2025-09-08T15:02:39,815 Created temporary directory: /tmp/pip-build-tracker-69ihyvz6 2025-09-08T15:02:39,816 Initialized build tracking at /tmp/pip-build-tracker-69ihyvz6 2025-09-08T15:02:39,816 Created build tracker: /tmp/pip-build-tracker-69ihyvz6 2025-09-08T15:02:39,816 Entered build tracker: /tmp/pip-build-tracker-69ihyvz6 2025-09-08T15:02:39,816 Created temporary directory: /tmp/pip-wheel-aw1wo65d 2025-09-08T15:02:39,819 Created temporary directory: /tmp/pip-ephem-wheel-cache-a2axvd4v 2025-09-08T15:02:39,878 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T15:02:39,881 2 location(s) to search for versions of pybedtools: 2025-09-08T15:02:39,881 * https://pypi.org/simple/pybedtools/ 2025-09-08T15:02:39,881 * https://www.piwheels.org/simple/pybedtools/ 2025-09-08T15:02:39,881 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2025-09-08T15:02:39,881 Getting page https://pypi.org/simple/pybedtools/ 2025-09-08T15:02:39,883 Found index url https://pypi.org/simple/ 2025-09-08T15:02:40,031 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2025-09-08T15:02:40,040 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 2025-09-08T15:02:40,040 Found link https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5dev 2025-09-08T15:02:40,041 Found link https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5rc1 2025-09-08T15:02:40,042 Found link https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5 2025-09-08T15:02:40,042 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 2025-09-08T15:02:40,042 Found link https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6rc1 2025-09-08T15:02:40,043 Found link https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6 2025-09-08T15:02:40,043 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 2025-09-08T15:02:40,044 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 2025-09-08T15:02:40,044 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 2025-09-08T15:02:40,045 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 2025-09-08T15:02:40,045 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 2025-09-08T15:02:40,046 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 2025-09-08T15:02:40,046 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 2025-09-08T15:02:40,047 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 2025-09-08T15:02:40,047 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 2025-09-08T15:02:40,048 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 2025-09-08T15:02:40,048 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 2025-09-08T15:02:40,049 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 2025-09-08T15:02:40,049 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 2025-09-08T15:02:40,049 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 2025-09-08T15:02:40,050 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 2025-09-08T15:02:40,050 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 2025-09-08T15:02:40,051 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 2025-09-08T15:02:40,051 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 2025-09-08T15:02:40,052 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 2025-09-08T15:02:40,052 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 2025-09-08T15:02:40,053 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 2025-09-08T15:02:40,053 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 2025-09-08T15:02:40,054 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 2025-09-08T15:02:40,054 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 2025-09-08T15:02:40,054 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 2025-09-08T15:02:40,054 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 2025-09-08T15:02:40,055 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2025-09-08T15:02:40,055 Getting page https://www.piwheels.org/simple/pybedtools/ 2025-09-08T15:02:40,056 Found index url https://www.piwheels.org/simple/ 2025-09-08T15:02:40,160 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 2025-09-08T15:02:40,175 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/) 2025-09-08T15:02:40,189 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/) 2025-09-08T15:02:40,189 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2025-09-08T15:02:40,189 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2025-09-08T15:02:40,214 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2025-09-08T15:02:40,215 Collecting pybedtools==0.8.0 2025-09-08T15:02:40,217 Created temporary directory: /tmp/pip-unpack-te8boj43 2025-09-08T15:02:40,358 Downloading pybedtools-0.8.0.tar.gz (12.5 MB) 2025-09-08T15:02:42,032 Added pybedtools==0.8.0 from https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz to build tracker '/tmp/pip-build-tracker-69ihyvz6' 2025-09-08T15:02:42,033 Running setup.py (path:/tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc/setup.py) egg_info for package pybedtools 2025-09-08T15:02:42,034 Created temporary directory: /tmp/pip-pip-egg-info-r9oradj6 2025-09-08T15:02:42,034 Preparing metadata (setup.py): started 2025-09-08T15:02:42,035 Running command python setup.py egg_info 2025-09-08T15:02:42,812 /tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc/setup.py:55: 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. 2025-09-08T15:02:42,812 import pkg_resources 2025-09-08T15:02:43,651 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T15:02:43,651 !! 2025-09-08T15:02:43,651 ******************************************************************************** 2025-09-08T15:02:43,651 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T15:02:43,652 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T15:02:43,652 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T15:02:43,652 ******************************************************************************** 2025-09-08T15:02:43,652 !! 2025-09-08T15:02:43,652 self._finalize_license_expression() 2025-09-08T15:02:43,727 running egg_info 2025-09-08T15:02:43,803 creating /tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info 2025-09-08T15:02:43,804 writing /tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info/PKG-INFO 2025-09-08T15:02:43,805 writing dependency_links to /tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info/dependency_links.txt 2025-09-08T15:02:43,805 writing requirements to /tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info/requires.txt 2025-09-08T15:02:43,806 writing top-level names to /tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info/top_level.txt 2025-09-08T15:02:43,806 writing manifest file '/tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info/SOURCES.txt' 2025-09-08T15:02:44,043 reading manifest file '/tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info/SOURCES.txt' 2025-09-08T15:02:44,044 adding license file 'LICENSE.txt' 2025-09-08T15:02:44,049 writing manifest file '/tmp/pip-pip-egg-info-r9oradj6/pybedtools.egg-info/SOURCES.txt' 2025-09-08T15:02:44,174 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T15:02:44,179 Source in /tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc has version 0.8.0, which satisfies requirement pybedtools==0.8.0 from https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz 2025-09-08T15:02:44,179 Removed pybedtools==0.8.0 from https://files.pythonhosted.org/packages/ca/b6/af143d5247cfe331e32c96ca92056293140eb8ce788d37842f6dcea734b4/pybedtools-0.8.0.tar.gz from build tracker '/tmp/pip-build-tracker-69ihyvz6' 2025-09-08T15:02:44,183 Created temporary directory: /tmp/pip-unpack-j30c6woi 2025-09-08T15:02:44,183 Created temporary directory: /tmp/pip-unpack-iwejgz9g 2025-09-08T15:02:44,184 Building wheels for collected packages: pybedtools 2025-09-08T15:02:44,185 Created temporary directory: /tmp/pip-wheel-435qmhy3 2025-09-08T15:02:44,186 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 2025-09-08T15:02:44,187 Building wheel for pybedtools (setup.py): started 2025-09-08T15:02:44,188 Destination directory: /tmp/pip-wheel-435qmhy3 2025-09-08T15:02:44,188 Running command python setup.py bdist_wheel 2025-09-08T15:02:44,944 /tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc/setup.py:55: 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. 2025-09-08T15:02:44,944 import pkg_resources 2025-09-08T15:02:45,692 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T15:02:45,692 !! 2025-09-08T15:02:45,692 ******************************************************************************** 2025-09-08T15:02:45,693 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T15:02:45,693 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T15:02:45,693 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T15:02:45,693 ******************************************************************************** 2025-09-08T15:02:45,693 !! 2025-09-08T15:02:45,693 self._finalize_license_expression() 2025-09-08T15:02:45,694 running bdist_wheel 2025-09-08T15:02:45,841 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2025-09-08T15:02:45,842 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:135: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated 2025-09-08T15:02:45,842 !! 2025-09-08T15:02:45,842 ******************************************************************************** 2025-09-08T15:02:45,842 With Python 2.7 end-of-life, support for building universal wheels 2025-09-08T15:02:45,842 (i.e., wheels that support both Python 2 and Python 3) 2025-09-08T15:02:45,843 is being obviated. 2025-09-08T15:02:45,843 Please discontinue using this option, or if you still need it, 2025-09-08T15:02:45,843 file an issue with pypa/setuptools describing your use case. 2025-09-08T15:02:45,843 This deprecation is overdue, please update your project and remove deprecated 2025-09-08T15:02:45,843 calls to avoid build errors in the future. 2025-09-08T15:02:45,843 ******************************************************************************** 2025-09-08T15:02:45,843 !! 2025-09-08T15:02:45,843 self.finalize_options() 2025-09-08T15:02:45,916 running build 2025-09-08T15:02:45,917 running build_py 2025-09-08T15:02:45,994 creating build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,994 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,995 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,996 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,996 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,997 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,998 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,998 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,999 copying pybedtools/__main__.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:45,999 copying pybedtools/paths.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,000 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,000 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,001 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,002 creating build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,002 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,003 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,003 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,004 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,004 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,005 copying pybedtools/test/test_issues.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,005 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,006 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,006 copying pybedtools/test/test1.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,007 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,007 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,008 copying pybedtools/test/test_scripts.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-08T15:02:46,009 creating build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,009 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,010 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,010 copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,011 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,011 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,012 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,012 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-08T15:02:46,013 creating build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,013 copying pybedtools/scripts/py_ms_example.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,014 copying pybedtools/scripts/intron_exon_reads.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,014 copying pybedtools/scripts/peak_pie.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,015 copying pybedtools/scripts/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,015 copying pybedtools/scripts/venn_gchart.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,016 copying pybedtools/scripts/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,016 copying pybedtools/scripts/annotate.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,017 copying pybedtools/scripts/venn_mpl.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,018 creating build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,018 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,018 running egg_info 2025-09-08T15:02:46,091 creating pybedtools.egg-info 2025-09-08T15:02:46,092 writing pybedtools.egg-info/PKG-INFO 2025-09-08T15:02:46,093 writing dependency_links to pybedtools.egg-info/dependency_links.txt 2025-09-08T15:02:46,094 writing requirements to pybedtools.egg-info/requires.txt 2025-09-08T15:02:46,094 writing top-level names to pybedtools.egg-info/top_level.txt 2025-09-08T15:02:46,094 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2025-09-08T15:02:46,179 reading manifest file 'pybedtools.egg-info/SOURCES.txt' 2025-09-08T15:02:46,180 adding license file 'LICENSE.txt' 2025-09-08T15:02:46,185 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2025-09-08T15:02:46,186 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. 2025-09-08T15:02:46,187 !! 2025-09-08T15:02:46,187 ******************************************************************************** 2025-09-08T15:02:46,187 ############################ 2025-09-08T15:02:46,187 # Package would be ignored # 2025-09-08T15:02:46,187 ############################ 2025-09-08T15:02:46,187 Python recognizes 'pybedtools.include' as an importable package[^1], 2025-09-08T15:02:46,187 but it is absent from setuptools' `packages` configuration. 2025-09-08T15:02:46,187 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T15:02:46,188 package, please make sure that 'pybedtools.include' is explicitly added 2025-09-08T15:02:46,188 to the `packages` configuration field. 2025-09-08T15:02:46,188 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T15:02:46,188 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T15:02:46,188 instead of `find_packages(...)`/`find:`). 2025-09-08T15:02:46,188 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T15:02:46,188 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T15:02:46,188 If you don't want 'pybedtools.include' to be distributed and are 2025-09-08T15:02:46,189 already explicitly excluding 'pybedtools.include' via 2025-09-08T15:02:46,189 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T15:02:46,189 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T15:02:46,189 combination with a more fine grained `package-data` configuration. 2025-09-08T15:02:46,189 You can read more about "package data files" on setuptools documentation page: 2025-09-08T15:02:46,189 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T15:02:46,189 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T15:02:46,190 even if it does not contain any `.py` files. 2025-09-08T15:02:46,190 On the other hand, currently there is no concept of package data 2025-09-08T15:02:46,190 directory, all directories are treated like packages. 2025-09-08T15:02:46,190 ******************************************************************************** 2025-09-08T15:02:46,190 !! 2025-09-08T15:02:46,190 check.warn(importable) 2025-09-08T15:02:46,190 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.scripts.examples' is absent from the `packages` configuration. 2025-09-08T15:02:46,190 !! 2025-09-08T15:02:46,190 ******************************************************************************** 2025-09-08T15:02:46,191 ############################ 2025-09-08T15:02:46,191 # Package would be ignored # 2025-09-08T15:02:46,191 ############################ 2025-09-08T15:02:46,191 Python recognizes 'pybedtools.scripts.examples' as an importable package[^1], 2025-09-08T15:02:46,191 but it is absent from setuptools' `packages` configuration. 2025-09-08T15:02:46,191 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T15:02:46,191 package, please make sure that 'pybedtools.scripts.examples' is explicitly added 2025-09-08T15:02:46,191 to the `packages` configuration field. 2025-09-08T15:02:46,191 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T15:02:46,192 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T15:02:46,192 instead of `find_packages(...)`/`find:`). 2025-09-08T15:02:46,192 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T15:02:46,192 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T15:02:46,192 If you don't want 'pybedtools.scripts.examples' to be distributed and are 2025-09-08T15:02:46,192 already explicitly excluding 'pybedtools.scripts.examples' via 2025-09-08T15:02:46,192 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T15:02:46,192 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T15:02:46,192 combination with a more fine grained `package-data` configuration. 2025-09-08T15:02:46,193 You can read more about "package data files" on setuptools documentation page: 2025-09-08T15:02:46,193 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T15:02:46,193 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T15:02:46,193 even if it does not contain any `.py` files. 2025-09-08T15:02:46,193 On the other hand, currently there is no concept of package data 2025-09-08T15:02:46,193 directory, all directories are treated like packages. 2025-09-08T15:02:46,193 ******************************************************************************** 2025-09-08T15:02:46,194 !! 2025-09-08T15:02:46,194 check.warn(importable) 2025-09-08T15:02:46,196 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,197 copying pybedtools/cbedtools.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,201 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,202 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,202 copying pybedtools/featurefuncs.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,204 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,205 creating build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-08T15:02:46,205 copying pybedtools/include/bedFile.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-08T15:02:46,206 copying pybedtools/include/fileType.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-08T15:02:46,206 copying pybedtools/include/gzstream.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-08T15:02:46,207 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,207 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,208 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,208 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,209 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,209 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,210 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,217 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,218 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,219 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,219 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,220 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,221 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,221 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,251 copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,252 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,253 copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,253 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,254 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,254 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,255 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,255 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,256 copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,256 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,257 copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,258 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,258 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,259 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,260 copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,261 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,261 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,262 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,262 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,263 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,264 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,264 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,265 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,265 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,266 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,267 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,268 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,278 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,280 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,280 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,281 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,281 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,282 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,283 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,283 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,284 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,286 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,286 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,287 copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,288 copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,288 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,289 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,289 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,290 copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,290 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,291 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,291 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,292 copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-08T15:02:46,292 copying pybedtools/scripts/pybedtools -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts 2025-09-08T15:02:46,293 creating build/lib.linux-armv7l-cpython-313/pybedtools/scripts/examples 2025-09-08T15:02:46,293 copying pybedtools/scripts/examples/pbt_plotting_example.py -> build/lib.linux-armv7l-cpython-313/pybedtools/scripts/examples 2025-09-08T15:02:46,306 running build_ext 2025-09-08T15:02:46,312 building 'pybedtools.cbedtools' extension 2025-09-08T15:02:46,314 creating build/temp.linux-armv7l-cpython-313/pybedtools 2025-09-08T15:02:46,314 creating build/temp.linux-armv7l-cpython-313/pybedtools/include 2025-09-08T15:02:46,315 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/cbedtools.o 2025-09-08T15:02:46,653 pybedtools/cbedtools.cpp:225:12: fatal error: longintrepr.h: No such file or directory 2025-09-08T15:02:46,654 225 | #include "longintrepr.h" 2025-09-08T15:02:46,654 | ^~~~~~~~~~~~~~~ 2025-09-08T15:02:46,654 compilation terminated. 2025-09-08T15:02:46,658 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-08T15:02:46,787 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T15:02:46,801 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T15:02:46,801 exec(compile('"'"''"'"''"'"' 2025-09-08T15:02:46,801 # This is -- a caller that pip uses to run setup.py 2025-09-08T15:02:46,801 # 2025-09-08T15:02:46,801 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T15:02:46,801 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T15:02:46,801 # - It provides a clear error message when setuptools is not installed. 2025-09-08T15:02:46,801 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T15:02:46,801 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T15:02:46,801 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T15:02:46,801 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T15:02:46,801 import os, sys, tokenize, traceback 2025-09-08T15:02:46,801 2025-09-08T15:02:46,801 try: 2025-09-08T15:02:46,801 import setuptools 2025-09-08T15:02:46,801 except ImportError: 2025-09-08T15:02:46,801 print( 2025-09-08T15:02:46,801 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T15:02:46,801 "the build environment with exception:", 2025-09-08T15:02:46,801 file=sys.stderr, 2025-09-08T15:02:46,801 ) 2025-09-08T15:02:46,801 traceback.print_exc() 2025-09-08T15:02:46,801 sys.exit(1) 2025-09-08T15:02:46,801 2025-09-08T15:02:46,801 __file__ = %r 2025-09-08T15:02:46,801 sys.argv[0] = __file__ 2025-09-08T15:02:46,801 2025-09-08T15:02:46,801 if os.path.exists(__file__): 2025-09-08T15:02:46,801 filename = __file__ 2025-09-08T15:02:46,801 with tokenize.open(__file__) as f: 2025-09-08T15:02:46,801 setup_py_code = f.read() 2025-09-08T15:02:46,801 else: 2025-09-08T15:02:46,801 filename = "" 2025-09-08T15:02:46,801 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T15:02:46,801 2025-09-08T15:02:46,801 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T15:02:46,801 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-435qmhy3[/] 2025-09-08T15:02:46,801 [bold magenta]cwd[/]: /tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc/ 2025-09-08T15:02:46,801 Building wheel for pybedtools (setup.py): finished with status 'error' 2025-09-08T15:02:46,802 ERROR: Failed building wheel for pybedtools 2025-09-08T15:02:46,803 Running setup.py clean for pybedtools 2025-09-08T15:02:46,804 Running command python setup.py clean 2025-09-08T15:02:47,561 /tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc/setup.py:55: 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. 2025-09-08T15:02:47,561 import pkg_resources 2025-09-08T15:02:48,332 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T15:02:48,332 !! 2025-09-08T15:02:48,332 ******************************************************************************** 2025-09-08T15:02:48,332 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T15:02:48,332 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T15:02:48,333 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T15:02:48,333 ******************************************************************************** 2025-09-08T15:02:48,333 !! 2025-09-08T15:02:48,333 self._finalize_license_expression() 2025-09-08T15:02:48,333 usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] 2025-09-08T15:02:48,333 or: setup.py --help [cmd1 cmd2 ...] 2025-09-08T15:02:48,333 or: setup.py --help-commands 2025-09-08T15:02:48,333 or: setup.py cmd --help 2025-09-08T15:02:48,334 error: option --all not recognized 2025-09-08T15:02:48,457 ERROR: python setup.py clean exited with 1 2025-09-08T15:02:48,462 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T15:02:48,462 exec(compile('"'"''"'"''"'"' 2025-09-08T15:02:48,462 # This is -- a caller that pip uses to run setup.py 2025-09-08T15:02:48,462 # 2025-09-08T15:02:48,462 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T15:02:48,462 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T15:02:48,462 # - It provides a clear error message when setuptools is not installed. 2025-09-08T15:02:48,462 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T15:02:48,462 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T15:02:48,462 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T15:02:48,462 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T15:02:48,462 import os, sys, tokenize, traceback 2025-09-08T15:02:48,462 2025-09-08T15:02:48,462 try: 2025-09-08T15:02:48,462 import setuptools 2025-09-08T15:02:48,462 except ImportError: 2025-09-08T15:02:48,462 print( 2025-09-08T15:02:48,462 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T15:02:48,462 "the build environment with exception:", 2025-09-08T15:02:48,462 file=sys.stderr, 2025-09-08T15:02:48,462 ) 2025-09-08T15:02:48,462 traceback.print_exc() 2025-09-08T15:02:48,462 sys.exit(1) 2025-09-08T15:02:48,462 2025-09-08T15:02:48,462 __file__ = %r 2025-09-08T15:02:48,462 sys.argv[0] = __file__ 2025-09-08T15:02:48,462 2025-09-08T15:02:48,462 if os.path.exists(__file__): 2025-09-08T15:02:48,462 filename = __file__ 2025-09-08T15:02:48,462 with tokenize.open(__file__) as f: 2025-09-08T15:02:48,462 setup_py_code = f.read() 2025-09-08T15:02:48,462 else: 2025-09-08T15:02:48,462 filename = "" 2025-09-08T15:02:48,462 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T15:02:48,462 2025-09-08T15:02:48,462 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T15:02:48,462 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc/setup.py'"'"',), "", "exec"))' clean --all[/] 2025-09-08T15:02:48,462 [bold magenta]cwd[/]: /tmp/pip-wheel-aw1wo65d/pybedtools_bff56d17644643218103e7c0c95c62fc 2025-09-08T15:02:48,462 ERROR: Failed cleaning build dir for pybedtools 2025-09-08T15:02:48,464 Failed to build pybedtools 2025-09-08T15:02:48,464 ERROR: Failed to build one or more wheels 2025-09-08T15:02:48,465 Exception information: 2025-09-08T15:02:48,465 Traceback (most recent call last): 2025-09-08T15:02:48,465 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T15:02:48,465 status = _inner_run() 2025-09-08T15:02:48,465 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T15:02:48,465 return self.run(options, args) 2025-09-08T15:02:48,465 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T15:02:48,465 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T15:02:48,465 return func(self, options, args) 2025-09-08T15:02:48,465 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T15:02:48,465 raise CommandError("Failed to build one or more wheels") 2025-09-08T15:02:48,465 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T15:02:48,470 Removed build tracker: '/tmp/pip-build-tracker-69ihyvz6'