2025-09-08T05:19:36,626 Created temporary directory: /tmp/pip-build-tracker-equx3c6n 2025-09-08T05:19:36,627 Initialized build tracking at /tmp/pip-build-tracker-equx3c6n 2025-09-08T05:19:36,627 Created build tracker: /tmp/pip-build-tracker-equx3c6n 2025-09-08T05:19:36,627 Entered build tracker: /tmp/pip-build-tracker-equx3c6n 2025-09-08T05:19:36,628 Created temporary directory: /tmp/pip-wheel-mgjnttoc 2025-09-08T05:19:36,631 Created temporary directory: /tmp/pip-ephem-wheel-cache-ksqqem40 2025-09-08T05:19:36,686 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T05:19:36,688 2 location(s) to search for versions of pybedtools: 2025-09-08T05:19:36,688 * https://pypi.org/simple/pybedtools/ 2025-09-08T05:19:36,688 * https://www.piwheels.org/simple/pybedtools/ 2025-09-08T05:19:36,688 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2025-09-08T05:19:36,689 Getting page https://pypi.org/simple/pybedtools/ 2025-09-08T05:19:36,690 Found index url https://pypi.org/simple/ 2025-09-08T05:19:36,841 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2025-09-08T05:19:36,850 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 2025-09-08T05:19:36,851 Found link https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5dev 2025-09-08T05:19:36,852 Found link https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5rc1 2025-09-08T05:19:36,852 Found link https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5 2025-09-08T05:19:36,853 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 2025-09-08T05:19:36,853 Found link https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6rc1 2025-09-08T05:19:36,854 Found link https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6 2025-09-08T05:19:36,854 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 2025-09-08T05:19:36,855 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 2025-09-08T05:19:36,855 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 2025-09-08T05:19:36,856 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 2025-09-08T05:19:36,856 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 2025-09-08T05:19:36,857 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 2025-09-08T05:19:36,857 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 2025-09-08T05:19:36,858 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 2025-09-08T05:19:36,858 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 2025-09-08T05:19:36,859 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 2025-09-08T05:19:36,859 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 2025-09-08T05:19:36,860 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 2025-09-08T05:19:36,860 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 2025-09-08T05:19:36,861 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 2025-09-08T05:19:36,861 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 2025-09-08T05:19:36,861 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 2025-09-08T05:19:36,862 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 2025-09-08T05:19:36,863 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 2025-09-08T05:19:36,863 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 2025-09-08T05:19:36,863 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 2025-09-08T05:19:36,864 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 2025-09-08T05:19:36,865 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 2025-09-08T05:19:36,865 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 2025-09-08T05:19:36,865 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 2025-09-08T05:19:36,865 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 2025-09-08T05:19:36,866 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 2025-09-08T05:19:36,866 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2025-09-08T05:19:36,866 Getting page https://www.piwheels.org/simple/pybedtools/ 2025-09-08T05:19:36,867 Found index url https://www.piwheels.org/simple/ 2025-09-08T05:19:36,966 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 2025-09-08T05:19:36,980 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/) 2025-09-08T05:19:36,992 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/) 2025-09-08T05:19:36,992 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2025-09-08T05:19:36,993 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2025-09-08T05:19:37,019 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2025-09-08T05:19:37,020 Collecting pybedtools==0.7.8 2025-09-08T05:19:37,022 Created temporary directory: /tmp/pip-unpack-e5hyx1nr 2025-09-08T05:19:37,269 Downloading pybedtools-0.7.8.tar.gz (14.5 MB) 2025-09-08T05:19:40,226 Added pybedtools==0.7.8 from https://files.pythonhosted.org/packages/2d/ee/aa19e50e03e06c817d00eadf8b56824b9e473da8c3e8ca3b33a11717ee6f/pybedtools-0.7.8.tar.gz to build tracker '/tmp/pip-build-tracker-equx3c6n' 2025-09-08T05:19:40,227 Running setup.py (path:/tmp/pip-wheel-mgjnttoc/pybedtools_26583135c0fd45b193d3d740331c4843/setup.py) egg_info for package pybedtools 2025-09-08T05:19:40,227 Created temporary directory: /tmp/pip-pip-egg-info-_sw5x4l4 2025-09-08T05:19:40,227 Preparing metadata (setup.py): started 2025-09-08T05:19:40,228 Running command python setup.py egg_info 2025-09-08T05:19:40,773 /tmp/pip-wheel-mgjnttoc/pybedtools_26583135c0fd45b193d3d740331c4843/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. 2025-09-08T05:19:40,773 import pkg_resources 2025-09-08T05:19:41,349 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T05:19:41,349 warnings.warn(msg) 2025-09-08T05:19:41,718 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T05:19:41,718 !! 2025-09-08T05:19:41,718 ******************************************************************************** 2025-09-08T05:19:41,719 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T05:19:41,719 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T05:19:41,719 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T05:19:41,719 ******************************************************************************** 2025-09-08T05:19:41,719 !! 2025-09-08T05:19:41,719 self._finalize_license_expression() 2025-09-08T05:19:41,792 running egg_info 2025-09-08T05:19:41,867 creating /tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info 2025-09-08T05:19:41,867 writing /tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info/PKG-INFO 2025-09-08T05:19:41,869 writing dependency_links to /tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info/dependency_links.txt 2025-09-08T05:19:41,869 writing requirements to /tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info/requires.txt 2025-09-08T05:19:41,870 writing top-level names to /tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info/top_level.txt 2025-09-08T05:19:41,870 writing manifest file '/tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info/SOURCES.txt' 2025-09-08T05:19:42,102 reading manifest file '/tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info/SOURCES.txt' 2025-09-08T05:19:42,103 reading manifest template 'MANIFEST.in' 2025-09-08T05:19:42,144 warning: no previously-included files matching '__pycache__' found under directory '*' 2025-09-08T05:19:42,145 warning: no previously-included files matching '*.py[co]' found under directory '*' 2025-09-08T05:19:42,145 adding license file 'LICENSE.txt' 2025-09-08T05:19:42,157 writing manifest file '/tmp/pip-pip-egg-info-_sw5x4l4/pybedtools.egg-info/SOURCES.txt' 2025-09-08T05:19:42,281 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T05:19:42,286 Source in /tmp/pip-wheel-mgjnttoc/pybedtools_26583135c0fd45b193d3d740331c4843 has version 0.7.8, which satisfies requirement pybedtools==0.7.8 from https://files.pythonhosted.org/packages/2d/ee/aa19e50e03e06c817d00eadf8b56824b9e473da8c3e8ca3b33a11717ee6f/pybedtools-0.7.8.tar.gz 2025-09-08T05:19:42,286 Removed pybedtools==0.7.8 from https://files.pythonhosted.org/packages/2d/ee/aa19e50e03e06c817d00eadf8b56824b9e473da8c3e8ca3b33a11717ee6f/pybedtools-0.7.8.tar.gz from build tracker '/tmp/pip-build-tracker-equx3c6n' 2025-09-08T05:19:42,290 Created temporary directory: /tmp/pip-unpack-kk74oqj7 2025-09-08T05:19:42,290 Created temporary directory: /tmp/pip-unpack-yito85gm 2025-09-08T05:19:42,290 Building wheels for collected packages: pybedtools 2025-09-08T05:19:42,291 Created temporary directory: /tmp/pip-wheel-s6arg99b 2025-09-08T05:19:42,292 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 2025-09-08T05:19:42,293 Building wheel for pybedtools (setup.py): started 2025-09-08T05:19:42,293 Destination directory: /tmp/pip-wheel-s6arg99b 2025-09-08T05:19:42,294 Running command python setup.py bdist_wheel 2025-09-08T05:19:42,864 /tmp/pip-wheel-mgjnttoc/pybedtools_26583135c0fd45b193d3d740331c4843/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. 2025-09-08T05:19:42,864 import pkg_resources 2025-09-08T05:19:43,426 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T05:19:43,426 warnings.warn(msg) 2025-09-08T05:19:43,794 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T05:19:43,794 !! 2025-09-08T05:19:43,794 ******************************************************************************** 2025-09-08T05:19:43,794 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T05:19:43,795 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T05:19:43,795 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T05:19:43,795 ******************************************************************************** 2025-09-08T05:19:43,795 !! 2025-09-08T05:19:43,795 self._finalize_license_expression() 2025-09-08T05:19:43,796 running bdist_wheel 2025-09-08T05:19:43,940 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2025-09-08T05:19:43,941 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:135: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated 2025-09-08T05:19:43,941 !! 2025-09-08T05:19:43,941 ******************************************************************************** 2025-09-08T05:19:43,941 With Python 2.7 end-of-life, support for building universal wheels 2025-09-08T05:19:43,941 (i.e., wheels that support both Python 2 and Python 3) 2025-09-08T05:19:43,942 is being obviated. 2025-09-08T05:19:43,942 Please discontinue using this option, or if you still need it, 2025-09-08T05:19:43,942 file an issue with pypa/setuptools describing your use case. 2025-09-08T05:19:43,942 This deprecation is overdue, please update your project and remove deprecated 2025-09-08T05:19:43,942 calls to avoid build errors in the future. 2025-09-08T05:19:43,942 ******************************************************************************** 2025-09-08T05:19:43,942 !! 2025-09-08T05:19:43,942 self.finalize_options() 2025-09-08T05:19:44,017 running build 2025-09-08T05:19:44,017 running build_py 2025-09-08T05:19:44,092 creating build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,093 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,093 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,094 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,095 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,096 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,096 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,096 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,097 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,098 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,098 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,099 copying pybedtools/__main__.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,100 creating build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,100 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,101 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,101 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,102 copying pybedtools/test/a.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,103 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,103 copying pybedtools/test/test_scripts.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,104 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,104 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,105 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,105 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,106 copying pybedtools/test/test1.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,106 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T05:19:44,107 creating build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,108 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,108 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,109 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,109 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,110 copying pybedtools/contrib/classifier.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,110 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,111 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,111 copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T05:19:44,112 creating build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,113 copying pybedtools/scripts/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,113 copying pybedtools/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,114 copying pybedtools/scripts/venn_gchart.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,114 copying pybedtools/scripts/annotate.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,115 copying pybedtools/scripts/intron_exon_reads.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,115 copying pybedtools/scripts/venn_mpl.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,116 copying pybedtools/scripts/peak_pie.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,116 copying pybedtools/scripts/py_ms_example.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T05:19:44,117 creating build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,117 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,125 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,126 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,127 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,127 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,128 copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,128 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,129 copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,129 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,130 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,130 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,131 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,131 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,132 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,132 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,133 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,134 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,134 copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,135 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,135 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,136 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,136 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,137 copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,137 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,138 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,138 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,139 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,170 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,170 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,171 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,172 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,172 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,173 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,174 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,176 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,176 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,177 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,177 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,178 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,179 copying pybedtools/test/data/dm3 -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,179 copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,180 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,181 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,182 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,182 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,183 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,183 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,184 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,185 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,186 copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,187 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,187 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,188 copying pybedtools/test/data/1000genomes-example.vcf.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,188 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,196 copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,196 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,197 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,197 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,198 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,200 copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,200 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,201 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,201 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,211 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T05:19:44,211 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,212 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,212 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,213 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,214 copying pybedtools/cbedtools.cxx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,217 copying pybedtools/featurefuncs.cxx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,219 copying pybedtools/_Window.c -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,223 running build_ext 2025-09-08T05:19:44,229 building 'pybedtools.cbedtools' extension 2025-09-08T05:19:44,230 creating build/temp.linux-armv7l-cpython-313/pybedtools 2025-09-08T05:19:44,231 creating build/temp.linux-armv7l-cpython-313/src 2025-09-08T05:19:44,231 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 2025-09-08T05:19:44,849 pybedtools/cbedtools.cxx:16304:12: fatal error: longintrepr.h: No such file or directory 2025-09-08T05:19:44,849 16304 | #include "longintrepr.h" 2025-09-08T05:19:44,849 | ^~~~~~~~~~~~~~~ 2025-09-08T05:19:44,849 compilation terminated. 2025-09-08T05:19:44,854 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-08T05:19:44,981 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T05:19:44,993 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T05:19:44,993 exec(compile('"'"''"'"''"'"' 2025-09-08T05:19:44,993 # This is -- a caller that pip uses to run setup.py 2025-09-08T05:19:44,993 # 2025-09-08T05:19:44,993 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T05:19:44,993 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T05:19:44,993 # - It provides a clear error message when setuptools is not installed. 2025-09-08T05:19:44,993 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T05:19:44,993 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T05:19:44,993 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T05:19:44,993 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T05:19:44,993 import os, sys, tokenize, traceback 2025-09-08T05:19:44,993 2025-09-08T05:19:44,993 try: 2025-09-08T05:19:44,993 import setuptools 2025-09-08T05:19:44,993 except ImportError: 2025-09-08T05:19:44,993 print( 2025-09-08T05:19:44,993 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T05:19:44,993 "the build environment with exception:", 2025-09-08T05:19:44,993 file=sys.stderr, 2025-09-08T05:19:44,993 ) 2025-09-08T05:19:44,993 traceback.print_exc() 2025-09-08T05:19:44,993 sys.exit(1) 2025-09-08T05:19:44,993 2025-09-08T05:19:44,993 __file__ = %r 2025-09-08T05:19:44,993 sys.argv[0] = __file__ 2025-09-08T05:19:44,993 2025-09-08T05:19:44,993 if os.path.exists(__file__): 2025-09-08T05:19:44,993 filename = __file__ 2025-09-08T05:19:44,993 with tokenize.open(__file__) as f: 2025-09-08T05:19:44,993 setup_py_code = f.read() 2025-09-08T05:19:44,993 else: 2025-09-08T05:19:44,993 filename = "" 2025-09-08T05:19:44,993 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T05:19:44,993 2025-09-08T05:19:44,993 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T05:19:44,993 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-mgjnttoc/pybedtools_26583135c0fd45b193d3d740331c4843/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-s6arg99b[/] 2025-09-08T05:19:44,993 [bold magenta]cwd[/]: /tmp/pip-wheel-mgjnttoc/pybedtools_26583135c0fd45b193d3d740331c4843/ 2025-09-08T05:19:44,993 Building wheel for pybedtools (setup.py): finished with status 'error' 2025-09-08T05:19:44,994 ERROR: Failed building wheel for pybedtools 2025-09-08T05:19:44,995 Running setup.py clean for pybedtools 2025-09-08T05:19:44,995 Running command python setup.py clean 2025-09-08T05:19:45,545 /tmp/pip-wheel-mgjnttoc/pybedtools_26583135c0fd45b193d3d740331c4843/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. 2025-09-08T05:19:45,545 import pkg_resources 2025-09-08T05:19:46,102 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T05:19:46,103 warnings.warn(msg) 2025-09-08T05:19:46,479 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T05:19:46,479 !! 2025-09-08T05:19:46,479 ******************************************************************************** 2025-09-08T05:19:46,480 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T05:19:46,480 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T05:19:46,480 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T05:19:46,480 ******************************************************************************** 2025-09-08T05:19:46,480 !! 2025-09-08T05:19:46,480 self._finalize_license_expression() 2025-09-08T05:19:46,481 running clean 2025-09-08T05:19:46,612 Failed to build pybedtools 2025-09-08T05:19:46,613 ERROR: Failed to build one or more wheels 2025-09-08T05:19:46,614 Exception information: 2025-09-08T05:19:46,614 Traceback (most recent call last): 2025-09-08T05:19:46,614 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T05:19:46,614 status = _inner_run() 2025-09-08T05:19:46,614 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T05:19:46,614 return self.run(options, args) 2025-09-08T05:19:46,614 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T05:19:46,614 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T05:19:46,614 return func(self, options, args) 2025-09-08T05:19:46,614 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T05:19:46,614 raise CommandError("Failed to build one or more wheels") 2025-09-08T05:19:46,614 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T05:19:46,618 Removed build tracker: '/tmp/pip-build-tracker-equx3c6n'