2026-08-27T00:06:05,473 Created temporary directory: /tmp/pip-ephem-wheel-cache-xa90j_3k 2026-08-27T00:06:05,475 Created temporary directory: /tmp/pip-build-tracker-2887lx2j 2026-08-27T00:06:05,476 Initialized build tracking at /tmp/pip-build-tracker-2887lx2j 2026-08-27T00:06:05,476 Created build tracker: /tmp/pip-build-tracker-2887lx2j 2026-08-27T00:06:05,477 Entered build tracker: /tmp/pip-build-tracker-2887lx2j 2026-08-27T00:06:05,477 Created temporary directory: /tmp/pip-wheel-qpwlutja 2026-08-27T00:06:05,480 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-08-27T00:06:05,483 Created temporary directory: /tmp/pip-ephem-wheel-cache-ps5coekp 2026-08-27T00:06:05,507 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-27T00:06:05,511 2 location(s) to search for versions of pybedtools: 2026-08-27T00:06:05,511 * https://pypi.org/simple/pybedtools/ 2026-08-27T00:06:05,511 * https://www.piwheels.org/simple/pybedtools/ 2026-08-27T00:06:05,511 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2026-08-27T00:06:05,512 Getting page https://pypi.org/simple/pybedtools/ 2026-08-27T00:06:05,514 Found index url https://pypi.org/simple 2026-08-27T00:06:05,759 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2026-08-27T00:06:05,773 Found link https://files.pythonhosted.org/packages/00/d9/aca9636b3e5b29f232fd6f60859f07f3420ec3c0712b50cb25c734a02a1f/pybedtools-0.2.2dev.tar.gz (from 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https://files.pythonhosted.org/packages/c2/a6/29fd41e86b38e7ca39eb7818c422e927534f2bd324c34cfd411cfca203b0/pybedtools-0.7.7.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.7 2026-08-27T00:06:05,789 Found link https://files.pythonhosted.org/packages/2d/ee/aa19e50e03e06c817d00eadf8b56824b9e473da8c3e8ca3b33a11717ee6f/pybedtools-0.7.8.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.8 2026-08-27T00:06:05,790 Found link https://files.pythonhosted.org/packages/7c/66/8aecffd830eddbd05c1c3e737f87220cef9f2a8358f1d692f85b30269520/pybedtools-0.7.9.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.9 2026-08-27T00:06:05,790 Found link https://files.pythonhosted.org/packages/09/57/e7668e8644c60413be05b8cc9c23aaea3a0717b4025843d8c26b7c4822af/pybedtools-0.7.10.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.10 2026-08-27T00:06:05,791 Found link https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.8.0 2026-08-27T00:06:05,792 Found link https://files.pythonhosted.org/packages/bf/14/152220f39cda6b9b72810eeed103c6ec78422429adabe3aafc3eaf6feb40/pybedtools-0.8.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.8.1 2026-08-27T00:06:05,792 Found link https://files.pythonhosted.org/packages/5b/57/46e9c8135954550d1d3a05db5b0462a264239f7f71c78af304bb47c5c900/pybedtools-0.8.2.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.8.2 2026-08-27T00:06:05,793 Found link https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.9.0 2026-08-27T00:06:05,794 Found link https://files.pythonhosted.org/packages/38/00/f07c17e25f9cc8e2d22b30aace73733e275b1804196f744f0178012a0d16/pybedtools-0.9.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.9.1 2026-08-27T00:06:05,795 Found link https://files.pythonhosted.org/packages/cc/90/cea4197772a029e925bd5d414108b5438d621dfbb1b0cc2627529d1ec524/pybedtools-0.10.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.10.0 2026-08-27T00:06:05,795 Found link https://files.pythonhosted.org/packages/93/c0/593dadfc238f1980cc7e612b9035f0f2890bea2b9a745c8dabadfe9d4da0/pybedtools-0.11.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.11.0 2026-08-27T00:06:05,796 Found link https://files.pythonhosted.org/packages/89/93/5878b1eed2e0b6662002d069763025e4374c16ad3d18d8e10a9fefac7b16/pybedtools-0.12.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.12.0 2026-08-27T00:06:05,797 Skipping link: No binaries permitted for pybedtools: 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https://files.pythonhosted.org/packages/91/f1/500be32a37e6722885b3a8d854a6e03eeff9fc612ab7ecd736ca3db3012f/pybedtools-0.12.1-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,799 Skipping link: No binaries permitted for pybedtools: https://files.pythonhosted.org/packages/ec/44/6964aa2f3cf63f7c81a7ff7127814db4aaa1a69202fc4f73950592ff7a0f/pybedtools-0.12.1-cp310-cp310-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,799 Skipping link: No binaries permitted for pybedtools: https://files.pythonhosted.org/packages/b7/bc/3d6f985e0872b13ee44b153021fed67e10b90b08be93a3bb19ad3b963a2b/pybedtools-0.12.1-cp310-cp310-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,800 Skipping link: No binaries permitted for pybedtools: 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https://files.pythonhosted.org/packages/26/74/34806dd01b64a6610eb1d6e798a38dd3bdea097a039c34186b1db0164621/pybedtools-0.12.1-cp314-cp314-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,811 Skipping link: No binaries permitted for pybedtools: https://files.pythonhosted.org/packages/d3/5b/77873cbfd90718d94467d07ee49df058cdfaa189923e7626dc058c18061b/pybedtools-0.12.1-cp314-cp314-macosx_11_0_arm64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,812 Skipping link: No binaries permitted for pybedtools: https://files.pythonhosted.org/packages/0c/e9/e83e1872a89c0008ece8f4259d087dfc61b49542c70744ae40625526c022/pybedtools-0.12.1-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,812 Skipping link: No binaries permitted for pybedtools: 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https://files.pythonhosted.org/packages/df/7c/7d0eeb87fc5f7db4c8291302eec8511c0a8ed1bcb46c918bd9666d4edd60/pybedtools-0.12.1-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,816 Skipping link: No binaries permitted for pybedtools: https://files.pythonhosted.org/packages/ab/22/8fdf092cf0bfb94eaf58632fd847f5e336a222977c64a31d4b8933cbde3c/pybedtools-0.12.1-cp39-cp39-musllinux_1_2_aarch64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,816 Skipping link: No binaries permitted for pybedtools: https://files.pythonhosted.org/packages/9a/bf/613e0fe341676943e16833636da58636cd0b757edfab9266cfd3977ef281/pybedtools-0.12.1-cp39-cp39-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/pybedtools/) 2026-08-27T00:06:05,817 Found link https://files.pythonhosted.org/packages/8c/0e/3b645561e25640cd5ffce29e7e1966e67b3ea49b7091910e5e2f43c203db/pybedtools-0.12.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.12.1 2026-08-27T00:06:05,818 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2026-08-27T00:06:05,819 Getting page https://www.piwheels.org/simple/pybedtools/ 2026-08-27T00:06:05,820 Found index url https://www.piwheels.org/simple 2026-08-27T00:06:06,039 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 2026-08-27T00:06:06,063 Skipping link: No binaries permitted for pybedtools: https://archive1.piwheels.org/simple/pybedtools/pybedtools-0.12.0-cp311-cp311-linux_armv6l.whl#sha256=9c87e5701fd763037dd3cee9811b7c9e1ac92592332d51f14cefffb2e7a19aa4 (from https://www.piwheels.org/simple/pybedtools/) 2026-08-27T00:06:06,064 Skipping link: No binaries permitted for pybedtools: https://archive1.piwheels.org/simple/pybedtools/pybedtools-0.12.0-cp311-cp311-linux_armv7l.whl#sha256=9c87e5701fd763037dd3cee9811b7c9e1ac92592332d51f14cefffb2e7a19aa4 (from https://www.piwheels.org/simple/pybedtools/) 2026-08-27T00:06:06,064 Skipping 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https://archive1.piwheels.org/simple/pybedtools/pybedtools-0.7.0-cp35-cp35m-linux_armv7l.whl#sha256=4a8563d567bdbcc4ae26db720acf3980bc4c63af83effdb6ca5e72145e8ddc6f (from https://www.piwheels.org/simple/pybedtools/) 2026-08-27T00:06:06,113 Skipping link: No binaries permitted for pybedtools: https://archive1.piwheels.org/simple/pybedtools/pybedtools-0.2.2.dev0-py3-none-any.whl#sha256=37efef7ea02a872e8d60cd34e5a36bd3e480eaccf7121bd8ac67647dd4550efc (from https://www.piwheels.org/simple/pybedtools/) 2026-08-27T00:06:06,114 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2026-08-27T00:06:06,114 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2026-08-27T00:06:06,137 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2026-08-27T00:06:06,155 Collecting pybedtools==0.12.1 2026-08-27T00:06:06,158 Created temporary directory: /tmp/pip-unpack-8ztukhp7 2026-08-27T00:06:06,819 Downloading pybedtools-0.12.1.tar.gz (12.7 MB) 2026-08-27T00:06:09,428 Added pybedtools==0.12.1 from https://files.pythonhosted.org/packages/8c/0e/3b645561e25640cd5ffce29e7e1966e67b3ea49b7091910e5e2f43c203db/pybedtools-0.12.1.tar.gz to build tracker '/tmp/pip-build-tracker-2887lx2j' 2026-08-27T00:06:09,433 Created temporary directory: /tmp/pip-build-env-py9y27ct 2026-08-27T00:06:09,438 Installing build dependencies: started 2026-08-27T00:06:09,439 Running command pip subprocess to install build dependencies 2026-08-27T00:06:10,567 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-08-27T00:06:11,023 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-08-27T00:06:11,046 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-08-27T00:06:12,856 Collecting setuptools>=61.0 2026-08-27T00:06:12,856 Obtaining dependency information for setuptools>=61.0 from https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata 2026-08-27T00:06:12,872 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl.metadata (6.6 kB) 2026-08-27T00:06:13,112 Collecting wheel 2026-08-27T00:06:13,113 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata 2026-08-27T00:06:13,127 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl.metadata (2.3 kB) 2026-08-27T00:06:15,324 Collecting Cython>=3.0 2026-08-27T00:06:15,325 Obtaining dependency information for Cython>=3.0 from https://www.piwheels.org/simple/cython/cython-3.3.0-cp311-cp311-linux_armv7l.whl.metadata 2026-08-27T00:06:15,344 Using cached https://www.piwheels.org/simple/cython/cython-3.3.0-cp311-cp311-linux_armv7l.whl.metadata (28 kB) 2026-08-27T00:06:15,536 Collecting packaging>=24.0 2026-08-27T00:06:15,536 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata 2026-08-27T00:06:15,551 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl.metadata (3.6 kB) 2026-08-27T00:06:15,821 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-08-27T00:06:16,636 Using cached https://www.piwheels.org/simple/cython/cython-3.3.0-cp311-cp311-linux_armv7l.whl (11.2 MB) 2026-08-27T00:06:16,845 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-08-27T00:06:16,917 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-27T00:06:16,948 Using cached https://www.piwheels.org/simple/wheel/wheel-0.48.0-py3-none-any.whl (33 kB) 2026-08-27T00:06:17,732 Using cached https://www.piwheels.org/simple/cython/cython-3.3.0-cp311-cp311-linux_armv7l.whl (11.2 MB) 2026-08-27T00:06:18,042 Using cached https://www.piwheels.org/simple/packaging/packaging-26.3-py3-none-any.whl (129 kB) 2026-08-27T00:06:18,121 Using cached https://www.piwheels.org/simple/setuptools/setuptools-84.0.0-py3-none-any.whl (818 kB) 2026-08-27T00:06:20,810 Installing collected packages: setuptools, packaging, Cython, wheel 2026-08-27T00:06:27,080 Creating /tmp/pip-build-env-py9y27ct/overlay/local/bin 2026-08-27T00:06:27,082 changing mode of /tmp/pip-build-env-py9y27ct/overlay/local/bin/cygdb to 755 2026-08-27T00:06:27,083 changing mode of /tmp/pip-build-env-py9y27ct/overlay/local/bin/cython to 755 2026-08-27T00:06:27,085 changing mode of /tmp/pip-build-env-py9y27ct/overlay/local/bin/cythonize to 755 2026-08-27T00:06:27,219 changing mode of /tmp/pip-build-env-py9y27ct/overlay/local/bin/wheel to 755 2026-08-27T00:06:27,248 Successfully installed Cython-3.3.0 packaging-26.3 setuptools-84.0.0 wheel-0.48.0 2026-08-27T00:06:27,643 Installing build dependencies: finished with status 'done' 2026-08-27T00:06:27,652 Getting requirements to build wheel: started 2026-08-27T00:06:27,654 Running command Getting requirements to build wheel 2026-08-27T00:06:28,553 /tmp/pip-build-env-py9y27ct/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T00:06:28,553 !! 2026-08-27T00:06:28,554 ******************************************************************************** 2026-08-27T00:06:28,554 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T00:06:28,555 License :: OSI Approved :: MIT License 2026-08-27T00:06:28,557 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T00:06:28,557 ******************************************************************************** 2026-08-27T00:06:28,558 !! 2026-08-27T00:06:28,559 dist._finalize_license_expression() 2026-08-27T00:06:28,560 /tmp/pip-build-env-py9y27ct/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T00:06:28,560 !! 2026-08-27T00:06:28,562 ******************************************************************************** 2026-08-27T00:06:28,562 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T00:06:28,564 License :: OSI Approved :: MIT License 2026-08-27T00:06:28,565 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T00:06:28,566 ******************************************************************************** 2026-08-27T00:06:28,567 !! 2026-08-27T00:06:28,568 self._finalize_license_expression() 2026-08-27T00:06:28,568 running egg_info 2026-08-27T00:06:28,569 writing pybedtools.egg-info/PKG-INFO 2026-08-27T00:06:28,572 writing dependency_links to pybedtools.egg-info/dependency_links.txt 2026-08-27T00:06:28,574 writing requirements to pybedtools.egg-info/requires.txt 2026-08-27T00:06:28,575 writing top-level names to pybedtools.egg-info/top_level.txt 2026-08-27T00:06:28,611 reading manifest file 'pybedtools.egg-info/SOURCES.txt' 2026-08-27T00:06:28,619 reading manifest template 'MANIFEST.in' 2026-08-27T00:06:28,746 warning: no files found matching '*.c' under directory 'pybedtools' 2026-08-27T00:06:28,748 warning: no previously-included files matching '__pycache__' found under directory '*' 2026-08-27T00:06:28,749 warning: no previously-included files matching '*.py[co]' found under directory '*' 2026-08-27T00:06:28,750 adding license file 'LICENSE.txt' 2026-08-27T00:06:28,759 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2026-08-27T00:06:28,881 Getting requirements to build wheel: finished with status 'done' 2026-08-27T00:06:28,885 Created temporary directory: /tmp/pip-modern-metadata-j9ud04_u 2026-08-27T00:06:28,887 Preparing metadata (pyproject.toml): started 2026-08-27T00:06:28,888 Running command Preparing metadata (pyproject.toml) 2026-08-27T00:06:29,972 /tmp/pip-build-env-py9y27ct/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T00:06:29,972 !! 2026-08-27T00:06:29,973 ******************************************************************************** 2026-08-27T00:06:29,973 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T00:06:29,974 License :: OSI Approved :: MIT License 2026-08-27T00:06:29,975 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T00:06:29,975 ******************************************************************************** 2026-08-27T00:06:29,976 !! 2026-08-27T00:06:29,977 dist._finalize_license_expression() 2026-08-27T00:06:29,977 /tmp/pip-build-env-py9y27ct/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T00:06:29,978 !! 2026-08-27T00:06:29,978 ******************************************************************************** 2026-08-27T00:06:29,979 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T00:06:29,980 License :: OSI Approved :: MIT License 2026-08-27T00:06:29,981 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T00:06:29,981 ******************************************************************************** 2026-08-27T00:06:29,982 !! 2026-08-27T00:06:29,983 self._finalize_license_expression() 2026-08-27T00:06:29,983 running dist_info 2026-08-27T00:06:29,995 creating /tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info 2026-08-27T00:06:29,996 writing /tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info/PKG-INFO 2026-08-27T00:06:29,999 writing dependency_links to /tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info/dependency_links.txt 2026-08-27T00:06:30,001 writing requirements to /tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info/requires.txt 2026-08-27T00:06:30,002 writing top-level names to /tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info/top_level.txt 2026-08-27T00:06:30,003 writing manifest file '/tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info/SOURCES.txt' 2026-08-27T00:06:30,034 reading manifest file '/tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info/SOURCES.txt' 2026-08-27T00:06:30,036 reading manifest template 'MANIFEST.in' 2026-08-27T00:06:30,164 warning: no files found matching '*.c' under directory 'pybedtools' 2026-08-27T00:06:30,166 warning: no previously-included files matching '__pycache__' found under directory '*' 2026-08-27T00:06:30,167 warning: no previously-included files matching '*.py[co]' found under directory '*' 2026-08-27T00:06:30,168 adding license file 'LICENSE.txt' 2026-08-27T00:06:30,176 writing manifest file '/tmp/pip-modern-metadata-j9ud04_u/pybedtools.egg-info/SOURCES.txt' 2026-08-27T00:06:30,177 creating '/tmp/pip-modern-metadata-j9ud04_u/pybedtools-0.12.1.dist-info' 2026-08-27T00:06:30,324 Preparing metadata (pyproject.toml): finished with status 'done' 2026-08-27T00:06:30,329 Source in /tmp/pip-wheel-qpwlutja/pybedtools_4b2fcbb5fd044674bce5aa59a2cc45bd has version 0.12.1, which satisfies requirement pybedtools==0.12.1 from https://files.pythonhosted.org/packages/8c/0e/3b645561e25640cd5ffce29e7e1966e67b3ea49b7091910e5e2f43c203db/pybedtools-0.12.1.tar.gz 2026-08-27T00:06:30,330 Removed pybedtools==0.12.1 from https://files.pythonhosted.org/packages/8c/0e/3b645561e25640cd5ffce29e7e1966e67b3ea49b7091910e5e2f43c203db/pybedtools-0.12.1.tar.gz from build tracker '/tmp/pip-build-tracker-2887lx2j' 2026-08-27T00:06:30,334 Created temporary directory: /tmp/pip-unpack-5pr5a2z2 2026-08-27T00:06:30,335 Building wheels for collected packages: pybedtools 2026-08-27T00:06:30,339 Created temporary directory: /tmp/pip-wheel-w3gnfrhx 2026-08-27T00:06:30,340 Destination directory: /tmp/pip-wheel-w3gnfrhx 2026-08-27T00:06:30,342 Building wheel for pybedtools (pyproject.toml): started 2026-08-27T00:06:30,343 Running command Building wheel for pybedtools (pyproject.toml) 2026-08-27T00:06:31,171 /tmp/pip-build-env-py9y27ct/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T00:06:31,171 !! 2026-08-27T00:06:31,172 ******************************************************************************** 2026-08-27T00:06:31,172 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T00:06:31,173 License :: OSI Approved :: MIT License 2026-08-27T00:06:31,174 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T00:06:31,175 ******************************************************************************** 2026-08-27T00:06:31,176 !! 2026-08-27T00:06:31,176 dist._finalize_license_expression() 2026-08-27T00:06:31,177 /tmp/pip-build-env-py9y27ct/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-08-27T00:06:31,177 !! 2026-08-27T00:06:31,178 ******************************************************************************** 2026-08-27T00:06:31,179 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-08-27T00:06:31,180 License :: OSI Approved :: MIT License 2026-08-27T00:06:31,181 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-08-27T00:06:31,181 ******************************************************************************** 2026-08-27T00:06:31,183 !! 2026-08-27T00:06:31,183 self._finalize_license_expression() 2026-08-27T00:06:31,184 running bdist_wheel 2026-08-27T00:06:31,189 running build 2026-08-27T00:06:31,190 running build_py 2026-08-27T00:06:31,197 creating build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,199 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,204 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,206 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,208 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,209 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,213 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,215 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,217 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,220 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,222 copying pybedtools/paths.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,223 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,226 creating build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,227 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,229 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,231 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,234 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,236 copying pybedtools/test/genomepy_integration.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,237 copying pybedtools/test/test_pathlib.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,239 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,241 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,243 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,245 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,246 copying pybedtools/test/test_1.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,250 copying pybedtools/test/test_issues.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,252 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,255 creating build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,256 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,259 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,261 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,263 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,265 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,267 copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,269 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib 2026-08-27T00:06:31,272 creating build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,273 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,274 running egg_info 2026-08-27T00:06:31,286 writing pybedtools.egg-info/PKG-INFO 2026-08-27T00:06:31,289 writing dependency_links to pybedtools.egg-info/dependency_links.txt 2026-08-27T00:06:31,291 writing requirements to pybedtools.egg-info/requires.txt 2026-08-27T00:06:31,291 writing top-level names to pybedtools.egg-info/top_level.txt 2026-08-27T00:06:31,317 reading manifest file 'pybedtools.egg-info/SOURCES.txt' 2026-08-27T00:06:31,325 reading manifest template 'MANIFEST.in' 2026-08-27T00:06:31,453 warning: no files found matching '*.c' under directory 'pybedtools' 2026-08-27T00:06:31,454 warning: no previously-included files matching '__pycache__' found under directory '*' 2026-08-27T00:06:31,456 warning: no previously-included files matching '*.py[co]' found under directory '*' 2026-08-27T00:06:31,457 adding license file 'LICENSE.txt' 2026-08-27T00:06:31,466 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2026-08-27T00:06:31,469 /tmp/pip-build-env-py9y27ct/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. 2026-08-27T00:06:31,469 !! 2026-08-27T00:06:31,470 ******************************************************************************** 2026-08-27T00:06:31,471 ############################ 2026-08-27T00:06:31,472 # Package would be ignored # 2026-08-27T00:06:31,472 ############################ 2026-08-27T00:06:31,473 Python recognizes 'pybedtools.include' as an importable package[^1], 2026-08-27T00:06:31,473 but it is absent from setuptools' `packages` configuration. 2026-08-27T00:06:31,475 This leads to an ambiguous overall configuration. If you want to distribute this 2026-08-27T00:06:31,475 package, please make sure that 'pybedtools.include' is explicitly added 2026-08-27T00:06:31,476 to the `packages` configuration field. 2026-08-27T00:06:31,477 Alternatively, you can also rely on setuptools' discovery methods 2026-08-27T00:06:31,477 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-08-27T00:06:31,477 instead of `find_packages(...)`/`find:`). 2026-08-27T00:06:31,478 You can read more about "package discovery" on setuptools documentation page: 2026-08-27T00:06:31,479 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-08-27T00:06:31,480 If you don't want 'pybedtools.include' to be distributed and are 2026-08-27T00:06:31,480 already explicitly excluding 'pybedtools.include' via 2026-08-27T00:06:31,481 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-08-27T00:06:31,481 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-08-27T00:06:31,481 combination with a more fine grained `package-data` configuration. 2026-08-27T00:06:31,482 You can read more about "package data files" on setuptools documentation page: 2026-08-27T00:06:31,483 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-08-27T00:06:31,484 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-08-27T00:06:31,485 even if it does not contain any `.py` files. 2026-08-27T00:06:31,485 On the other hand, currently there is no concept of package data 2026-08-27T00:06:31,486 directory, all directories are treated like packages. 2026-08-27T00:06:31,486 ******************************************************************************** 2026-08-27T00:06:31,487 !! 2026-08-27T00:06:31,488 check.warn(importable) 2026-08-27T00:06:31,488 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,490 copying pybedtools/cbedtools.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,515 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,517 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,520 copying pybedtools/featurefuncs.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,535 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools 2026-08-27T00:06:31,538 creating build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,539 copying pybedtools/include/bedFile.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,542 copying pybedtools/include/bedFile.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,545 copying pybedtools/include/fileType.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,548 copying pybedtools/include/fileType.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,550 copying pybedtools/include/gzstream.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,553 copying pybedtools/include/gzstream.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,556 copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include 2026-08-27T00:06:31,558 copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,560 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,563 copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,566 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,569 copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,571 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,573 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,576 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,578 copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,580 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,583 copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,585 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,589 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,591 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,594 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,596 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,599 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,648 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,650 copying pybedtools/test/data/issue319.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,652 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,654 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,656 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,658 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,661 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,663 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,779 copying pybedtools/test/data/genome.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,781 copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,783 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,785 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,793 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,796 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,798 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,800 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,802 copying pybedtools/test/data/gdc.cram -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,804 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,808 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,812 copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,814 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,816 copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,818 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,820 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,822 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,824 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,826 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,828 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,831 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,835 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,837 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,839 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,841 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,845 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,848 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,850 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,880 copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,882 copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,884 copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,889 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,891 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,897 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,899 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,901 copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,904 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,913 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,915 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,919 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,921 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,923 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,925 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data 2026-08-27T00:06:31,929 copying pybedtools/test/gchart-expected.png -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,931 copying pybedtools/test/mpl-expected.png -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,934 copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,936 copying pybedtools/test/test_cases.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,939 copying pybedtools/test/test_merge215.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,941 copying pybedtools/test/test_merge227.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,943 copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,945 copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test 2026-08-27T00:06:31,975 running build_ext 2026-08-27T00:06:33,167 building 'pybedtools.cbedtools' extension 2026-08-27T00:06:33,170 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o 2026-08-27T00:06:37,155 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx_Unpacked___Pyx_PyLong_AndObjC(PyObject*, PyObject*, long int, int, int)’: 2026-08-27T00:06:37,156 pybedtools/cbedtools.cpp:28855:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2026-08-27T00:06:37,157 28855 | if ((intval & PyLong_MASK) == intval) { 2026-08-27T00:06:37,158 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2026-08-27T00:07:06,633 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o 2026-08-27T00:07:14,743 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o 2026-08-27T00:07:16,448 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o 2026-08-27T00:07:18,231 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so 2026-08-27T00:07:18,645 building 'pybedtools.featurefuncs' extension 2026-08-27T00:07:18,646 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/featurefuncs.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/featurefuncs.o 2026-08-27T00:07:37,094 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o 2026-08-27T00:07:45,236 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o 2026-08-27T00:07:46,925 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o 2026-08-27T00:07:48,710 arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/pybedtools/featurefuncs.o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so 2026-08-27T00:07:49,083 installing to build/bdist.linux-armv7l/wheel 2026-08-27T00:07:49,083 running install 2026-08-27T00:07:49,106 running install_lib 2026-08-27T00:07:49,112 creating build/bdist.linux-armv7l/wheel 2026-08-27T00:07:49,116 creating build/bdist.linux-armv7l/wheel/pybedtools 2026-08-27T00:07:49,117 copying build/lib.linux-armv7l-cpython-311/pybedtools/bedtool.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,122 copying build/lib.linux-armv7l-cpython-311/pybedtools/logger.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,124 copying build/lib.linux-armv7l-cpython-311/pybedtools/_Window.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,127 copying build/lib.linux-armv7l-cpython-311/pybedtools/filenames.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,129 copying build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,131 copying build/lib.linux-armv7l-cpython-311/pybedtools/stats.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,135 creating build/bdist.linux-armv7l/wheel/pybedtools/contrib 2026-08-27T00:07:49,136 copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/plotting.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib 2026-08-27T00:07:49,139 copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib 2026-08-27T00:07:49,141 copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/bigwig.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib 2026-08-27T00:07:49,143 copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/venn_maker.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib 2026-08-27T00:07:49,145 copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib 2026-08-27T00:07:49,147 copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib 2026-08-27T00:07:49,150 copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/bigbed.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib 2026-08-27T00:07:49,152 copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,184 copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,238 creating build/bdist.linux-armv7l/wheel/pybedtools/include 2026-08-27T00:07:49,239 copying build/lib.linux-armv7l-cpython-311/pybedtools/include/fileType.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include 2026-08-27T00:07:49,241 copying build/lib.linux-armv7l-cpython-311/pybedtools/include/gzstream.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include 2026-08-27T00:07:49,244 copying build/lib.linux-armv7l-cpython-311/pybedtools/include/gzstream.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include 2026-08-27T00:07:49,246 copying build/lib.linux-armv7l-cpython-311/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include 2026-08-27T00:07:49,248 copying build/lib.linux-armv7l-cpython-311/pybedtools/include/bedFile.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include 2026-08-27T00:07:49,251 copying build/lib.linux-armv7l-cpython-311/pybedtools/include/fileType.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include 2026-08-27T00:07:49,253 copying build/lib.linux-armv7l-cpython-311/pybedtools/include/bedFile.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include 2026-08-27T00:07:49,255 copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.pxd -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,257 copying build/lib.linux-armv7l-cpython-311/pybedtools/genome_registry.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,261 copying build/lib.linux-armv7l-cpython-311/pybedtools/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,263 copying build/lib.linux-armv7l-cpython-311/pybedtools/version.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,265 copying build/lib.linux-armv7l-cpython-311/pybedtools/helpers.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,268 creating build/bdist.linux-armv7l/wheel/pybedtools/test 2026-08-27T00:07:49,269 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/tfuncs.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,271 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,274 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_iter.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,276 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_contrib.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,278 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_gzip_support.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,280 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/genomepy_integration.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,282 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/gchart-expected.png -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,286 creating build/bdist.linux-armv7l/wheel/pybedtools/test/data 2026-08-27T00:07:49,287 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,289 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/venn.b.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,291 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,293 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,295 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/164.gtf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,297 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/m1.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,299 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/a.links.html -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,301 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,303 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,304 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,306 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,308 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,311 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/b.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,313 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,315 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/exons.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,317 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test.fa -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,319 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/x.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,361 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,362 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue319.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,364 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,366 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,368 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/a.igv_script -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,370 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/venn.c.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,372 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/bedpe.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,374 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,501 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/genome.fa -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,503 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,504 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/small.fastq -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,506 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,514 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test.fa.fai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,516 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/y.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,518 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/d.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,520 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/v.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,522 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.cram -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,523 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,526 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,528 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,532 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,534 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,536 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,537 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,539 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,541 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,542 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,544 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/expand_test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,546 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,549 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,554 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,555 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,557 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,559 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,563 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,566 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/c.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,567 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/x.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,598 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue_121.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,600 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,602 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,607 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,609 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/hg19.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,615 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,617 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,619 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,622 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,633 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,635 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,639 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/a.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,641 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/reads.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,643 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/small.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,645 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data 2026-08-27T00:07:49,650 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_pathlib.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,652 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/mpl-expected.png -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,655 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,657 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/regression_tests.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,660 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_merge227.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,662 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_helpers.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,665 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_len_leak.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,667 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_merge215.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,669 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,672 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_cases.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,675 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_1.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,678 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_issues.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,681 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_cbedtools.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,684 copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test 2026-08-27T00:07:49,686 copying build/lib.linux-armv7l-cpython-311/pybedtools/settings.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,689 copying build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,727 copying build/lib.linux-armv7l-cpython-311/pybedtools/paths.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,729 copying build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,744 copying build/lib.linux-armv7l-cpython-311/pybedtools/parallel.py -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,747 copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools 2026-08-27T00:07:49,749 running install_egg_info 2026-08-27T00:07:49,755 Copying pybedtools.egg-info to build/bdist.linux-armv7l/wheel/./pybedtools-0.12.1-py3.11.egg-info 2026-08-27T00:07:49,768 running install_scripts 2026-08-27T00:07:49,789 creating build/bdist.linux-armv7l/wheel/pybedtools-0.12.1.dist-info/WHEEL 2026-08-27T00:07:49,793 creating '/tmp/pip-wheel-w3gnfrhx/.tmp-plvnvlx9/pybedtools-0.12.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-08-27T00:07:49,797 adding 'pybedtools/_Window.pyx' 2026-08-27T00:07:49,799 adding 'pybedtools/__init__.py' 2026-08-27T00:07:49,816 adding 'pybedtools/bedtool.py' 2026-08-27T00:07:49,924 adding 'pybedtools/cbedtools.cpp' 2026-08-27T00:07:50,470 adding 'pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so' 2026-08-27T00:07:50,488 adding 'pybedtools/cbedtools.pxd' 2026-08-27T00:07:50,492 adding 'pybedtools/cbedtools.pyx' 2026-08-27T00:07:50,559 adding 'pybedtools/featurefuncs.cpp' 2026-08-27T00:07:50,892 adding 'pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so' 2026-08-27T00:07:50,906 adding 'pybedtools/featurefuncs.pyx' 2026-08-27T00:07:50,908 adding 'pybedtools/filenames.py' 2026-08-27T00:07:50,917 adding 'pybedtools/genome_registry.py' 2026-08-27T00:07:50,921 adding 'pybedtools/helpers.py' 2026-08-27T00:07:50,923 adding 'pybedtools/logger.py' 2026-08-27T00:07:50,925 adding 'pybedtools/parallel.py' 2026-08-27T00:07:50,927 adding 'pybedtools/paths.py' 2026-08-27T00:07:50,929 adding 'pybedtools/settings.py' 2026-08-27T00:07:50,930 adding 'pybedtools/stats.py' 2026-08-27T00:07:50,932 adding 'pybedtools/version.py' 2026-08-27T00:07:50,934 adding 'pybedtools/contrib/__init__.py' 2026-08-27T00:07:50,936 adding 'pybedtools/contrib/bigbed.py' 2026-08-27T00:07:50,938 adding 'pybedtools/contrib/bigwig.py' 2026-08-27T00:07:50,940 adding 'pybedtools/contrib/intersection_matrix.py' 2026-08-27T00:07:50,943 adding 'pybedtools/contrib/long_range_interaction.py' 2026-08-27T00:07:50,946 adding 'pybedtools/contrib/plotting.py' 2026-08-27T00:07:50,949 adding 'pybedtools/contrib/venn_maker.py' 2026-08-27T00:07:50,952 adding 'pybedtools/include/bedFile.cpp' 2026-08-27T00:07:50,955 adding 'pybedtools/include/bedFile.h' 2026-08-27T00:07:50,957 adding 'pybedtools/include/fileType.cpp' 2026-08-27T00:07:50,958 adding 'pybedtools/include/fileType.h' 2026-08-27T00:07:50,960 adding 'pybedtools/include/gzstream.cpp' 2026-08-27T00:07:50,962 adding 'pybedtools/include/gzstream.h' 2026-08-27T00:07:50,964 adding 'pybedtools/include/lineFileUtilities.h' 2026-08-27T00:07:50,967 adding 'pybedtools/test/__init__.py' 2026-08-27T00:07:50,969 adding 'pybedtools/test/gchart-expected.png' 2026-08-27T00:07:50,971 adding 'pybedtools/test/genomepy_integration.py' 2026-08-27T00:07:50,974 adding 'pybedtools/test/mpl-expected.png' 2026-08-27T00:07:50,976 adding 'pybedtools/test/prevent_open_file_regression' 2026-08-27T00:07:50,978 adding 'pybedtools/test/regression_tests.py' 2026-08-27T00:07:50,984 adding 'pybedtools/test/test_1.py' 2026-08-27T00:07:50,988 adding 'pybedtools/test/test_cases.yaml' 2026-08-27T00:07:50,990 adding 'pybedtools/test/test_cbedtools.py' 2026-08-27T00:07:50,992 adding 'pybedtools/test/test_contrib.py' 2026-08-27T00:07:50,994 adding 'pybedtools/test/test_gzip_support.py' 2026-08-27T00:07:50,996 adding 'pybedtools/test/test_helpers.py' 2026-08-27T00:07:51,000 adding 'pybedtools/test/test_issues.py' 2026-08-27T00:07:51,003 adding 'pybedtools/test/test_iter.py' 2026-08-27T00:07:51,004 adding 'pybedtools/test/test_len_leak.py' 2026-08-27T00:07:51,006 adding 'pybedtools/test/test_merge215.yaml' 2026-08-27T00:07:51,007 adding 'pybedtools/test/test_merge227.yaml' 2026-08-27T00:07:51,009 adding 'pybedtools/test/test_pathlib.py' 2026-08-27T00:07:51,011 adding 'pybedtools/test/test_shuffle215.yaml' 2026-08-27T00:07:51,012 adding 'pybedtools/test/test_shuffle227.yaml' 2026-08-27T00:07:51,013 adding 'pybedtools/test/tfuncs.py' 2026-08-27T00:07:51,016 adding 'pybedtools/test/data/1000genomes-example.vcf' 2026-08-27T00:07:51,017 adding 'pybedtools/test/data/164.gtf' 2026-08-27T00:07:51,030 adding 'pybedtools/test/data/BEAF_Kc_Bushey_2009.bed' 2026-08-27T00:07:51,043 adding 'pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed' 2026-08-27T00:07:51,053 adding 'pybedtools/test/data/CTCF_Kc_Bushey_2009.bed' 2026-08-27T00:07:51,065 adding 'pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed' 2026-08-27T00:07:51,087 adding 'pybedtools/test/data/Cp190_Kc_Bushey_2009.bed' 2026-08-27T00:07:51,110 adding 'pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed' 2026-08-27T00:07:51,126 adding 'pybedtools/test/data/SuHw_Kc_Bushey_2009.bed' 2026-08-27T00:07:51,141 adding 'pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed' 2026-08-27T00:07:51,143 adding 'pybedtools/test/data/__init__.py' 2026-08-27T00:07:51,144 adding 'pybedtools/test/data/a.bed' 2026-08-27T00:07:51,145 adding 'pybedtools/test/data/a.igv_script' 2026-08-27T00:07:51,146 adding 'pybedtools/test/data/a.links.html' 2026-08-27T00:07:51,147 adding 'pybedtools/test/data/b.bed' 2026-08-27T00:07:51,148 adding 'pybedtools/test/data/bedpe.bed' 2026-08-27T00:07:51,149 adding 'pybedtools/test/data/bedpe2.bed' 2026-08-27T00:07:51,151 adding 'pybedtools/test/data/c.gff' 2026-08-27T00:07:51,152 adding 'pybedtools/test/data/d.gff' 2026-08-27T00:07:51,153 adding 'pybedtools/test/data/democonfig.yaml' 2026-08-27T00:07:51,199 adding 'pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz' 2026-08-27T00:07:51,248 adding 'pybedtools/test/data/dm3-chr2L-5M.gff.gz' 2026-08-27T00:07:51,251 adding 'pybedtools/test/data/example.narrowPeak' 2026-08-27T00:07:51,253 adding 'pybedtools/test/data/exons.gff' 2026-08-27T00:07:51,254 adding 'pybedtools/test/data/expand_test.bed' 2026-08-27T00:07:51,255 adding 'pybedtools/test/data/gdc.1.100.bam' 2026-08-27T00:07:51,256 adding 'pybedtools/test/data/gdc.1.100.bam.bai' 2026-08-27T00:07:51,257 adding 'pybedtools/test/data/gdc.50.200.bam' 2026-08-27T00:07:51,258 adding 'pybedtools/test/data/gdc.50.200.bam.bai' 2026-08-27T00:07:51,260 adding 'pybedtools/test/data/gdc.bam' 2026-08-27T00:07:51,261 adding 'pybedtools/test/data/gdc.bed' 2026-08-27T00:07:51,262 adding 'pybedtools/test/data/gdc.cram' 2026-08-27T00:07:51,263 adding 'pybedtools/test/data/gdc.gff' 2026-08-27T00:07:51,264 adding 'pybedtools/test/data/gdc.gff.gz' 2026-08-27T00:07:51,266 adding 'pybedtools/test/data/gdc.othersort.bam' 2026-08-27T00:07:51,267 adding 'pybedtools/test/data/gdc.sorted.bam' 2026-08-27T00:07:51,268 adding 'pybedtools/test/data/gdc.sorted.bam.bai' 2026-08-27T00:07:51,269 adding 'pybedtools/test/data/genome.fa' 2026-08-27T00:07:51,293 adding 'pybedtools/test/data/hg19.gff' 2026-08-27T00:07:51,295 adding 'pybedtools/test/data/hg38-base.bed' 2026-08-27T00:07:51,297 adding 'pybedtools/test/data/hg38-problem.bed' 2026-08-27T00:07:51,298 adding 'pybedtools/test/data/issue319.bed' 2026-08-27T00:07:51,308 adding 'pybedtools/test/data/issue319.out.bed' 2026-08-27T00:07:51,312 adding 'pybedtools/test/data/issue319.vcf.gz' 2026-08-27T00:07:51,314 adding 'pybedtools/test/data/issue_121.bam' 2026-08-27T00:07:51,315 adding 'pybedtools/test/data/m1.bed' 2026-08-27T00:07:51,316 adding 'pybedtools/test/data/mm9.bed12' 2026-08-27T00:07:51,317 adding 'pybedtools/test/data/multibamcov_test.bed' 2026-08-27T00:07:51,319 adding 'pybedtools/test/data/reads.bam' 2026-08-27T00:07:51,324 adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed' 2026-08-27T00:07:51,327 adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz' 2026-08-27T00:07:51,328 adding 'pybedtools/test/data/small.bam' 2026-08-27T00:07:51,329 adding 'pybedtools/test/data/small.fastq' 2026-08-27T00:07:52,264 adding 'pybedtools/test/data/snps.bed.gz' 2026-08-27T00:07:52,318 adding 'pybedtools/test/data/tag_test1.bed' 2026-08-27T00:07:52,319 adding 'pybedtools/test/data/tag_test2.bed' 2026-08-27T00:07:52,320 adding 'pybedtools/test/data/test.fa' 2026-08-27T00:07:52,321 adding 'pybedtools/test/data/test.fa.fai' 2026-08-27T00:07:52,322 adding 'pybedtools/test/data/test_bedpe.bed' 2026-08-27T00:07:52,323 adding 'pybedtools/test/data/test_peaks.bed' 2026-08-27T00:07:52,324 adding 'pybedtools/test/data/test_tsses.bed' 2026-08-27T00:07:52,325 adding 'pybedtools/test/data/v.vcf' 2026-08-27T00:07:52,326 adding 'pybedtools/test/data/vcf-stderr-test.bed' 2026-08-27T00:07:52,328 adding 'pybedtools/test/data/vcf-stderr-test.vcf' 2026-08-27T00:07:52,329 adding 'pybedtools/test/data/venn.b.bed' 2026-08-27T00:07:52,331 adding 'pybedtools/test/data/venn.c.bed' 2026-08-27T00:07:52,536 adding 'pybedtools/test/data/x.bam' 2026-08-27T00:07:52,881 adding 'pybedtools/test/data/x.bed' 2026-08-27T00:07:52,898 adding 'pybedtools/test/data/y.bam' 2026-08-27T00:07:52,901 adding 'pybedtools-0.12.1.dist-info/licenses/LICENSE.txt' 2026-08-27T00:07:52,902 adding 'pybedtools-0.12.1.dist-info/METADATA' 2026-08-27T00:07:52,903 adding 'pybedtools-0.12.1.dist-info/WHEEL' 2026-08-27T00:07:52,904 adding 'pybedtools-0.12.1.dist-info/top_level.txt' 2026-08-27T00:07:52,906 adding 'pybedtools-0.12.1.dist-info/RECORD' 2026-08-27T00:07:53,063 removing build/bdist.linux-armv7l/wheel 2026-08-27T00:07:53,312 Building wheel for pybedtools (pyproject.toml): finished with status 'done' 2026-08-27T00:07:53,624 Created wheel for pybedtools: filename=pybedtools-0.12.1-cp311-cp311-linux_armv7l.whl size=14387295 sha256=3a8b1c1cc569a215c9715f8e842a7d59417fdef096c8e12dbbfa705fd3d6e29f 2026-08-27T00:07:53,626 Stored in directory: /tmp/pip-ephem-wheel-cache-ps5coekp/wheels/b2/88/11/60ce4d5c9314f5dc747502f258cb69a4610ca3100658cba3b9 2026-08-27T00:07:53,644 Successfully built pybedtools 2026-08-27T00:07:53,993 Removed build tracker: '/tmp/pip-build-tracker-2887lx2j'