor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/table_summarizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/metadata_exporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/table_head.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/metadata_adder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/table_converter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> copying biom/cli/installation_informer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/cli
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_show_install_info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_normalizer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_table_converter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_add_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_subset_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_uc_processor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_summarize_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> copying biom/tests/test_cli/test_validate_table.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli
> running 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
> 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
> writing manifest file 'biom_format.egg-info/SOURCES.txt'
> copying biom/_filter.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/_filter.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/_subsample.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/_subsample.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/_transform.c -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> copying biom/_transform.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/assets
> copying biom/assets/exercise_api.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/assets
> copying biom/assets/exercise_cli.sh -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/assets
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/bench_tables
> copying biom/tests/test_data/bad_table.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/bad_table.txt.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/empty.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/no-contents.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> copying biom/tests/test_data/test.json.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.biom -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
> copying biom/tests/test_cli/test_data/test.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_cli/test_data
> running build_ext
> building 'biom._filter' extension
> creating build/temp.linux-x86_64-3.8
> creating build/temp.linux-x86_64-3.8/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 -fdebug-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/python3.8 -c biom/_filter.c -o build/temp.linux-x86_64-3.8/biom/_filter.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
> 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:617:
> /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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/biom/_filter.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/_filter.cpython-38-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 -fdebug-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/python3.8 -c biom/_transform.c -o build/temp.linux-x86_64-3.8/biom/_transform.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
> 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:617:
> /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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/biom/_transform.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/_transform.cpython-38-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 -fdebug-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/python3.8 -c biom/_subsample.c -o build/temp.linux-x86_64-3.8/biom/_subsample.o
> In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
> 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:617:
> /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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/biom/_subsample.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_biom-format/build/biom/_subsample.cpython-38-x86_64-linux-gnu.so
> # indep:
> PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html doc build/html
> Running Sphinx v1.8.5
> making output directory...
> [autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst
> Failed to import 'biom.table': no module named biom.table
> Failed to import 'biom': no module named biom
> building [mo]: targets for 0 po files that are out of date
> building [html]: targets for 12 source files that are out of date
> updating environment: 12 added, 0 changed, 0 removed
> reading sources... [ 8%] BIOM_LICENSE
> reading sources... [ 16%] documentation/adding_metadata
> reading sources... [ 25%] documentation/biom_conversion
> reading sources... [ 33%] documentation/biom_format
> reading sources... [ 41%] documentation/format_versions/biom-1.0
> reading sources... [ 50%] documentation/format_versions/biom-2.0
> reading sources... [ 58%] documentation/format_versions/biom-2.1
> reading sources... [ 66%] documentation/index
> reading sources... [ 75%] documentation/quick_usage_examples
> reading sources... [ 83%] documentation/summarizing_biom_tables
> reading sources... [ 91%] documentation/table_objects
> reading sources... [100%] index
>
> WARNING: autodoc: failed to import module 'biom'; the following exception was raised:
> No module named 'matplotlib'
> WARNING: autodoc: failed to import module 'table' from module 'biom'; the following exception was raised:
> No module named 'matplotlib'
> looking for now-outdated files... none found
> pickling environment... done
> checking consistency... done
> preparing documents... done
> writing output... [ 8%] BIOM_LICENSE
> writing output... [ 16%] documentation/adding_metadata
> writing output... [ 25%] documentation/biom_conversion
> writing output... [ 33%] documentation/biom_format
> writing output... [ 41%] documentation/format_versions/biom-1.0
> writing output... [ 50%] documentation/format_versions/biom-2.0
> writing output... [ 58%] documentation/format_versions/biom-2.1
> writing output... [ 66%] documentation/index
> writing output... [ 75%] documentation/quick_usage_examples
> writing output... [ 83%] documentation/summarizing_biom_tables
> writing output... [ 91%] documentation/table_objects
> writing output... [100%] index
>
> /<<PKGBUILDDIR>>/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated
> /<<PKGBUILDDIR>>/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated
> /<<PKGBUILDDIR>>/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/quick_usage_examples' that doesn't have a title: no link will be generated
> /<<PKGBUILDDIR>>/doc/documentation/index.rst:11: WARNING: toctree contains reference to document 'documentation/table_objects' that doesn't have a title: no link will be generated
> generating indices...
> writing additional pages... search
> copying images... [100%] _static/biom-format.png
>
> copying static files... done
> copying extra files... done
> dumping search index in English (code: en) ... done
> dumping object inventory... done
> build succeeded, 6 warnings.
>
> The HTML pages are in build/html.
> PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b man doc build/man
> Running Sphinx v1.8.5
> making output directory...
> [autosummary] generating autosummary for: BIOM_LICENSE.rst, documentation/adding_metadata.rst, documentation/biom_conversion.rst, documentation/biom_format.rst, documentation/index.rst, documentation/quick_usage_examples.rst, documentation/summarizing_biom_tables.rst, documentation/table_objects.rst, index.rst
> Failed to import 'biom.table': no module named biom.table
> Failed to import 'biom': no module named biom
> building [mo]: targets for 0 po files that are out of date
> building [man]: all manpages
> updating environment: 12 added, 0 changed, 0 removed
> reading sources... [ 8%] BIOM_LICENSE
> reading sources... [ 16%] documentation/adding_metadata
> reading sources... [ 25%] documentation/biom_conversion
> reading sources... [ 33%] documentation/biom_format
> reading sources... [ 41%] documentation/format_versions/biom-1.0
> reading sources... [ 50%] documentation/format_versions/biom-2.0
> reading sources... [ 58%] documentation/format_versions/biom-2.1
> reading sources... [ 66%] documentation/index
> reading sources... [ 75%] documentation/quick_usage_examples
> reading sources... [ 83%] documentation/summarizing_biom_tables
> reading sources... [ 91%] documentation/table_objects
> reading sources... [100%] index
>
> WARNING: autodoc: failed to import module 'biom'; the following exception was raised:
> No module named 'matplotlib'
> WARNING: autodoc: failed to import module 'table' from module 'biom'; the following exception was raised:
> No module named 'matplotlib'
> looking for now-outdated files... none found
> pickling environment... done
> checking consistency... done
> writing... biom.1 { documentation/index documentation/biom_format documentation/format_versions/biom-1.0 documentation/format_versions/biom-2.0 documentation/format_versions/biom-2.1 documentation/quick_usage_examples documentation/table_objects documentation/biom_conversion documentation/adding_metadata documentation/summarizing_biom_tables BIOM_LICENSE }
> build succeeded, 2 warnings.
>
> The manual pages are in build/man.
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test -O--buildsystem=pybuild
> pybuild --test --test-nose -i python{version} -p "3.7 3.8"
> I: pybuild pybuild:284: cp -r /<<PKGBUILDDIR>>/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build
> I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build; python3.7 -m nose -v
> Failure: ModuleNotFoundError (No module named 'matplotlib') ... ERROR
>
> ======================================================================
> ERROR: Failure: ModuleNotFoundError (No module named 'matplotlib')
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
> raise self.exc_val.with_traceback(self.tb)
> File "/usr/lib/python3/dist-packages/nose/loader.py", line 417, in loadTestsFromName
> addr.filename, addr.module)
> File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
> return self.importFromDir(dir_path, fqname)
> File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
> mod = load_module(part_fqname, fh, filename, desc)
> File "/usr/lib/python3.7/imp.py", line 244, in load_module
> return load_package(name, filename)
> File "/usr/lib/python3.7/imp.py", line 216, in load_package
> return _load(spec)
> File "<frozen importlib._bootstrap>", line 696, in _load
> File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
> File "<frozen importlib._bootstrap_external>", line 728, in exec_module
> File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/__init__.py", line 53, in <module>
> from .table import Table
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build/biom/table.py", line 189, in <module>
> import pandas as pd
> File "/usr/lib/python3/dist-packages/pandas/__init__.py", line 182, in <module>
> import pandas.testing
> File "/usr/lib/python3/dist-packages/pandas/testing.py", line 7, in <module>
> from pandas.util.testing import (
> File "/usr/lib/python3/dist-packages/pandas/util/testing.py", line 18, in <module>
> from matplotlib.cbook import MatplotlibDeprecationWarning
> ModuleNotFoundError: No module named 'matplotlib'
>
> ----------------------------------------------------------------------
> Ran 1 test in 0.360s
>
> FAILED (errors=1)
> E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_biom-format/build; python3.7 -m nose -v
> dh_auto_test: error: pybuild --test --test-nose -i python{version} -p "3.7 3.8" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2020/04/02/python-biom-format_2.1.8+dfsg-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!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
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