(lEFSE) [lefse-1.1.2] pip install lefse Defaulting to user installation because normal site-packages is not writeable Collecting lefse Using cached lefse-1.1.2-py3-none-any.whl (60 kB) Collecting biom-format Using cached biom-format-2.1.10.tar.gz (11.7 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Collecting rpy2 Using cached rpy2-3.4.5.tar.gz (194 kB) Requirement already satisfied: numpy in /usr/lib64/python3.9/site-packages (from lefse) (1.20.1) Collecting matplotlib Using cached matplotlib-3.4.3-cp39-cp39-manylinux1_x86_64.whl (10.3 MB) Requirement already satisfied: six>=1.10.0 in /usr/lib/python3.9/site-packages (from biom-format->lefse) (1.15.0) Collecting h5py Using cached h5py-3.4.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) Collecting future>=0.16.0 Using cached future-0.18.2-py3-none-any.whl Collecting scipy>=1.3.1 Using cached scipy-1.7.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.5 MB) Collecting cython Using cached Cython-0.29.24-cp39-cp39-manylinux1_x86_64.whl (1.9 MB) Collecting pandas>=0.20.0 Using cached pandas-1.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.5 MB) Requirement already satisfied: click in /usr/lib/python3.9/site-packages (from biom-format->lefse) (7.1.2) Requirement already satisfied: pytz>=2017.3 in /usr/lib/python3.9/site-packages (from pandas>=0.20.0->biom-format->lefse) (2021.1) Requirement already satisfied: python-dateutil>=2.7.3 in /usr/lib/python3.9/site-packages (from pandas>=0.20.0->biom-format->lefse) (2.8.1) Collecting cycler>=0.10 Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Requirement already satisfied: pyparsing>=2.2.1 in /usr/lib/python3.9/site-packages (from matplotlib->lefse) (2.4.7) Requirement already satisfied: pillow>=6.2.0 in /usr/lib64/python3.9/site-packages (from matplotlib->lefse) (8.1.2) Collecting kiwisolver>=1.0.1 Using cached kiwisolver-1.3.1-cp39-cp39-manylinux1_x86_64.whl (1.2 MB) Requirement already satisfied: cffi>=1.10.0 in /usr/lib64/python3.9/site-packages (from rpy2->lefse) (1.14.5) Requirement already satisfied: jinja2 in /usr/lib/python3.9/site-packages (from rpy2->lefse) (2.11.3) Collecting tzlocal Using cached tzlocal-3.0-py3-none-any.whl (16 kB) Requirement already satisfied: pycparser in /usr/lib/python3.9/site-packages (from cffi>=1.10.0->rpy2->lefse) (2.20) Requirement already satisfied: MarkupSafe>=0.23 in /usr/lib64/python3.9/site-packages (from jinja2->rpy2->lefse) (1.1.1) Requirement already satisfied: ply==3.11 in /usr/lib/python3.9/site-packages (from pycparser->cffi>=1.10.0->rpy2->lefse) (3.11) Building wheels for collected packages: biom-format, rpy2 Building wheel for biom-format (PEP 517) ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3 /home/andrespara/.local/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpw54qdw3d cwd: /tmp/pip-install-hw4umimb/biom-format_9a1838e974b0451390558b19c7000e3a Complete output (188 lines): running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.9 creating build/lib.linux-x86_64-3.9/biom copying biom/err.py -> build/lib.linux-x86_64-3.9/biom copying biom/parse.py -> build/lib.linux-x86_64-3.9/biom copying biom/table.py -> build/lib.linux-x86_64-3.9/biom copying biom/__init__.py -> build/lib.linux-x86_64-3.9/biom copying biom/util.py -> build/lib.linux-x86_64-3.9/biom copying biom/exception.py -> build/lib.linux-x86_64-3.9/biom creating build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/table_ids.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/table_head.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/table_summarizer.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/table_converter.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/metadata_adder.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/uc_processor.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/table_normalizer.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/table_validator.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/metadata_exporter.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/__init__.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/util.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/table_subsetter.py -> build/lib.linux-x86_64-3.9/biom/cli copying biom/cli/installation_informer.py -> build/lib.linux-x86_64-3.9/biom/cli creating build/lib.linux-x86_64-3.9/biom/tests copying biom/tests/test_err.py -> build/lib.linux-x86_64-3.9/biom/tests copying biom/tests/test_util.py -> build/lib.linux-x86_64-3.9/biom/tests copying biom/tests/__init__.py -> build/lib.linux-x86_64-3.9/biom/tests copying biom/tests/test_table.py -> build/lib.linux-x86_64-3.9/biom/tests copying biom/tests/test_parse.py -> build/lib.linux-x86_64-3.9/biom/tests copying biom/tests/long_lines.py -> build/lib.linux-x86_64-3.9/biom/tests creating build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/__init__.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> build/lib.linux-x86_64-3.9/biom/tests/test_cli creating build/lib.linux-x86_64-3.9/biom/tests/test_data copying biom/tests/test_data/__init__.py -> build/lib.linux-x86_64-3.9/biom/tests/test_data 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 adding license file 'COPYING.txt' writing manifest file 'biom_format.egg-info/SOURCES.txt' copying biom/_filter.pyx -> build/lib.linux-x86_64-3.9/biom copying biom/_subsample.pyx -> build/lib.linux-x86_64-3.9/biom copying biom/_transform.pyx -> build/lib.linux-x86_64-3.9/biom creating build/lib.linux-x86_64-3.9/biom/assets copying biom/assets/exercise_api.py -> build/lib.linux-x86_64-3.9/biom/assets copying biom/assets/exercise_cli.sh -> build/lib.linux-x86_64-3.9/biom/assets creating build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.9/biom/tests/bench_tables creating build/lib.linux-x86_64-3.9/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/lib.linux-x86_64-3.9/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/lib.linux-x86_64-3.9/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> build/lib.linux-x86_64-3.9/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> build/lib.linux-x86_64-3.9/biom/tests/test_cli/test_data copying biom/tests/test_data/bad_table.txt -> build/lib.linux-x86_64-3.9/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> build/lib.linux-x86_64-3.9/biom/tests/test_data copying biom/tests/test_data/empty.biom -> build/lib.linux-x86_64-3.9/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> build/lib.linux-x86_64-3.9/biom/tests/test_data copying biom/tests/test_data/test.biom -> build/lib.linux-x86_64-3.9/biom/tests/test_data copying biom/tests/test_data/test.json -> build/lib.linux-x86_64-3.9/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> build/lib.linux-x86_64-3.9/biom/tests/test_data running build_ext building 'biom._filter' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/biom gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/tmp/pip-build-env-98fc1dm4/overlay/lib64/python3.9/site-packages/numpy/core/include -I/tmp/pip-build-env-98fc1dm4/overlay/lib64/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c biom/_filter.c -o build/temp.linux-x86_64-3.9/biom/_filter.o biom/_filter.c:28:10: error fatal: Python.h: No existe el fichero o el directorio 28 | #include "Python.h" | ^~~~~~~~~~ compilación terminada. error: command '/usr/bin/gcc' failed with exit code 1 ---------------------------------------- ERROR: Failed building wheel for biom-format Building wheel for rpy2 (setup.py) ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-hw4umimb/rpy2_e438aac0140d4cbfb9632cfdf753fd57/setup.py'"'"'; __file__='"'"'/tmp/pip-install-hw4umimb/rpy2_e438aac0140d4cbfb9632cfdf753fd57/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-v4nvlhpo cwd: /tmp/pip-install-hw4umimb/rpy2_e438aac0140d4cbfb9632cfdf753fd57/ Complete output (152 lines): ['cffi>=1.10.0', 'jinja2', 'pytz', 'tzlocal'] running bdist_wheel running build cffi mode: CFFI_MODE.ANY running build_py file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found creating build creating build/lib.linux-x86_64-3.9 creating build/lib.linux-x86_64-3.9/rpy2 copying ./rpy2/situation.py -> build/lib.linux-x86_64-3.9/rpy2 copying ./rpy2/rinterface.py -> build/lib.linux-x86_64-3.9/rpy2 copying ./rpy2/_rinterface_cffi_build.py -> build/lib.linux-x86_64-3.9/rpy2 copying ./rpy2/__init__.py -> build/lib.linux-x86_64-3.9/rpy2 creating build/lib.linux-x86_64-3.9/rpy2/rlike copying ./rpy2/rlike/indexing.py -> build/lib.linux-x86_64-3.9/rpy2/rlike copying ./rpy2/rlike/functional.py -> build/lib.linux-x86_64-3.9/rpy2/rlike copying ./rpy2/rlike/container.py -> build/lib.linux-x86_64-3.9/rpy2/rlike copying ./rpy2/rlike/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/rlike creating build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/sexp.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/openrlib.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/na_values.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/memorymanagement.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/ffi_proxy.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/embedded_mswin.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/embedded.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/conversion.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/callbacks.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/bufferprotocol.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/_rinterface_capi.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib creating build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/vectors.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/robject.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/pandas2ri.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/packages_utils.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/packages.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/numpy2ri.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/methods.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/language.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/help.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/functions.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/environments.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/conversion.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/constants.py -> build/lib.linux-x86_64-3.9/rpy2/robjects copying ./rpy2/robjects/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/robjects creating build/lib.linux-x86_64-3.9/rpy2/robjects/lib copying ./rpy2/robjects/lib/tidyr.py -> build/lib.linux-x86_64-3.9/rpy2/robjects/lib copying ./rpy2/robjects/lib/grid.py -> build/lib.linux-x86_64-3.9/rpy2/robjects/lib copying ./rpy2/robjects/lib/grdevices.py -> build/lib.linux-x86_64-3.9/rpy2/robjects/lib copying ./rpy2/robjects/lib/ggplot2.py -> build/lib.linux-x86_64-3.9/rpy2/robjects/lib copying ./rpy2/robjects/lib/dplyr.py -> build/lib.linux-x86_64-3.9/rpy2/robjects/lib copying ./rpy2/robjects/lib/dbplyr.py -> build/lib.linux-x86_64-3.9/rpy2/robjects/lib copying ./rpy2/robjects/lib/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/robjects/lib creating build/lib.linux-x86_64-3.9/rpy2/interactive copying ./rpy2/interactive/process_revents.py -> build/lib.linux-x86_64-3.9/rpy2/interactive copying ./rpy2/interactive/packages.py -> build/lib.linux-x86_64-3.9/rpy2/interactive copying ./rpy2/interactive/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/interactive creating build/lib.linux-x86_64-3.9/rpy2/ipython copying ./rpy2/ipython/rmagic.py -> build/lib.linux-x86_64-3.9/rpy2/ipython copying ./rpy2/ipython/html.py -> build/lib.linux-x86_64-3.9/rpy2/ipython copying ./rpy2/ipython/ggplot.py -> build/lib.linux-x86_64-3.9/rpy2/ipython copying ./rpy2/ipython/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/ipython creating build/lib.linux-x86_64-3.9/rpy2/tests copying ./rpy2/tests/utils.py -> build/lib.linux-x86_64-3.9/rpy2/tests copying ./rpy2/tests/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/tests creating build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vectors.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_str.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_pairlist.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_numpy.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_list.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_lang.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_int.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_float.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_complex.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_byte.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_vector_bool.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_threading.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_symbol.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_sexp.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_openrlib.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_noinitialization.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_na.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_memorymanagement.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_functions.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_externalptr.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_environment.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_endr.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_embedded_r.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_callbacks.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/test_bufferprotocol.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface copying ./rpy2/tests/rinterface/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rinterface package init file './rpy2/tests/rlike/__init__.py' not found (or not a regular file) creating build/lib.linux-x86_64-3.9/rpy2/tests/rlike copying ./rpy2/tests/rlike/test_indexing.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rlike copying ./rpy2/tests/rlike/test_functional.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rlike copying ./rpy2/tests/rlike/test_container.py -> build/lib.linux-x86_64-3.9/rpy2/tests/rlike creating build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_vector_factor.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_vector_extractdelegator.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_vector_datetime.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_vector.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_translated_function.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_serialization.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_rs4.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_robjects.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_pandas_conversions.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_packages_utils.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_packages.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_methods.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_language.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_help.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_function.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_formula.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_environment.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_dataframe.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_conversion_numpy.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_conversion.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/test_array.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects copying ./rpy2/tests/robjects/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects creating build/lib.linux-x86_64-3.9/rpy2/tests/ipython copying ./rpy2/tests/ipython/test_rmagic.py -> build/lib.linux-x86_64-3.9/rpy2/tests/ipython copying ./rpy2/tests/ipython/test_html.py -> build/lib.linux-x86_64-3.9/rpy2/tests/ipython copying ./rpy2/tests/ipython/test_ggplot.py -> build/lib.linux-x86_64-3.9/rpy2/tests/ipython copying ./rpy2/tests/ipython/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/tests/ipython creating build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/tests/robjects/lib/test_tidyr.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/tests/robjects/lib/test_grid.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/tests/robjects/lib/test_grdevices.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/tests/robjects/lib/test_ggplot2.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/tests/robjects/lib/test_dplyr.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/tests/robjects/lib/test_dbplyr.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/tests/robjects/lib/__init__.py -> build/lib.linux-x86_64-3.9/rpy2/tests/robjects/lib copying ./rpy2/rinterface_lib/R_API.h -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/R_API_eventloop.h -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/R_API_eventloop.c -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib copying ./rpy2/rinterface_lib/RPY2.h -> build/lib.linux-x86_64-3.9/rpy2/rinterface_lib file _rinterface_cffi_abi.py (for module _rinterface_cffi_abi) not found generating cffi module 'build/lib.linux-x86_64-3.9/_rinterface_cffi_abi.py' running build_ext generating cffi module 'build/temp.linux-x86_64-3.9/_rinterface_cffi_api.c' creating build/temp.linux-x86_64-3.9 building '_rinterface_cffi_api' extension creating build/temp.linux-x86_64-3.9/build creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9 gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DRPY2_RLEN_LONG=True -DR_INTERFACE_PTRS=True -Irpy2/rinterface_lib/ -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/_rinterface_cffi_api.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/_rinterface_cffi_api.o build/temp.linux-x86_64-3.9/_rinterface_cffi_api.c:50:14: error fatal: pyconfig.h: No existe el fichero o el directorio 50 | # include | ^~~~~~~~~~~~ compilación terminada. error: command '/usr/bin/gcc' failed with exit code 1 ---------------------------------------- ERROR: Failed building wheel for rpy2 Running setup.py clean for rpy2 Failed to build biom-format rpy2 ERROR: Could not build wheels for biom-format which use PEP 517 and cannot be installed directly