2025-09-08T02:58:23,619 Created temporary directory: /tmp/pip-build-tracker-sea9z2cu 2025-09-08T02:58:23,620 Initialized build tracking at /tmp/pip-build-tracker-sea9z2cu 2025-09-08T02:58:23,620 Created build tracker: /tmp/pip-build-tracker-sea9z2cu 2025-09-08T02:58:23,620 Entered build tracker: /tmp/pip-build-tracker-sea9z2cu 2025-09-08T02:58:23,621 Created temporary directory: /tmp/pip-wheel-emvatnva 2025-09-08T02:58:23,624 Created temporary directory: /tmp/pip-ephem-wheel-cache-8scg8gom 2025-09-08T02:58:23,686 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T02:58:23,688 2 location(s) to search for versions of pybedtools: 2025-09-08T02:58:23,688 * https://pypi.org/simple/pybedtools/ 2025-09-08T02:58:23,688 * https://www.piwheels.org/simple/pybedtools/ 2025-09-08T02:58:23,688 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2025-09-08T02:58:23,689 Getting page https://pypi.org/simple/pybedtools/ 2025-09-08T02:58:23,690 Found index url https://pypi.org/simple/ 2025-09-08T02:58:23,759 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2025-09-08T02:58:23,763 Found link https://files.pythonhosted.org/packages/00/d9/aca9636b3e5b29f232fd6f60859f07f3420ec3c0712b50cb25c734a02a1f/pybedtools-0.2.2dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.2.2dev 2025-09-08T02:58:23,764 Found link https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5dev 2025-09-08T02:58:23,764 Found link https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5rc1 2025-09-08T02:58:23,764 Found link https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5 2025-09-08T02:58:23,764 Found link https://files.pythonhosted.org/packages/e7/9b/f082d2db470a0c9ba777a0d661fd5a7292c367840880040940de4a705e1f/pybedtools-0.5.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5.5 2025-09-08T02:58:23,764 Found link https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6rc1 2025-09-08T02:58:23,765 Found link https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6 2025-09-08T02:58:23,765 Found link https://files.pythonhosted.org/packages/ac/25/c971ba83c6df08cbd17626339ec637df57a0aa409ba3042408ff349dd710/pybedtools-0.6.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.1 2025-09-08T02:58:23,765 Found link https://files.pythonhosted.org/packages/3e/71/cb09c7b874a87803f9fb9a9b679d02a82879b9cadca4c93756e05e65a439/pybedtools-0.6.2.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.2 2025-09-08T02:58:23,765 Found link https://files.pythonhosted.org/packages/28/0b/15291a1aac0a2a1eb814a0c883ccebf2eebaebbef9923bfa0444df0cb3a8/pybedtools-0.6.3.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.3 2025-09-08T02:58:23,766 Found link https://files.pythonhosted.org/packages/7a/12/73027be04fc57dd3340e2120f0148c0aca569b16e62333f32a40b2b06ee0/pybedtools-0.6.4.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.4 2025-09-08T02:58:23,766 Found link https://files.pythonhosted.org/packages/a4/98/dab963ff44ddd40849a01b145b6d769158d9794b979fdbfd173728e06e5b/pybedtools-0.6.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.5 2025-09-08T02:58:23,766 Found link https://files.pythonhosted.org/packages/a3/91/02e900caea18ee909665440727222a9f37c9a532170c52684123f07d6e21/pybedtools-0.6.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.6 2025-09-08T02:58:23,766 Found link https://files.pythonhosted.org/packages/af/ff/7d488b19b8e4109bbaf7b7e4c5dc53207f2c4354d7729cf73f17a79fa104/pybedtools-0.6.7.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.7 2025-09-08T02:58:23,766 Found link https://files.pythonhosted.org/packages/aa/e9/c92a7e58326bf76534af1fbd4074def6999130b1838b4dcc51e9f3ba5e17/pybedtools-0.6.8.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.8 2025-09-08T02:58:23,767 Found link https://files.pythonhosted.org/packages/79/20/2a0861cc9ffc41043efd814cdf860828f4b2213573c82ea6138eb6cb221b/pybedtools-0.6.9.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6.9 2025-09-08T02:58:23,767 Found link https://files.pythonhosted.org/packages/e6/8d/06beb4e8a9e9a4ce042af337a5b855a789da586072d0c418ed9cb9398628/pybedtools-0.7.0.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.0 2025-09-08T02:58:23,767 Found link https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.1 2025-09-08T02:58:23,767 Found link https://files.pythonhosted.org/packages/a2/43/d80dbf32da421c78ea84a386402e1840dd06f3aba7e5fe73e8134e1ce50a/pybedtools-0.7.4.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.4 2025-09-08T02:58:23,768 Found link https://files.pythonhosted.org/packages/ed/f1/2caa4dc57b62707f0df147c0820d1fc8565e439c5f5c86778df7a2fec59f/pybedtools-0.7.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.5 2025-09-08T02:58:23,768 Found link https://files.pythonhosted.org/packages/f4/49/ce7ccc0ad79189eb8b8eec170c350643e7a209f98e34dae239a954d6fdb0/pybedtools-0.7.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.6 2025-09-08T02:58:23,768 Found link https://files.pythonhosted.org/packages/c2/a6/29fd41e86b38e7ca39eb7818c422e927534f2bd324c34cfd411cfca203b0/pybedtools-0.7.7.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.7.7 2025-09-08T02:58:23,768 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 2025-09-08T02:58:23,768 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 2025-09-08T02:58:23,769 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 2025-09-08T02:58:23,769 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 2025-09-08T02:58:23,769 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 2025-09-08T02:58:23,769 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 2025-09-08T02:58:23,769 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 2025-09-08T02:58:23,770 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 2025-09-08T02:58:23,770 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 2025-09-08T02:58:23,770 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 2025-09-08T02:58:23,770 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 2025-09-08T02:58:23,771 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2025-09-08T02:58:23,771 Getting page https://www.piwheels.org/simple/pybedtools/ 2025-09-08T02:58:23,772 Found index url https://www.piwheels.org/simple/ 2025-09-08T02:58:23,855 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 2025-09-08T02:58:23,872 Skipping link: No binaries permitted for pybedtools: 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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/) 2025-09-08T02:58:23,884 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/) 2025-09-08T02:58:23,884 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2025-09-08T02:58:23,884 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2025-09-08T02:58:23,910 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2025-09-08T02:58:23,911 Collecting pybedtools==0.7.1 2025-09-08T02:58:23,912 Created temporary directory: /tmp/pip-unpack-dk4w1mp7 2025-09-08T02:58:24,323 Downloading pybedtools-0.7.1.tar.gz (12.6 MB) 2025-09-08T02:58:26,971 Added pybedtools==0.7.1 from https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz to build tracker '/tmp/pip-build-tracker-sea9z2cu' 2025-09-08T02:58:26,973 Running setup.py (path:/tmp/pip-wheel-emvatnva/pybedtools_350fb863542347f0b3ad40362f576311/setup.py) egg_info for package pybedtools 2025-09-08T02:58:26,973 Created temporary directory: /tmp/pip-pip-egg-info-cby8taw1 2025-09-08T02:58:26,973 Preparing metadata (setup.py): started 2025-09-08T02:58:26,974 Running command python setup.py egg_info 2025-09-08T02:58:27,535 /tmp/pip-wheel-emvatnva/pybedtools_350fb863542347f0b3ad40362f576311/setup.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T02:58:27,535 import pkg_resources 2025-09-08T02:58:28,114 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T02:58:28,114 warnings.warn(msg) 2025-09-08T02:58:28,492 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T02:58:28,492 !! 2025-09-08T02:58:28,493 ******************************************************************************** 2025-09-08T02:58:28,493 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T02:58:28,493 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T02:58:28,493 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T02:58:28,493 ******************************************************************************** 2025-09-08T02:58:28,493 !! 2025-09-08T02:58:28,493 self._finalize_license_expression() 2025-09-08T02:58:28,568 running egg_info 2025-09-08T02:58:28,643 creating /tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info 2025-09-08T02:58:28,643 writing /tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info/PKG-INFO 2025-09-08T02:58:28,644 writing dependency_links to /tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info/dependency_links.txt 2025-09-08T02:58:28,645 writing requirements to /tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info/requires.txt 2025-09-08T02:58:28,645 writing top-level names to /tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info/top_level.txt 2025-09-08T02:58:28,646 writing manifest file '/tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info/SOURCES.txt' 2025-09-08T02:58:28,884 reading manifest file '/tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info/SOURCES.txt' 2025-09-08T02:58:28,885 reading manifest template 'MANIFEST.in' 2025-09-08T02:58:28,923 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-09-08T02:58:28,924 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-09-08T02:58:28,924 adding license file 'LICENSE.txt' 2025-09-08T02:58:28,936 writing manifest file '/tmp/pip-pip-egg-info-cby8taw1/pybedtools.egg-info/SOURCES.txt' 2025-09-08T02:58:29,059 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T02:58:29,064 Source in /tmp/pip-wheel-emvatnva/pybedtools_350fb863542347f0b3ad40362f576311 has version 0.7.1, which satisfies requirement pybedtools==0.7.1 from https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz 2025-09-08T02:58:29,065 Removed pybedtools==0.7.1 from https://files.pythonhosted.org/packages/b5/1c/1b7e66668105e5b84cc6224a54ce552c6a6113e9b34c980fc436140e6be1/pybedtools-0.7.1.tar.gz from build tracker '/tmp/pip-build-tracker-sea9z2cu' 2025-09-08T02:58:29,068 Created temporary directory: /tmp/pip-unpack-zq8djr7q 2025-09-08T02:58:29,069 Created temporary directory: /tmp/pip-unpack-jssaaxhg 2025-09-08T02:58:29,069 Building wheels for collected packages: pybedtools 2025-09-08T02:58:29,070 Created temporary directory: /tmp/pip-wheel-6w7idbpt 2025-09-08T02:58:29,071 DEPRECATION: Building 'pybedtools' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pybedtools'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T02:58:29,072 Building wheel for pybedtools (setup.py): started 2025-09-08T02:58:29,073 Destination directory: /tmp/pip-wheel-6w7idbpt 2025-09-08T02:58:29,073 Running command python setup.py bdist_wheel 2025-09-08T02:58:29,625 /tmp/pip-wheel-emvatnva/pybedtools_350fb863542347f0b3ad40362f576311/setup.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T02:58:29,626 import pkg_resources 2025-09-08T02:58:30,220 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T02:58:30,221 warnings.warn(msg) 2025-09-08T02:58:30,594 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T02:58:30,594 !! 2025-09-08T02:58:30,594 ******************************************************************************** 2025-09-08T02:58:30,594 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T02:58:30,595 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T02:58:30,595 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T02:58:30,595 ******************************************************************************** 2025-09-08T02:58:30,595 !! 2025-09-08T02:58:30,595 self._finalize_license_expression() 2025-09-08T02:58:30,596 running bdist_wheel 2025-09-08T02:58:30,743 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2025-09-08T02:58:30,744 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:135: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated 2025-09-08T02:58:30,744 !! 2025-09-08T02:58:30,744 ******************************************************************************** 2025-09-08T02:58:30,744 With Python 2.7 end-of-life, support for building universal wheels 2025-09-08T02:58:30,744 (i.e., wheels that support both Python 2 and Python 3) 2025-09-08T02:58:30,744 is being obviated. 2025-09-08T02:58:30,745 Please discontinue using this option, or if you still need it, 2025-09-08T02:58:30,745 file an issue with pypa/setuptools describing your use case. 2025-09-08T02:58:30,745 This deprecation is overdue, please update your project and remove deprecated 2025-09-08T02:58:30,745 calls to avoid build errors in the future. 2025-09-08T02:58:30,745 ******************************************************************************** 2025-09-08T02:58:30,745 !! 2025-09-08T02:58:30,745 self.finalize_options() 2025-09-08T02:58:30,819 running build 2025-09-08T02:58:30,819 running build_py 2025-09-08T02:58:30,896 creating build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,897 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,897 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,898 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,899 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,899 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,900 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,900 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,901 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,902 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,902 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,903 copying pybedtools/__main__.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:30,904 creating build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,904 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,905 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,905 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,906 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,906 copying pybedtools/test/test_scripts.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,907 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,907 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,908 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,908 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,909 copying pybedtools/test/test1.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,909 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T02:58:30,910 creating build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,911 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,911 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,912 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,912 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,913 copying pybedtools/contrib/classifier.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,913 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,914 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T02:58:30,915 creating build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,915 copying pybedtools/scripts/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,915 copying pybedtools/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,916 copying pybedtools/scripts/venn_gchart.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,916 copying pybedtools/scripts/annotate.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,917 copying pybedtools/scripts/intron_exon_reads.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,917 copying pybedtools/scripts/venn_mpl.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,918 copying pybedtools/scripts/peak_pie.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,918 copying pybedtools/scripts/py_ms_example.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T02:58:30,919 creating build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,920 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,927 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,928 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,929 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,929 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,930 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,930 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,931 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,931 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,932 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,932 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,933 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,934 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,934 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,935 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,935 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,936 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,937 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,937 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,938 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,938 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,939 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,939 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,970 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,970 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,971 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,971 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,972 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,973 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,974 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,976 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,976 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,977 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,977 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,978 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,979 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,980 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,981 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,981 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,982 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,982 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,983 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,984 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,985 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,986 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,986 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,994 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,994 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,995 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,995 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,997 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,998 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:30,998 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:31,008 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T02:58:31,008 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,009 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,010 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,010 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,011 copying pybedtools/cbedtools.cxx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,014 copying pybedtools/featurefuncs.cxx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,016 copying pybedtools/_Window.c -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,019 running build_ext 2025-09-08T02:58:31,025 building 'pybedtools.cbedtools' extension 2025-09-08T02:58:31,026 creating build/temp.linux-armv7l-cpython-313/pybedtools 2025-09-08T02:58:31,027 creating build/temp.linux-armv7l-cpython-313/src 2025-09-08T02:58:31,027 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Isrc/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cxx -o build/temp.linux-armv7l-cpython-313/pybedtools/cbedtools.o 2025-09-08T02:58:33,258 In file included from pybedtools/cbedtools.cxx:256: 2025-09-08T02:58:33,258 src/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: 2025-09-08T02:58:33,258 src/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2025-09-08T02:58:33,258 92 | for (register short i = 0; i < _binLevels; ++i) { 2025-09-08T02:58:33,258 | ^ 2025-09-08T02:58:33,311 In file included from /usr/include/python3.13/Python.h:72, 2025-09-08T02:58:33,311 from pybedtools/cbedtools.cxx:16: 2025-09-08T02:58:33,311 pybedtools/cbedtools.cxx: In function ‘int __Pyx_ListComp_Append(PyObject*, PyObject*)’: 2025-09-08T02:58:33,311 /usr/include/python3.13/object.h:357:30: error: lvalue required as left operand of assignment 2025-09-08T02:58:33,311 357 | # define Py_SIZE(ob) Py_SIZE(_PyObject_CAST(ob)) 2025-09-08T02:58:33,311 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,311 pybedtools/cbedtools.cxx:669:9: note: in expansion of macro ‘Py_SIZE’ 2025-09-08T02:58:33,312 669 | Py_SIZE(list) = len+1; 2025-09-08T02:58:33,312 | ^~~~~~~ 2025-09-08T02:58:33,312 pybedtools/cbedtools.cxx: In function ‘int __Pyx_PyList_Append(PyObject*, PyObject*)’: 2025-09-08T02:58:33,312 /usr/include/python3.13/object.h:357:30: error: lvalue required as left operand of assignment 2025-09-08T02:58:33,313 357 | # define Py_SIZE(ob) Py_SIZE(_PyObject_CAST(ob)) 2025-09-08T02:58:33,313 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,313 pybedtools/cbedtools.cxx:700:9: note: in expansion of macro ‘Py_SIZE’ 2025-09-08T02:58:33,313 700 | Py_SIZE(list) = len+1; 2025-09-08T02:58:33,313 | ^~~~~~~ 2025-09-08T02:58:33,342 pybedtools/cbedtools.cxx: In function ‘int __Pyx_PyList_Extend(PyObject*, PyObject*)’: 2025-09-08T02:58:33,342 pybedtools/cbedtools.cxx:711:22: error: ‘_PyList_Extend’ was not declared in this scope; did you mean ‘PyList_Extend’? 2025-09-08T02:58:33,342 711 | PyObject* none = _PyList_Extend((PyListObject*)L, v); 2025-09-08T02:58:33,342 | ^~~~~~~~~~~~~~ 2025-09-08T02:58:33,342 | PyList_Extend 2025-09-08T02:58:33,865 pybedtools/cbedtools.cxx: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_Interval(PyObject*)’: 2025-09-08T02:58:33,865 pybedtools/cbedtools.cxx:12945:45: error: ‘_PyGC_FINALIZED’ was not declared in this scope 2025-09-08T02:58:33,866 12945 | if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { 2025-09-08T02:58:33,866 | ^~~~~~~~~~~~~~~ 2025-09-08T02:58:33,866 /usr/include/python3.13/object.h:335:34: error: lvalue required as increment operand 2025-09-08T02:58:33,866 335 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2025-09-08T02:58:33,866 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,866 pybedtools/cbedtools.cxx:12953:7: note: in expansion of macro ‘Py_REFCNT’ 2025-09-08T02:58:33,866 12953 | ++Py_REFCNT(o); 2025-09-08T02:58:33,866 | ^~~~~~~~~ 2025-09-08T02:58:33,866 /usr/include/python3.13/object.h:335:34: error: lvalue required as decrement operand 2025-09-08T02:58:33,867 335 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2025-09-08T02:58:33,867 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,867 pybedtools/cbedtools.cxx:12955:7: note: in expansion of macro ‘Py_REFCNT’ 2025-09-08T02:58:33,867 12955 | --Py_REFCNT(o); 2025-09-08T02:58:33,867 | ^~~~~~~~~ 2025-09-08T02:58:33,917 pybedtools/cbedtools.cxx: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalIterator(PyObject*)’: 2025-09-08T02:58:33,917 pybedtools/cbedtools.cxx:13313:45: error: ‘_PyGC_FINALIZED’ was not declared in this scope 2025-09-08T02:58:33,917 13313 | if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { 2025-09-08T02:58:33,917 | ^~~~~~~~~~~~~~~ 2025-09-08T02:58:33,961 pybedtools/cbedtools.cxx: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalFile(PyObject*)’: 2025-09-08T02:58:33,961 pybedtools/cbedtools.cxx:13419:75: error: ‘_PyGC_FINALIZED’ was not declared in this scope 2025-09-08T02:58:33,962 13419 | if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { 2025-09-08T02:58:33,962 | ^~~~~~~~~~~~~~~ 2025-09-08T02:58:33,962 /usr/include/python3.13/object.h:335:34: error: lvalue required as increment operand 2025-09-08T02:58:33,962 335 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2025-09-08T02:58:33,962 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,962 pybedtools/cbedtools.cxx:13426:7: note: in expansion of macro ‘Py_REFCNT’ 2025-09-08T02:58:33,962 13426 | ++Py_REFCNT(o); 2025-09-08T02:58:33,962 | ^~~~~~~~~ 2025-09-08T02:58:33,962 /usr/include/python3.13/object.h:335:34: error: lvalue required as decrement operand 2025-09-08T02:58:33,963 335 | # define Py_REFCNT(ob) Py_REFCNT(_PyObject_CAST(ob)) 2025-09-08T02:58:33,963 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,963 pybedtools/cbedtools.cxx:13428:7: note: in expansion of macro ‘Py_REFCNT’ 2025-09-08T02:58:33,963 13428 | --Py_REFCNT(o); 2025-09-08T02:58:33,963 | ^~~~~~~~~ 2025-09-08T02:58:33,983 pybedtools/cbedtools.cxx: In function ‘int __Pyx_InitCachedConstants()’: 2025-09-08T02:58:33,983 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:33,983 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:33,984 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,984 pybedtools/cbedtools.cxx:13782:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:33,984 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:33,984 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,984 In file included from /usr/include/python3.13/Python.h:101: 2025-09-08T02:58:33,984 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:33,984 213 | PyCode_New( 2025-09-08T02:58:33,984 | ^~~~~~~~~~ 2025-09-08T02:58:33,986 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:33,986 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:33,986 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,986 pybedtools/cbedtools.cxx:13782:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:33,986 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:33,986 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,987 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:33,987 213 | PyCode_New( 2025-09-08T02:58:33,987 | ^~~~~~~~~~ 2025-09-08T02:58:33,987 pybedtools/cbedtools.cxx:13782:237: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-08T02:58:33,987 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:33,987 | ^~~ 2025-09-08T02:58:33,987 | | 2025-09-08T02:58:33,987 | int 2025-09-08T02:58:33,987 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:33,987 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:33,987 | ^~~~~ 2025-09-08T02:58:33,989 pybedtools/cbedtools.cxx:13782:242: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2025-09-08T02:58:33,989 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:33,989 | ^~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,989 | | 2025-09-08T02:58:33,989 | PyObject* {aka _object*} 2025-09-08T02:58:33,989 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:33,989 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:33,990 | ^~~~ 2025-09-08T02:58:33,991 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2025-09-08T02:58:33,991 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:33,992 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,992 pybedtools/cbedtools.cxx:13782:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:33,992 13782 | __pyx_codeobj__15 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__14, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_cmp, 280, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:33,992 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:33,992 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:33,992 213 | PyCode_New( 2025-09-08T02:58:33,992 | ^~~~~~~~~~ 2025-09-08T02:58:34,006 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,006 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,006 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,006 pybedtools/cbedtools.cxx:14183:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,006 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,006 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,006 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,006 213 | PyCode_New( 2025-09-08T02:58:34,006 | ^~~~~~~~~~ 2025-09-08T02:58:34,008 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,008 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,008 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,008 pybedtools/cbedtools.cxx:14183:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,008 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,008 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,008 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,008 213 | PyCode_New( 2025-09-08T02:58:34,009 | ^~~~~~~~~~ 2025-09-08T02:58:34,009 pybedtools/cbedtools.cxx:14183:238: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-08T02:58:34,009 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,009 | ^~~ 2025-09-08T02:58:34,009 | | 2025-09-08T02:58:34,009 | int 2025-09-08T02:58:34,009 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,009 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,009 | ^~~~~ 2025-09-08T02:58:34,010 pybedtools/cbedtools.cxx:14183:243: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2025-09-08T02:58:34,011 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,011 | ^~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,011 | | 2025-09-08T02:58:34,011 | PyObject* {aka _object*} 2025-09-08T02:58:34,011 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,011 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,011 | ^~~~ 2025-09-08T02:58:34,013 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2025-09-08T02:58:34,013 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,013 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,013 pybedtools/cbedtools.cxx:14183:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,013 14183 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_init, 145, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,013 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,013 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,013 213 | PyCode_New( 2025-09-08T02:58:34,013 | ^~~~~~~~~~ 2025-09-08T02:58:34,016 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,016 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,016 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,016 pybedtools/cbedtools.cxx:14198:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,016 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,016 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,017 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,017 213 | PyCode_New( 2025-09-08T02:58:34,017 | ^~~~~~~~~~ 2025-09-08T02:58:34,018 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,018 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,018 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,018 pybedtools/cbedtools.cxx:14198:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,019 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,019 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,019 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,019 213 | PyCode_New( 2025-09-08T02:58:34,019 | ^~~~~~~~~~ 2025-09-08T02:58:34,019 pybedtools/cbedtools.cxx:14198:237: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-08T02:58:34,019 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,019 | ^~~ 2025-09-08T02:58:34,019 | | 2025-09-08T02:58:34,019 | int 2025-09-08T02:58:34,019 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,020 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,020 | ^~~~~ 2025-09-08T02:58:34,021 pybedtools/cbedtools.cxx:14198:242: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2025-09-08T02:58:34,021 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,021 | ^~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,021 | | 2025-09-08T02:58:34,021 | PyObject* {aka _object*} 2025-09-08T02:58:34,021 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,021 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,021 | ^~~~ 2025-09-08T02:58:34,023 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2025-09-08T02:58:34,023 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,023 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,023 pybedtools/cbedtools.cxx:14198:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,023 14198 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_str, 181, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,024 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,024 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,024 213 | PyCode_New( 2025-09-08T02:58:34,024 | ^~~~~~~~~~ 2025-09-08T02:58:34,026 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,026 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,026 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,026 pybedtools/cbedtools.cxx:14210:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,026 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,026 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,027 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,027 213 | PyCode_New( 2025-09-08T02:58:34,027 | ^~~~~~~~~~ 2025-09-08T02:58:34,028 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,028 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,028 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,028 pybedtools/cbedtools.cxx:14210:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,029 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,029 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,029 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,029 213 | PyCode_New( 2025-09-08T02:58:34,029 | ^~~~~~~~~~ 2025-09-08T02:58:34,029 pybedtools/cbedtools.cxx:14210:241: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-08T02:58:34,029 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,029 | ^~~ 2025-09-08T02:58:34,029 | | 2025-09-08T02:58:34,029 | int 2025-09-08T02:58:34,030 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,030 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,030 | ^~~~~ 2025-09-08T02:58:34,031 pybedtools/cbedtools.cxx:14210:246: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2025-09-08T02:58:34,031 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,031 | ^~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,031 | | 2025-09-08T02:58:34,031 | PyObject* {aka _object*} 2025-09-08T02:58:34,031 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,031 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,031 | ^~~~ 2025-09-08T02:58:34,033 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2025-09-08T02:58:34,033 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,033 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,033 pybedtools/cbedtools.cxx:14210:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,034 14210 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_ryan_proj_pybedtools_pybed, __pyx_n_s_overlap, 708, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T02:58:34,034 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,034 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,034 213 | PyCode_New( 2025-09-08T02:58:34,034 | ^~~~~~~~~~ 2025-09-08T02:58:34,043 pybedtools/cbedtools.cxx: In function ‘PyObject* PyInit_cbedtools()’: 2025-09-08T02:58:34,043 pybedtools/cbedtools.cxx:14327:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T02:58:34,043 14327 | __pyx_type_10pybedtools_9cbedtools_Interval.tp_print = 0; 2025-09-08T02:58:34,043 | ^~~~~~~~ 2025-09-08T02:58:34,045 pybedtools/cbedtools.cxx:14342:55: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T02:58:34,045 14342 | __pyx_type_10pybedtools_9cbedtools_IntervalIterator.tp_print = 0; 2025-09-08T02:58:34,045 | ^~~~~~~~ 2025-09-08T02:58:34,045 pybedtools/cbedtools.cxx:14346:51: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T02:58:34,045 14346 | __pyx_type_10pybedtools_9cbedtools_IntervalFile.tp_print = 0; 2025-09-08T02:58:34,045 | ^~~~~~~~ 2025-09-08T02:58:34,119 pybedtools/cbedtools.cxx: In function ‘PyObject* __Pyx_decode_c_bytes(const char*, Py_ssize_t, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’: 2025-09-08T02:58:34,119 pybedtools/cbedtools.cxx:15279:16: error: ‘PyUnicode_FromUnicode’ was not declared in this scope; did you mean ‘PyInt_FromUnicode’? 2025-09-08T02:58:34,119 15279 | return PyUnicode_FromUnicode(NULL, 0); 2025-09-08T02:58:34,119 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,120 | PyInt_FromUnicode 2025-09-08T02:58:34,147 pybedtools/cbedtools.cxx: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2025-09-08T02:58:34,147 pybedtools/cbedtools.cxx:15349:22: error: ‘PyUnicode_GET_SIZE’ was not declared in this scope; did you mean ‘PyDict_GET_SIZE’? 2025-09-08T02:58:34,147 15349 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T02:58:34,147 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,147 | PyDict_GET_SIZE 2025-09-08T02:58:34,173 pybedtools/cbedtools.cxx:15365:26: error: ‘PyUnicode_GET_SIZE’ was not declared in this scope; did you mean ‘PyDict_GET_SIZE’? 2025-09-08T02:58:34,173 15365 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T02:58:34,173 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,173 | PyDict_GET_SIZE 2025-09-08T02:58:34,218 pybedtools/cbedtools.cxx: In function ‘int __Pyx_PyUnicode_Equals(PyObject*, PyObject*, int)’: 2025-09-08T02:58:34,218 pybedtools/cbedtools.cxx:84:51: error: ‘_PyUnicode_Ready’ was not declared in this scope; did you mean ‘PyUnicode_READY’? 2025-09-08T02:58:34,218 84 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-08T02:58:34,218 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,219 pybedtools/cbedtools.cxx:421:43: note: in definition of macro ‘unlikely’ 2025-09-08T02:58:34,219 421 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T02:58:34,219 | ^ 2025-09-08T02:58:34,219 pybedtools/cbedtools.cxx:15498:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-08T02:58:34,219 15498 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-08T02:58:34,219 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,226 pybedtools/cbedtools.cxx: In function ‘int __Pyx_IterFinish()’: 2025-09-08T02:58:34,226 pybedtools/cbedtools.cxx:15625:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,226 15625 | PyObject* exc_type = tstate->curexc_type; 2025-09-08T02:58:34,226 | ^~~~~~~~~~~ 2025-09-08T02:58:34,226 pybedtools/cbedtools.cxx:15629:33: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,226 15629 | exc_value = tstate->curexc_value; 2025-09-08T02:58:34,226 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,227 pybedtools/cbedtools.cxx:15630:30: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,227 15630 | exc_tb = tstate->curexc_traceback; 2025-09-08T02:58:34,227 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,227 pybedtools/cbedtools.cxx:15631:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,227 15631 | tstate->curexc_type = 0; 2025-09-08T02:58:34,227 | ^~~~~~~~~~~ 2025-09-08T02:58:34,227 pybedtools/cbedtools.cxx:15632:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,227 15632 | tstate->curexc_value = 0; 2025-09-08T02:58:34,227 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,227 pybedtools/cbedtools.cxx:15633:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,228 15633 | tstate->curexc_traceback = 0; 2025-09-08T02:58:34,228 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,230 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ExceptionSave(PyObject**, PyObject**, PyObject**)’: 2025-09-08T02:58:34,230 pybedtools/cbedtools.cxx:15695:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T02:58:34,230 15695 | *type = tstate->exc_type; 2025-09-08T02:58:34,230 | ^~~~~~~~ 2025-09-08T02:58:34,230 | exc_state 2025-09-08T02:58:34,230 pybedtools/cbedtools.cxx:15696:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T02:58:34,230 15696 | *value = tstate->exc_value; 2025-09-08T02:58:34,230 | ^~~~~~~~~ 2025-09-08T02:58:34,230 pybedtools/cbedtools.cxx:15697:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T02:58:34,231 15697 | *tb = tstate->exc_traceback; 2025-09-08T02:58:34,231 | ^~~~~~~~~~~~~ 2025-09-08T02:58:34,231 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ExceptionReset(PyObject*, PyObject*, PyObject*)’: 2025-09-08T02:58:34,231 pybedtools/cbedtools.cxx:15709:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T02:58:34,231 15709 | tmp_type = tstate->exc_type; 2025-09-08T02:58:34,231 | ^~~~~~~~ 2025-09-08T02:58:34,231 | exc_state 2025-09-08T02:58:34,231 pybedtools/cbedtools.cxx:15710:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T02:58:34,231 15710 | tmp_value = tstate->exc_value; 2025-09-08T02:58:34,231 | ^~~~~~~~~ 2025-09-08T02:58:34,232 pybedtools/cbedtools.cxx:15711:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T02:58:34,232 15711 | tmp_tb = tstate->exc_traceback; 2025-09-08T02:58:34,232 | ^~~~~~~~~~~~~ 2025-09-08T02:58:34,232 pybedtools/cbedtools.cxx:15712:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T02:58:34,232 15712 | tstate->exc_type = type; 2025-09-08T02:58:34,232 | ^~~~~~~~ 2025-09-08T02:58:34,232 | exc_state 2025-09-08T02:58:34,232 pybedtools/cbedtools.cxx:15713:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T02:58:34,232 15713 | tstate->exc_value = value; 2025-09-08T02:58:34,232 | ^~~~~~~~~ 2025-09-08T02:58:34,233 pybedtools/cbedtools.cxx:15714:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T02:58:34,233 15714 | tstate->exc_traceback = tb; 2025-09-08T02:58:34,233 | ^~~~~~~~~~~~~ 2025-09-08T02:58:34,279 pybedtools/cbedtools.cxx: In function ‘PyObject* __Pyx_CyFunction_Call(PyObject*, PyObject*, PyObject*)’: 2025-09-08T02:58:34,279 pybedtools/cbedtools.cxx:16220:16: error: ‘PyCFunction_Call’ was not declared in this scope; did you mean ‘PyCFunction_Type’? 2025-09-08T02:58:34,279 16220 | return PyCFunction_Call(func, arg, kw); 2025-09-08T02:58:34,279 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,279 | PyCFunction_Type 2025-09-08T02:58:34,304 pybedtools/cbedtools.cxx: In function ‘int __Pyx_CyFunction_init()’: 2025-09-08T02:58:34,304 pybedtools/cbedtools.cxx:16285:41: error: ‘PyCFunction_Call’ was not declared in this scope; did you mean ‘PyCFunction_Type’? 2025-09-08T02:58:34,305 16285 | __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; 2025-09-08T02:58:34,305 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,305 | PyCFunction_Type 2025-09-08T02:58:34,307 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ErrRestore(PyObject*, PyObject*, PyObject*)’: 2025-09-08T02:58:34,307 pybedtools/cbedtools.cxx:16339:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,307 16339 | tmp_type = tstate->curexc_type; 2025-09-08T02:58:34,307 | ^~~~~~~~~~~ 2025-09-08T02:58:34,307 pybedtools/cbedtools.cxx:16340:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,307 16340 | tmp_value = tstate->curexc_value; 2025-09-08T02:58:34,307 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,307 pybedtools/cbedtools.cxx:16341:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,308 16341 | tmp_tb = tstate->curexc_traceback; 2025-09-08T02:58:34,308 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,308 pybedtools/cbedtools.cxx:16342:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,308 16342 | tstate->curexc_type = type; 2025-09-08T02:58:34,308 | ^~~~~~~~~~~ 2025-09-08T02:58:34,308 pybedtools/cbedtools.cxx:16343:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,308 16343 | tstate->curexc_value = value; 2025-09-08T02:58:34,308 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,308 pybedtools/cbedtools.cxx:16344:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,308 16344 | tstate->curexc_traceback = tb; 2025-09-08T02:58:34,309 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,309 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ErrFetch(PyObject**, PyObject**, PyObject**)’: 2025-09-08T02:58:34,309 pybedtools/cbedtools.cxx:16355:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,309 16355 | *type = tstate->curexc_type; 2025-09-08T02:58:34,309 | ^~~~~~~~~~~ 2025-09-08T02:58:34,309 pybedtools/cbedtools.cxx:16356:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,309 16356 | *value = tstate->curexc_value; 2025-09-08T02:58:34,309 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,309 pybedtools/cbedtools.cxx:16357:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,309 16357 | *tb = tstate->curexc_traceback; 2025-09-08T02:58:34,310 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,310 pybedtools/cbedtools.cxx:16358:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,310 16358 | tstate->curexc_type = 0; 2025-09-08T02:58:34,310 | ^~~~~~~~~~~ 2025-09-08T02:58:34,310 pybedtools/cbedtools.cxx:16359:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,310 16359 | tstate->curexc_value = 0; 2025-09-08T02:58:34,310 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,310 pybedtools/cbedtools.cxx:16360:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,310 16360 | tstate->curexc_traceback = 0; 2025-09-08T02:58:34,311 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,313 pybedtools/cbedtools.cxx: In function ‘void __Pyx_Raise(PyObject*, PyObject*, PyObject*, PyObject*)’: 2025-09-08T02:58:34,314 pybedtools/cbedtools.cxx:16509:36: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,314 16509 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T02:58:34,314 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,314 pybedtools/cbedtools.cxx:16512:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,314 16512 | tstate->curexc_traceback = tb; 2025-09-08T02:58:34,314 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,315 pybedtools/cbedtools.cxx: In function ‘int __Pyx_GetException(PyObject**, PyObject**, PyObject**)’: 2025-09-08T02:58:34,315 pybedtools/cbedtools.cxx:16528:26: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,315 16528 | local_type = tstate->curexc_type; 2025-09-08T02:58:34,315 | ^~~~~~~~~~~ 2025-09-08T02:58:34,316 pybedtools/cbedtools.cxx:16529:27: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,316 16529 | local_value = tstate->curexc_value; 2025-09-08T02:58:34,316 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,316 pybedtools/cbedtools.cxx:16530:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,316 16530 | local_tb = tstate->curexc_traceback; 2025-09-08T02:58:34,316 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,316 pybedtools/cbedtools.cxx:16531:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,316 16531 | tstate->curexc_type = 0; 2025-09-08T02:58:34,316 | ^~~~~~~~~~~ 2025-09-08T02:58:34,316 pybedtools/cbedtools.cxx:16532:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T02:58:34,317 16532 | tstate->curexc_value = 0; 2025-09-08T02:58:34,317 | ^~~~~~~~~~~~ 2025-09-08T02:58:34,317 pybedtools/cbedtools.cxx:16533:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T02:58:34,317 16533 | tstate->curexc_traceback = 0; 2025-09-08T02:58:34,317 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,317 pybedtools/cbedtools.cxx:16539:26: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T02:58:34,317 16539 | if (unlikely(tstate->curexc_type)) 2025-09-08T02:58:34,317 | ^~~~~~~~~~~ 2025-09-08T02:58:34,317 pybedtools/cbedtools.cxx:421:43: note: in definition of macro ‘unlikely’ 2025-09-08T02:58:34,317 421 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T02:58:34,317 | ^ 2025-09-08T02:58:34,319 pybedtools/cbedtools.cxx:16557:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T02:58:34,319 16557 | tmp_type = tstate->exc_type; 2025-09-08T02:58:34,319 | ^~~~~~~~ 2025-09-08T02:58:34,320 | exc_state 2025-09-08T02:58:34,320 pybedtools/cbedtools.cxx:16558:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T02:58:34,320 16558 | tmp_value = tstate->exc_value; 2025-09-08T02:58:34,320 | ^~~~~~~~~ 2025-09-08T02:58:34,320 pybedtools/cbedtools.cxx:16559:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T02:58:34,320 16559 | tmp_tb = tstate->exc_traceback; 2025-09-08T02:58:34,320 | ^~~~~~~~~~~~~ 2025-09-08T02:58:34,320 pybedtools/cbedtools.cxx:16560:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T02:58:34,320 16560 | tstate->exc_type = local_type; 2025-09-08T02:58:34,320 | ^~~~~~~~ 2025-09-08T02:58:34,321 | exc_state 2025-09-08T02:58:34,321 pybedtools/cbedtools.cxx:16561:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T02:58:34,321 16561 | tstate->exc_value = local_value; 2025-09-08T02:58:34,321 | ^~~~~~~~~ 2025-09-08T02:58:34,321 pybedtools/cbedtools.cxx:16562:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T02:58:34,321 16562 | tstate->exc_traceback = local_tb; 2025-09-08T02:58:34,321 | ^~~~~~~~~~~~~ 2025-09-08T02:58:34,392 pybedtools/cbedtools.cxx: In function ‘PyObject* __Pyx_PyIter_Next2(PyObject*, PyObject*)’: 2025-09-08T02:58:34,392 pybedtools/cbedtools.cxx:16858:31: error: ‘_PyObject_NextNotImplemented’ was not declared in this scope; did you mean ‘PyObject_HashNotImplemented’? 2025-09-08T02:58:34,392 16858 | if (unlikely(iternext == &_PyObject_NextNotImplemented)) 2025-09-08T02:58:34,392 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,392 pybedtools/cbedtools.cxx:421:43: note: in definition of macro ‘unlikely’ 2025-09-08T02:58:34,392 421 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T02:58:34,393 | ^ 2025-09-08T02:58:34,396 pybedtools/cbedtools.cxx: In function ‘void __Pyx_ExceptionSwap(PyObject**, PyObject**, PyObject**)’: 2025-09-08T02:58:34,396 pybedtools/cbedtools.cxx:16886:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T02:58:34,396 16886 | tmp_type = tstate->exc_type; 2025-09-08T02:58:34,396 | ^~~~~~~~ 2025-09-08T02:58:34,396 | exc_state 2025-09-08T02:58:34,397 pybedtools/cbedtools.cxx:16887:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T02:58:34,397 16887 | tmp_value = tstate->exc_value; 2025-09-08T02:58:34,397 | ^~~~~~~~~ 2025-09-08T02:58:34,397 pybedtools/cbedtools.cxx:16888:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T02:58:34,397 16888 | tmp_tb = tstate->exc_traceback; 2025-09-08T02:58:34,397 | ^~~~~~~~~~~~~ 2025-09-08T02:58:34,397 pybedtools/cbedtools.cxx:16889:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T02:58:34,397 16889 | tstate->exc_type = *type; 2025-09-08T02:58:34,397 | ^~~~~~~~ 2025-09-08T02:58:34,397 | exc_state 2025-09-08T02:58:34,398 pybedtools/cbedtools.cxx:16890:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T02:58:34,398 16890 | tstate->exc_value = *value; 2025-09-08T02:58:34,398 | ^~~~~~~~~ 2025-09-08T02:58:34,398 pybedtools/cbedtools.cxx:16891:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T02:58:34,398 16891 | tstate->exc_traceback = *tb; 2025-09-08T02:58:34,398 | ^~~~~~~~~~~~~ 2025-09-08T02:58:34,413 pybedtools/cbedtools.cxx: In function ‘PyCodeObject* __Pyx_CreateCodeObjectForTraceback(const char*, int, int, const char*)’: 2025-09-08T02:58:34,413 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,413 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,413 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,414 pybedtools/cbedtools.cxx:17190:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,414 17190 | py_code = __Pyx_PyCode_New( 2025-09-08T02:58:34,414 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,414 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,414 213 | PyCode_New( 2025-09-08T02:58:34,414 | ^~~~~~~~~~ 2025-09-08T02:58:34,415 pybedtools/cbedtools.cxx:70:21: warning: ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ is deprecated [-Wdeprecated-declarations] 2025-09-08T02:58:34,416 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,416 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,416 pybedtools/cbedtools.cxx:17190:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,416 17190 | py_code = __Pyx_PyCode_New( 2025-09-08T02:58:34,416 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,416 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,416 213 | PyCode_New( 2025-09-08T02:58:34,416 | ^~~~~~~~~~ 2025-09-08T02:58:34,416 pybedtools/cbedtools.cxx:17204:9: error: invalid conversion from ‘int’ to ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-08T02:58:34,416 17204 | py_line, 2025-09-08T02:58:34,417 | ^~~~~~~ 2025-09-08T02:58:34,417 | | 2025-09-08T02:58:34,417 | int 2025-09-08T02:58:34,417 pybedtools/cbedtools.cxx:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,417 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,417 | ^~~~~ 2025-09-08T02:58:34,418 pybedtools/cbedtools.cxx:17205:9: error: invalid conversion from ‘PyObject*’ {aka ‘_object*’} to ‘int’ [-fpermissive] 2025-09-08T02:58:34,419 17205 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-08T02:58:34,419 | ^~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,419 | | 2025-09-08T02:58:34,419 | PyObject* {aka _object*} 2025-09-08T02:58:34,419 pybedtools/cbedtools.cxx:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,419 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,419 | ^~~~ 2025-09-08T02:58:34,421 pybedtools/cbedtools.cxx:70:21: error: too few arguments to function ‘PyCodeObject* PyCode_New(int, int, int, int, int, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, PyObject*, int, PyObject*, PyObject*)’ 2025-09-08T02:58:34,421 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T02:58:34,421 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,421 pybedtools/cbedtools.cxx:17190:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T02:58:34,422 17190 | py_code = __Pyx_PyCode_New( 2025-09-08T02:58:34,422 | ^~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,422 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T02:58:34,422 213 | PyCode_New( 2025-09-08T02:58:34,422 | ^~~~~~~~~~ 2025-09-08T02:58:34,423 pybedtools/cbedtools.cxx: In function ‘void __Pyx_AddTraceback(const char*, int, int, const char*)’: 2025-09-08T02:58:34,423 pybedtools/cbedtools.cxx:17233:13: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T02:58:34,423 17233 | py_frame->f_lineno = py_line; 2025-09-08T02:58:34,423 | ^~ 2025-09-08T02:58:34,423 In file included from /usr/include/python3.13/Python.h:67: 2025-09-08T02:58:34,423 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T02:58:34,423 22 | typedef struct _frame PyFrameObject; 2025-09-08T02:58:34,424 | ^~~~~~ 2025-09-08T02:58:34,428 pybedtools/cbedtools.cxx: In function ‘int __Pyx_PyInt_As_int(PyObject*)’: 2025-09-08T02:58:34,428 pybedtools/cbedtools.cxx:17401:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-08T02:58:34,428 17401 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T02:58:34,428 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,428 17402 | bytes, sizeof(val), 2025-09-08T02:58:34,428 | ~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,429 17403 | is_little, !is_unsigned); 2025-09-08T02:58:34,429 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,429 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-08T02:58:34,429 from /usr/include/python3.13/Python.h:81: 2025-09-08T02:58:34,429 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T02:58:34,429 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T02:58:34,429 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,433 pybedtools/cbedtools.cxx: In function ‘CHRPOS __Pyx_PyInt_As_CHRPOS(PyObject*)’: 2025-09-08T02:58:34,433 pybedtools/cbedtools.cxx:17496:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-08T02:58:34,433 17496 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T02:58:34,433 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,434 17497 | bytes, sizeof(val), 2025-09-08T02:58:34,434 | ~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,434 17498 | is_little, !is_unsigned); 2025-09-08T02:58:34,434 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,434 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T02:58:34,434 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T02:58:34,434 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,438 pybedtools/cbedtools.cxx: In function ‘size_t __Pyx_PyInt_As_size_t(PyObject*)’: 2025-09-08T02:58:34,438 pybedtools/cbedtools.cxx:17591:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-08T02:58:34,438 17591 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T02:58:34,438 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,438 17592 | bytes, sizeof(val), 2025-09-08T02:58:34,438 | ~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,438 17593 | is_little, !is_unsigned); 2025-09-08T02:58:34,438 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,438 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T02:58:34,439 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T02:58:34,439 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,445 pybedtools/cbedtools.cxx: In function ‘long unsigned int __Pyx_PyInt_As_unsigned_long(PyObject*)’: 2025-09-08T02:58:34,445 pybedtools/cbedtools.cxx:17764:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-08T02:58:34,445 17764 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T02:58:34,445 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,445 17765 | bytes, sizeof(val), 2025-09-08T02:58:34,445 | ~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,445 17766 | is_little, !is_unsigned); 2025-09-08T02:58:34,445 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,445 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T02:58:34,446 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T02:58:34,446 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,449 pybedtools/cbedtools.cxx: In function ‘long int __Pyx_PyInt_As_long(PyObject*)’: 2025-09-08T02:58:34,449 pybedtools/cbedtools.cxx:17859:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-08T02:58:34,449 17859 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T02:58:34,449 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,449 17860 | bytes, sizeof(val), 2025-09-08T02:58:34,450 | ~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,450 17861 | is_little, !is_unsigned); 2025-09-08T02:58:34,450 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:34,450 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T02:58:34,450 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T02:58:34,450 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:35,066 pybedtools/cbedtools.cxx: At global scope: 2025-09-08T02:58:35,066 pybedtools/cbedtools.cxx:7940:12: warning: ‘int __pyx_pw_10pybedtools_9cbedtools_8Interval_33__nonzero__(PyObject*)’ defined but not used [-Wunused-function] 2025-09-08T02:58:35,066 7940 | static int __pyx_pw_10pybedtools_9cbedtools_8Interval_33__nonzero__(PyObject *__pyx_v_self) { 2025-09-08T02:58:35,067 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T02:58:35,083 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-08T02:58:35,207 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T02:58:35,219 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T02:58:35,219 exec(compile('"'"''"'"''"'"' 2025-09-08T02:58:35,219 # This is -- a caller that pip uses to run setup.py 2025-09-08T02:58:35,219 # 2025-09-08T02:58:35,219 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T02:58:35,219 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T02:58:35,219 # - It provides a clear error message when setuptools is not installed. 2025-09-08T02:58:35,219 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T02:58:35,219 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T02:58:35,219 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T02:58:35,219 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T02:58:35,219 import os, sys, tokenize, traceback 2025-09-08T02:58:35,219 2025-09-08T02:58:35,219 try: 2025-09-08T02:58:35,219 import setuptools 2025-09-08T02:58:35,219 except ImportError: 2025-09-08T02:58:35,219 print( 2025-09-08T02:58:35,219 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T02:58:35,219 "the build environment with exception:", 2025-09-08T02:58:35,219 file=sys.stderr, 2025-09-08T02:58:35,219 ) 2025-09-08T02:58:35,219 traceback.print_exc() 2025-09-08T02:58:35,219 sys.exit(1) 2025-09-08T02:58:35,219 2025-09-08T02:58:35,219 __file__ = %r 2025-09-08T02:58:35,219 sys.argv[0] = __file__ 2025-09-08T02:58:35,219 2025-09-08T02:58:35,219 if os.path.exists(__file__): 2025-09-08T02:58:35,219 filename = __file__ 2025-09-08T02:58:35,219 with tokenize.open(__file__) as f: 2025-09-08T02:58:35,219 setup_py_code = f.read() 2025-09-08T02:58:35,219 else: 2025-09-08T02:58:35,219 filename = "" 2025-09-08T02:58:35,219 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T02:58:35,219 2025-09-08T02:58:35,219 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T02:58:35,219 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-emvatnva/pybedtools_350fb863542347f0b3ad40362f576311/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-6w7idbpt[/] 2025-09-08T02:58:35,219 [bold magenta]cwd[/]: /tmp/pip-wheel-emvatnva/pybedtools_350fb863542347f0b3ad40362f576311/ 2025-09-08T02:58:35,219 Building wheel for pybedtools (setup.py): finished with status 'error' 2025-09-08T02:58:35,220 ERROR: Failed building wheel for pybedtools 2025-09-08T02:58:35,221 Running setup.py clean for pybedtools 2025-09-08T02:58:35,221 Running command python setup.py clean 2025-09-08T02:58:35,761 /tmp/pip-wheel-emvatnva/pybedtools_350fb863542347f0b3ad40362f576311/setup.py:25: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-08T02:58:35,761 import pkg_resources 2025-09-08T02:58:36,331 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T02:58:36,331 warnings.warn(msg) 2025-09-08T02:58:36,721 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T02:58:36,721 !! 2025-09-08T02:58:36,722 ******************************************************************************** 2025-09-08T02:58:36,722 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T02:58:36,722 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T02:58:36,722 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T02:58:36,722 ******************************************************************************** 2025-09-08T02:58:36,722 !! 2025-09-08T02:58:36,722 self._finalize_license_expression() 2025-09-08T02:58:36,723 running clean 2025-09-08T02:58:36,854 Failed to build pybedtools 2025-09-08T02:58:36,855 ERROR: Failed to build one or more wheels 2025-09-08T02:58:36,856 Exception information: 2025-09-08T02:58:36,856 Traceback (most recent call last): 2025-09-08T02:58:36,856 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T02:58:36,856 status = _inner_run() 2025-09-08T02:58:36,856 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T02:58:36,856 return self.run(options, args) 2025-09-08T02:58:36,856 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T02:58:36,856 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T02:58:36,856 return func(self, options, args) 2025-09-08T02:58:36,856 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T02:58:36,856 raise CommandError("Failed to build one or more wheels") 2025-09-08T02:58:36,856 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T02:58:36,861 Removed build tracker: '/tmp/pip-build-tracker-sea9z2cu'