2025-09-10T05:16:52,926 Created temporary directory: /tmp/pip-build-tracker-zwo802pp 2025-09-10T05:16:52,927 Initialized build tracking at /tmp/pip-build-tracker-zwo802pp 2025-09-10T05:16:52,927 Created build tracker: /tmp/pip-build-tracker-zwo802pp 2025-09-10T05:16:52,927 Entered build tracker: /tmp/pip-build-tracker-zwo802pp 2025-09-10T05:16:52,927 Created temporary directory: /tmp/pip-wheel-q54nh1kg 2025-09-10T05:16:52,931 Created temporary directory: /tmp/pip-ephem-wheel-cache-rhjafr9t 2025-09-10T05:16:52,990 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-10T05:16:52,993 2 location(s) to search for versions of pybedtools: 2025-09-10T05:16:52,993 * https://pypi.org/simple/pybedtools/ 2025-09-10T05:16:52,993 * https://www.piwheels.org/simple/pybedtools/ 2025-09-10T05:16:52,993 Fetching project page and analyzing links: https://pypi.org/simple/pybedtools/ 2025-09-10T05:16:52,994 Getting page https://pypi.org/simple/pybedtools/ 2025-09-10T05:16:52,995 Found index url https://pypi.org/simple/ 2025-09-10T05:16:53,146 Fetched page https://pypi.org/simple/pybedtools/ as application/vnd.pypi.simple.v1+json 2025-09-10T05:16:53,150 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 2025-09-10T05:16:53,151 Found link https://files.pythonhosted.org/packages/44/19/a9bebb9eccd8d64d58202d5b3a151de81ffc7703a47503161b7615554703/pybedtools-0.5dev.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5dev 2025-09-10T05:16:53,151 Found link https://files.pythonhosted.org/packages/e4/2f/e842c6b1165d706ebc62c931c11d4dfffe60e6b045ecf80eef7ea78d7afc/pybedtools-0.5rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5rc1 2025-09-10T05:16:53,151 Found link https://files.pythonhosted.org/packages/85/17/c89028c00537638629ca21be7f1b84e963fc8b63c1e9a5fda9884f86fb90/pybedtools-0.5.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.5 2025-09-10T05:16:53,151 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 2025-09-10T05:16:53,152 Found link https://files.pythonhosted.org/packages/3c/e7/365015ec8104195329635cb75ef745bff45d905271cd165f5048efaf48e3/pybedtools-0.6rc1.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6rc1 2025-09-10T05:16:53,152 Found link https://files.pythonhosted.org/packages/04/ce/0e1480725fe80eb9a401f59e1bcc28fce721f6c2c5d7be233894d0154551/pybedtools-0.6.tar.gz (from https://pypi.org/simple/pybedtools/), version: 0.6 2025-09-10T05:16:53,152 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 2025-09-10T05:16:53,153 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 2025-09-10T05:16:53,153 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 2025-09-10T05:16:53,153 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 2025-09-10T05:16:53,153 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 2025-09-10T05:16:53,154 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 2025-09-10T05:16:53,154 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 2025-09-10T05:16:53,154 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 2025-09-10T05:16:53,155 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 2025-09-10T05:16:53,155 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 2025-09-10T05:16:53,155 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 2025-09-10T05:16:53,155 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 2025-09-10T05:16:53,156 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 2025-09-10T05:16:53,156 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 2025-09-10T05:16:53,156 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 2025-09-10T05:16:53,156 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 2025-09-10T05:16:53,157 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 2025-09-10T05:16:53,157 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 2025-09-10T05:16:53,157 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 2025-09-10T05:16:53,157 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 2025-09-10T05:16:53,158 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 2025-09-10T05:16:53,158 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 2025-09-10T05:16:53,158 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 2025-09-10T05:16:53,158 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 2025-09-10T05:16:53,159 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 2025-09-10T05:16:53,159 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 2025-09-10T05:16:53,159 Fetching project page and analyzing links: https://www.piwheels.org/simple/pybedtools/ 2025-09-10T05:16:53,160 Getting page https://www.piwheels.org/simple/pybedtools/ 2025-09-10T05:16:53,161 Found index url https://www.piwheels.org/simple/ 2025-09-10T05:16:53,255 Fetched page https://www.piwheels.org/simple/pybedtools/ as text/html 2025-09-10T05:16:53,272 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/) 2025-09-10T05:16:53,283 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/) 2025-09-10T05:16:53,283 Skipping link: not a file: https://www.piwheels.org/simple/pybedtools/ 2025-09-10T05:16:53,284 Skipping link: not a file: https://pypi.org/simple/pybedtools/ 2025-09-10T05:16:53,309 Given no hashes to check 1 links for project 'pybedtools': discarding no candidates 2025-09-10T05:16:53,311 Collecting pybedtools==0.9.0 2025-09-10T05:16:53,312 Created temporary directory: /tmp/pip-unpack-fcnrydv3 2025-09-10T05:16:53,456 Downloading pybedtools-0.9.0.tar.gz (12.5 MB) 2025-09-10T05:16:55,183 Added pybedtools==0.9.0 from https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz to build tracker '/tmp/pip-build-tracker-zwo802pp' 2025-09-10T05:16:55,185 Running setup.py (path:/tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e/setup.py) egg_info for package pybedtools 2025-09-10T05:16:55,185 Created temporary directory: /tmp/pip-pip-egg-info-d72ad5xs 2025-09-10T05:16:55,185 Preparing metadata (setup.py): started 2025-09-10T05:16:55,186 Running command python setup.py egg_info 2025-09-10T05:16:56,007 /tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e/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. 2025-09-10T05:16:56,007 import pkg_resources 2025-09-10T05:16:56,928 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-10T05:16:56,928 !! 2025-09-10T05:16:56,929 ******************************************************************************** 2025-09-10T05:16:56,929 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-10T05:16:56,929 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-10T05:16:56,929 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-10T05:16:56,929 ******************************************************************************** 2025-09-10T05:16:56,930 !! 2025-09-10T05:16:56,930 self._finalize_license_expression() 2025-09-10T05:16:57,024 running egg_info 2025-09-10T05:16:57,116 creating /tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info 2025-09-10T05:16:57,116 writing /tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info/PKG-INFO 2025-09-10T05:16:57,118 writing dependency_links to /tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info/dependency_links.txt 2025-09-10T05:16:57,119 writing requirements to /tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info/requires.txt 2025-09-10T05:16:57,119 writing top-level names to /tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info/top_level.txt 2025-09-10T05:16:57,120 writing manifest file '/tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info/SOURCES.txt' 2025-09-10T05:16:57,325 reading manifest file '/tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info/SOURCES.txt' 2025-09-10T05:16:57,325 adding license file 'LICENSE.txt' 2025-09-10T05:16:57,331 writing manifest file '/tmp/pip-pip-egg-info-d72ad5xs/pybedtools.egg-info/SOURCES.txt' 2025-09-10T05:16:57,489 Preparing metadata (setup.py): finished with status 'done' 2025-09-10T05:16:57,495 Source in /tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e has version 0.9.0, which satisfies requirement pybedtools==0.9.0 from https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz 2025-09-10T05:16:57,495 Removed pybedtools==0.9.0 from https://files.pythonhosted.org/packages/58/e2/410bb188b47582e2fd2f7176173b7b7bf46e122bb17fb4422552f4a6c604/pybedtools-0.9.0.tar.gz from build tracker '/tmp/pip-build-tracker-zwo802pp' 2025-09-10T05:16:57,499 Created temporary directory: /tmp/pip-unpack-tpz6wymh 2025-09-10T05:16:57,499 Created temporary directory: /tmp/pip-unpack-xzn9t3_1 2025-09-10T05:16:57,500 Building wheels for collected packages: pybedtools 2025-09-10T05:16:57,501 Created temporary directory: /tmp/pip-wheel-6zutxrxu 2025-09-10T05:16:57,501 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 2025-09-10T05:16:57,503 Building wheel for pybedtools (setup.py): started 2025-09-10T05:16:57,504 Destination directory: /tmp/pip-wheel-6zutxrxu 2025-09-10T05:16:57,504 Running command python setup.py bdist_wheel 2025-09-10T05:16:58,325 /tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e/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. 2025-09-10T05:16:58,325 import pkg_resources 2025-09-10T05:16:59,242 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-10T05:16:59,242 !! 2025-09-10T05:16:59,242 ******************************************************************************** 2025-09-10T05:16:59,242 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-10T05:16:59,243 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-10T05:16:59,243 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-10T05:16:59,243 ******************************************************************************** 2025-09-10T05:16:59,243 !! 2025-09-10T05:16:59,243 self._finalize_license_expression() 2025-09-10T05:16:59,244 running bdist_wheel 2025-09-10T05:16:59,430 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2025-09-10T05:16:59,431 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:135: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated 2025-09-10T05:16:59,431 !! 2025-09-10T05:16:59,432 ******************************************************************************** 2025-09-10T05:16:59,432 With Python 2.7 end-of-life, support for building universal wheels 2025-09-10T05:16:59,432 (i.e., wheels that support both Python 2 and Python 3) 2025-09-10T05:16:59,432 is being obviated. 2025-09-10T05:16:59,432 Please discontinue using this option, or if you still need it, 2025-09-10T05:16:59,432 file an issue with pypa/setuptools describing your use case. 2025-09-10T05:16:59,432 This deprecation is overdue, please update your project and remove deprecated 2025-09-10T05:16:59,433 calls to avoid build errors in the future. 2025-09-10T05:16:59,433 ******************************************************************************** 2025-09-10T05:16:59,433 !! 2025-09-10T05:16:59,433 self.finalize_options() 2025-09-10T05:16:59,526 running build 2025-09-10T05:16:59,527 running build_py 2025-09-10T05:16:59,626 creating build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,627 copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,627 copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,628 copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,629 copying pybedtools/paths.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,629 copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,630 copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,631 copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,632 copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,633 copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,634 copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,635 copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,636 creating build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,637 copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,637 copying pybedtools/test/test_pathlib.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,638 copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,639 copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,639 copying pybedtools/test/test_issues.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,640 copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,641 copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,642 copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,642 copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,643 copying pybedtools/test/test_1.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,644 copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,645 copying pybedtools/test/genomepy_integration.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,646 copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test 2025-09-10T05:16:59,647 creating build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,647 copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,648 copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,649 copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,649 copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,650 copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,651 copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,652 copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib 2025-09-10T05:16:59,653 creating build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,653 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,654 running egg_info 2025-09-10T05:16:59,750 creating pybedtools.egg-info 2025-09-10T05:16:59,750 writing pybedtools.egg-info/PKG-INFO 2025-09-10T05:16:59,752 writing dependency_links to pybedtools.egg-info/dependency_links.txt 2025-09-10T05:16:59,753 writing requirements to pybedtools.egg-info/requires.txt 2025-09-10T05:16:59,754 writing top-level names to pybedtools.egg-info/top_level.txt 2025-09-10T05:16:59,754 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2025-09-10T05:16:59,868 reading manifest file 'pybedtools.egg-info/SOURCES.txt' 2025-09-10T05:16:59,869 adding license file 'LICENSE.txt' 2025-09-10T05:16:59,875 writing manifest file 'pybedtools.egg-info/SOURCES.txt' 2025-09-10T05:16:59,876 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. 2025-09-10T05:16:59,876 !! 2025-09-10T05:16:59,877 ******************************************************************************** 2025-09-10T05:16:59,877 ############################ 2025-09-10T05:16:59,877 # Package would be ignored # 2025-09-10T05:16:59,877 ############################ 2025-09-10T05:16:59,877 Python recognizes 'pybedtools.include' as an importable package[^1], 2025-09-10T05:16:59,877 but it is absent from setuptools' `packages` configuration. 2025-09-10T05:16:59,877 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-10T05:16:59,877 package, please make sure that 'pybedtools.include' is explicitly added 2025-09-10T05:16:59,878 to the `packages` configuration field. 2025-09-10T05:16:59,878 Alternatively, you can also rely on setuptools' discovery methods 2025-09-10T05:16:59,878 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-10T05:16:59,878 instead of `find_packages(...)`/`find:`). 2025-09-10T05:16:59,878 You can read more about "package discovery" on setuptools documentation page: 2025-09-10T05:16:59,878 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-10T05:16:59,879 If you don't want 'pybedtools.include' to be distributed and are 2025-09-10T05:16:59,879 already explicitly excluding 'pybedtools.include' via 2025-09-10T05:16:59,879 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-10T05:16:59,879 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-10T05:16:59,879 combination with a more fine grained `package-data` configuration. 2025-09-10T05:16:59,879 You can read more about "package data files" on setuptools documentation page: 2025-09-10T05:16:59,879 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-10T05:16:59,880 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-10T05:16:59,880 even if it does not contain any `.py` files. 2025-09-10T05:16:59,880 On the other hand, currently there is no concept of package data 2025-09-10T05:16:59,880 directory, all directories are treated like packages. 2025-09-10T05:16:59,880 ******************************************************************************** 2025-09-10T05:16:59,880 !! 2025-09-10T05:16:59,880 check.warn(importable) 2025-09-10T05:16:59,888 copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,888 copying pybedtools/cbedtools.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,893 copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,894 copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,895 copying pybedtools/featurefuncs.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,897 copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:16:59,898 creating build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-10T05:16:59,898 copying pybedtools/include/bedFile.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-10T05:16:59,899 copying pybedtools/include/fileType.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-10T05:16:59,900 copying pybedtools/include/gzstream.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include 2025-09-10T05:16:59,901 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,901 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,912 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,921 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,921 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,922 copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,923 copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,924 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,924 copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,925 copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,926 copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,927 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,927 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,928 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,929 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,929 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,964 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,965 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,966 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,966 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,967 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,968 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,969 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,969 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,970 copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,971 copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,972 copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,973 copying pybedtools/test/data/issue319.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,974 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,975 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,975 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,977 copying pybedtools/test/data/genome.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,978 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,978 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,979 copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,980 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,981 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,981 copying pybedtools/test/data/gdc.cram -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,982 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,983 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,983 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,984 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,985 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,985 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,986 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,987 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,988 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,990 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,993 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,993 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,994 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,995 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,995 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,996 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,997 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,998 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,998 copying pybedtools/test/data/a.bed.gz.tbi -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:16:59,999 copying pybedtools/test/data/a.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,000 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,000 copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,001 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,002 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,003 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,005 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,006 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,007 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,008 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,009 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,010 copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,011 copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,012 copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,012 copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,013 copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,014 copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,015 copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,016 copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,017 copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,019 copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,020 copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,021 copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,022 copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,023 copying pybedtools/test/data/a.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,024 copying pybedtools/test/data/a.bed.gz.tbi -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,024 copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,025 copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,026 copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,027 copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,027 copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,028 copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,029 copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,030 copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,030 copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,033 copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,035 copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,036 copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,037 copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,038 copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,038 copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,039 copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,040 copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,040 copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,041 copying pybedtools/test/data/gdc.cram -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,042 copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,043 copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,044 copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,044 copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,045 copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,046 copying pybedtools/test/data/genome.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,047 copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,048 copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,049 copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,050 copying pybedtools/test/data/issue319.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,051 copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,052 copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,053 copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,054 copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,054 copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,055 copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,056 copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,057 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,057 copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,058 copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,059 copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,060 copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,096 copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,097 copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,098 copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,098 copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,099 copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,100 copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,100 copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,101 copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,102 copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,103 copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,104 copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,104 copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,105 copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,114 copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,126 copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data 2025-09-10T05:17:00,128 running build_ext 2025-09-10T05:17:00,136 building 'pybedtools.cbedtools' extension 2025-09-10T05:17:00,138 creating build/temp.linux-armv7l-cpython-313/pybedtools 2025-09-10T05:17:00,138 creating build/temp.linux-armv7l-cpython-313/pybedtools/include 2025-09-10T05:17:00,139 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 2025-09-10T05:17:02,821 In file included from pybedtools/cbedtools.cpp:731: 2025-09-10T05:17:02,822 pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: 2025-09-10T05:17:02,822 pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 2025-09-10T05:17:02,822 92 | for (register short i = 0; i < _binLevels; ++i) { 2025-09-10T05:17:02,822 | ^ 2025-09-10T05:17:02,881 pybedtools/cbedtools.cpp: At global scope: 2025-09-10T05:17:02,881 pybedtools/cbedtools.cpp:810:72: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:02,881 810 | static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { 2025-09-10T05:17:02,881 | ^ 2025-09-10T05:17:02,882 In file included from /usr/include/python3.13/unicodeobject.h:1014, 2025-09-10T05:17:02,882 from /usr/include/python3.13/Python.h:79, 2025-09-10T05:17:02,882 from pybedtools/cbedtools.cpp:35: 2025-09-10T05:17:02,882 /usr/include/python3.13/cpython/unicodeobject.h:10:37: note: declared here 2025-09-10T05:17:02,882 10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE; 2025-09-10T05:17:02,882 | ^~~~~~~~~~ 2025-09-10T05:17:02,882 pybedtools/cbedtools.cpp: In function ‘size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE*)’: 2025-09-10T05:17:02,883 pybedtools/cbedtools.cpp:811:23: warning: ‘Py_UNICODE’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:02,883 811 | const Py_UNICODE *u_end = u; 2025-09-10T05:17:02,883 | ^~~~~ 2025-09-10T05:17:02,883 /usr/include/python3.13/cpython/unicodeobject.h:10:37: note: declared here 2025-09-10T05:17:02,883 10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE; 2025-09-10T05:17:02,883 | ^~~~~~~~~~ 2025-09-10T05:17:02,920 pybedtools/cbedtools.cpp: In function ‘int __Pyx_PyList_Extend(PyObject*, PyObject*)’: 2025-09-10T05:17:02,920 pybedtools/cbedtools.cpp:1394:22: error: ‘_PyList_Extend’ was not declared in this scope; did you mean ‘PyList_Extend’? 2025-09-10T05:17:02,920 1394 | PyObject* none = _PyList_Extend((PyListObject*)L, v); 2025-09-10T05:17:02,920 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:02,920 | PyList_Extend 2025-09-10T05:17:03,076 pybedtools/cbedtools.cpp: In function ‘PyObject* __pyx_pf_10pybedtools_9cbedtools_8Interval_6__richcmp__(__pyx_obj_10pybedtools_9cbedtools_Interval*, PyObject*, int)’: 2025-09-10T05:17:03,077 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,077 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,077 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,077 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,077 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,077 | ^ 2025-09-10T05:17:03,077 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,077 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,077 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,078 pybedtools/cbedtools.cpp:5008:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,078 5008 | __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 303, __pyx_L7_error) 2025-09-10T05:17:03,078 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,078 In file included from /usr/include/python3.13/dictobject.h:101, 2025-09-10T05:17:03,078 from /usr/include/python3.13/Python.h:90: 2025-09-10T05:17:03,078 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,078 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,078 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,078 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,078 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,079 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,079 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,079 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,079 | ^ 2025-09-10T05:17:03,079 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,079 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,079 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,079 pybedtools/cbedtools.cpp:5008:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,079 5008 | __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 303, __pyx_L7_error) 2025-09-10T05:17:03,079 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,080 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,080 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,080 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,080 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,080 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,080 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,080 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,081 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,081 | ^ 2025-09-10T05:17:03,081 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,081 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,081 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,081 pybedtools/cbedtools.cpp:5008:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,081 5008 | __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 303, __pyx_L7_error) 2025-09-10T05:17:03,081 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,081 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,082 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,082 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,085 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,085 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,085 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,085 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,085 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,085 | ^ 2025-09-10T05:17:03,085 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,085 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,085 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,085 pybedtools/cbedtools.cpp:5063:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,086 5063 | __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 307, __pyx_L7_error) 2025-09-10T05:17:03,086 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,086 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,086 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,086 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,086 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,086 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,086 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,086 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,087 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,087 | ^ 2025-09-10T05:17:03,087 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,087 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,087 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,087 pybedtools/cbedtools.cpp:5063:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,087 5063 | __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 307, __pyx_L7_error) 2025-09-10T05:17:03,087 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,087 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,088 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,088 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,088 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,088 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,088 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,088 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,088 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,088 | ^ 2025-09-10T05:17:03,089 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,089 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,089 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,089 pybedtools/cbedtools.cpp:5063:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,089 5063 | __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 307, __pyx_L7_error) 2025-09-10T05:17:03,089 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,089 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,089 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,090 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,091 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,091 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,091 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,091 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,091 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,091 | ^ 2025-09-10T05:17:03,091 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,092 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,092 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,092 pybedtools/cbedtools.cpp:5124:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,092 5124 | __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 311, __pyx_L7_error) 2025-09-10T05:17:03,092 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,092 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,092 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,092 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,092 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,093 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,093 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,093 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,093 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,093 | ^ 2025-09-10T05:17:03,093 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,093 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,093 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,093 pybedtools/cbedtools.cpp:5124:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,093 5124 | __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 311, __pyx_L7_error) 2025-09-10T05:17:03,094 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,094 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,094 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,094 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,094 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,094 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,094 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,095 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,095 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,095 | ^ 2025-09-10T05:17:03,095 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,095 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,095 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,095 pybedtools/cbedtools.cpp:5124:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,095 5124 | __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_PROFILES_TRUE); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 311, __pyx_L7_error) 2025-09-10T05:17:03,096 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,096 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,096 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,096 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,159 pybedtools/cbedtools.cpp: In function ‘PyObject* __pyx_pf_10pybedtools_9cbedtools_8Interval_5attrs___get__(__pyx_obj_10pybedtools_9cbedtools_Interval*)’: 2025-09-10T05:17:03,159 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,159 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,159 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,159 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,159 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,159 | ^ 2025-09-10T05:17:03,159 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,159 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,160 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,160 pybedtools/cbedtools.cpp:6542:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,160 6542 | __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 393, __pyx_L1_error) 2025-09-10T05:17:03,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,160 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,160 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,160 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,160 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,160 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,160 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,161 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,161 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,161 | ^ 2025-09-10T05:17:03,161 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,161 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,161 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,161 pybedtools/cbedtools.cpp:6542:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,161 6542 | __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 393, __pyx_L1_error) 2025-09-10T05:17:03,161 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,161 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,162 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,162 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,162 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,162 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,162 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,162 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,162 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,163 | ^ 2025-09-10T05:17:03,163 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,163 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,163 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,163 pybedtools/cbedtools.cpp:6542:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,163 6542 | __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 393, __pyx_L1_error) 2025-09-10T05:17:03,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,163 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,163 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,164 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,166 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,167 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,167 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,167 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,167 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,167 | ^ 2025-09-10T05:17:03,167 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,167 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,167 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,167 pybedtools/cbedtools.cpp:6586:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,168 6586 | __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 395, __pyx_L1_error) 2025-09-10T05:17:03,168 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,168 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,168 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,168 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,168 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,168 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,168 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,168 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,168 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,169 | ^ 2025-09-10T05:17:03,169 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,169 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,169 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,169 pybedtools/cbedtools.cpp:6586:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,169 6586 | __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 395, __pyx_L1_error) 2025-09-10T05:17:03,169 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,169 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,169 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,169 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,170 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,170 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,170 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,170 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,170 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,170 | ^ 2025-09-10T05:17:03,170 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,171 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,171 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,171 pybedtools/cbedtools.cpp:6586:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,171 6586 | __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_Attributes); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 395, __pyx_L1_error) 2025-09-10T05:17:03,171 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,171 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,171 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,171 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,286 pybedtools/cbedtools.cpp: In function ‘PyObject* __pyx_f_10pybedtools_9cbedtools_isdigit(PyObject*)’: 2025-09-10T05:17:03,286 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,286 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,286 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,286 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,287 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,287 | ^ 2025-09-10T05:17:03,287 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,287 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,287 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,287 pybedtools/cbedtools.cpp:9414:3: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,287 9414 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_integer_types); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 577, __pyx_L1_error) 2025-09-10T05:17:03,287 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,287 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,287 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,288 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,288 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,288 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,288 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,288 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,288 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,288 | ^ 2025-09-10T05:17:03,288 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,288 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,288 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,289 pybedtools/cbedtools.cpp:9414:3: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,289 9414 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_integer_types); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 577, __pyx_L1_error) 2025-09-10T05:17:03,289 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,289 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,289 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,289 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,289 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,289 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,290 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,290 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,290 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,290 | ^ 2025-09-10T05:17:03,290 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,290 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,290 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,290 pybedtools/cbedtools.cpp:9414:3: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,291 9414 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_integer_types); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 577, __pyx_L1_error) 2025-09-10T05:17:03,291 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,291 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,291 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,291 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,399 pybedtools/cbedtools.cpp: In function ‘__pyx_obj_10pybedtools_9cbedtools_Interval* __pyx_f_10pybedtools_9cbedtools_create_interval_from_list(PyObject*, int)’: 2025-09-10T05:17:03,399 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,399 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,400 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,400 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,400 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,400 | ^ 2025-09-10T05:17:03,400 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,400 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,400 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,400 pybedtools/cbedtools.cpp:10726:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,400 10726 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 699, __pyx_L1_error) 2025-09-10T05:17:03,400 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,400 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,401 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,401 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,401 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,401 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,401 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,401 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,402 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,402 | ^ 2025-09-10T05:17:03,402 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,402 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,402 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,402 pybedtools/cbedtools.cpp:10726:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,402 10726 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 699, __pyx_L1_error) 2025-09-10T05:17:03,402 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,402 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,403 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,403 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,403 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,403 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,404 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,404 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,404 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,404 | ^ 2025-09-10T05:17:03,404 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,404 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,404 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,404 pybedtools/cbedtools.cpp:10726:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,405 10726 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 699, __pyx_L1_error) 2025-09-10T05:17:03,405 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,405 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,405 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,405 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,410 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,410 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,410 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,410 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,411 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,411 | ^ 2025-09-10T05:17:03,411 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,411 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,411 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,411 pybedtools/cbedtools.cpp:10777:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,411 10777 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 702, __pyx_L1_error) 2025-09-10T05:17:03,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,411 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,411 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,412 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,412 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,412 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,412 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,412 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,412 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,412 | ^ 2025-09-10T05:17:03,413 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,413 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,413 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,413 pybedtools/cbedtools.cpp:10777:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,413 10777 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 702, __pyx_L1_error) 2025-09-10T05:17:03,413 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,413 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,413 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,413 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,414 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,414 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,414 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,414 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,414 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,414 | ^ 2025-09-10T05:17:03,415 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,415 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,415 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,415 pybedtools/cbedtools.cpp:10777:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,415 10777 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 702, __pyx_L1_error) 2025-09-10T05:17:03,415 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,415 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,415 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,416 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,502 pybedtools/cbedtools.cpp: In function ‘PyObject* __pyx_pf_10pybedtools_9cbedtools_16IntervalIterator_8__reduce_cython__(__pyx_obj_10pybedtools_9cbedtools_IntervalIterator*)’: 2025-09-10T05:17:03,502 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,502 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,502 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,502 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,502 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,503 | ^ 2025-09-10T05:17:03,503 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,503 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,503 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,503 pybedtools/cbedtools.cpp:12401:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,503 12401 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) 2025-09-10T05:17:03,503 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,503 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,503 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,504 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,504 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,504 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,504 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,504 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,504 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,504 | ^ 2025-09-10T05:17:03,505 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,505 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,505 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,505 pybedtools/cbedtools.cpp:12401:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,505 12401 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) 2025-09-10T05:17:03,505 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,505 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,505 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,505 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,506 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,506 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,506 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,506 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,507 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,507 | ^ 2025-09-10T05:17:03,507 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,507 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,507 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,507 pybedtools/cbedtools.cpp:12401:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,507 12401 | __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 13, __pyx_L1_error) 2025-09-10T05:17:03,507 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,508 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,508 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,508 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,511 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,511 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,511 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,511 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,511 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,512 | ^ 2025-09-10T05:17:03,512 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,512 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,512 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,512 pybedtools/cbedtools.cpp:12447:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,512 12447 | __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 15, __pyx_L1_error) 2025-09-10T05:17:03,512 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,512 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,513 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,513 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,513 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,513 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,513 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,513 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,514 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,514 | ^ 2025-09-10T05:17:03,514 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,514 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,514 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,514 pybedtools/cbedtools.cpp:12447:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,514 12447 | __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 15, __pyx_L1_error) 2025-09-10T05:17:03,514 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,514 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,515 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,515 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,515 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,515 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,516 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,516 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,516 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,516 | ^ 2025-09-10T05:17:03,516 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,516 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,516 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,516 pybedtools/cbedtools.cpp:12447:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,517 12447 | __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_IntervalIterator); if (unlikely(!__pyx_t_5)) __PYX_ERR(1, 15, __pyx_L1_error) 2025-09-10T05:17:03,517 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,517 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,517 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,517 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,533 pybedtools/cbedtools.cpp: In function ‘PyObject* __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_6__next__(__pyx_obj_10pybedtools_9cbedtools_IntervalFile*)’: 2025-09-10T05:17:03,533 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,533 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,533 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,533 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,533 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,533 | ^ 2025-09-10T05:17:03,534 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,534 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,534 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,534 pybedtools/cbedtools.cpp:12857:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,534 12857 | __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_BedToolsFileError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 825, __pyx_L1_error) 2025-09-10T05:17:03,534 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,534 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,534 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,534 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,535 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,535 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,535 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,535 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,535 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,535 | ^ 2025-09-10T05:17:03,535 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,536 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,536 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,536 pybedtools/cbedtools.cpp:12857:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,536 12857 | __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_BedToolsFileError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 825, __pyx_L1_error) 2025-09-10T05:17:03,536 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,536 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,536 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,536 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,537 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,537 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,537 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,537 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,538 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,538 | ^ 2025-09-10T05:17:03,538 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,538 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,538 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,538 pybedtools/cbedtools.cpp:12857:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,538 12857 | __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_BedToolsFileError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 825, __pyx_L1_error) 2025-09-10T05:17:03,538 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,539 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,539 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,539 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,544 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,544 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,544 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,544 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,545 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,545 | ^ 2025-09-10T05:17:03,545 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,545 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,545 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,545 pybedtools/cbedtools.cpp:12993:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,545 12993 | __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 835, __pyx_L1_error) 2025-09-10T05:17:03,545 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,545 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,545 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,546 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,546 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,547 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,547 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,547 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,547 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,547 | ^ 2025-09-10T05:17:03,547 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,547 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,547 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,547 pybedtools/cbedtools.cpp:12993:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,547 12993 | __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 835, __pyx_L1_error) 2025-09-10T05:17:03,548 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,548 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,548 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,548 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,549 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,549 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,549 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,549 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,549 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,549 | ^ 2025-09-10T05:17:03,549 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,550 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,550 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,550 pybedtools/cbedtools.cpp:12993:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,550 12993 | __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 835, __pyx_L1_error) 2025-09-10T05:17:03,550 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,550 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,550 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,550 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,560 pybedtools/cbedtools.cpp: In function ‘PyObject* __pyx_pf_10pybedtools_9cbedtools_12IntervalFile_9file_type___get__(__pyx_obj_10pybedtools_9cbedtools_IntervalFile*)’: 2025-09-10T05:17:03,560 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,560 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,560 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,560 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,560 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,561 | ^ 2025-09-10T05:17:03,561 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,561 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,561 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,561 pybedtools/cbedtools.cpp:13216:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,561 13216 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_six); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 847, __pyx_L4_error) 2025-09-10T05:17:03,561 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,561 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,561 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,561 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,562 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,562 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,562 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,562 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,563 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,563 | ^ 2025-09-10T05:17:03,563 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,563 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,563 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,563 pybedtools/cbedtools.cpp:13216:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,563 13216 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_six); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 847, __pyx_L4_error) 2025-09-10T05:17:03,563 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,563 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,564 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,564 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,564 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,565 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,565 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,565 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,565 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,565 | ^ 2025-09-10T05:17:03,565 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,565 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,565 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,566 pybedtools/cbedtools.cpp:13216:9: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,566 13216 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_six); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 847, __pyx_L4_error) 2025-09-10T05:17:03,566 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,566 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,566 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,566 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,571 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,571 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,571 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,572 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,572 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,572 | ^ 2025-09-10T05:17:03,572 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,572 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,572 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,572 pybedtools/cbedtools.cpp:13297:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,572 13297 | __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 851, __pyx_L6_except_error) 2025-09-10T05:17:03,572 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,573 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,573 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,573 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,573 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,574 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,574 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,574 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,574 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,574 | ^ 2025-09-10T05:17:03,574 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,574 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,574 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,574 pybedtools/cbedtools.cpp:13297:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,574 13297 | __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 851, __pyx_L6_except_error) 2025-09-10T05:17:03,575 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,575 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,575 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,575 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,575 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,576 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,576 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,576 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,576 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,576 | ^ 2025-09-10T05:17:03,576 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,576 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,577 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,577 pybedtools/cbedtools.cpp:13297:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,577 13297 | __Pyx_GetModuleGlobalName(__pyx_t_8, __pyx_n_s_MalformedBedLineError); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 851, __pyx_L6_except_error) 2025-09-10T05:17:03,577 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,577 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,577 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,577 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,734 pybedtools/cbedtools.cpp: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_Interval(PyObject*)’: 2025-09-10T05:17:03,734 pybedtools/cbedtools.cpp:15667:104: error: ‘_PyGC_FINALIZED’ was not declared in this scope 2025-09-10T05:17:03,734 15667 | if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { 2025-09-10T05:17:03,734 | ^~~~~~~~~~~~~~~ 2025-09-10T05:17:03,791 pybedtools/cbedtools.cpp: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalIterator(PyObject*)’: 2025-09-10T05:17:03,791 pybedtools/cbedtools.cpp:16068:104: error: ‘_PyGC_FINALIZED’ was not declared in this scope 2025-09-10T05:17:03,791 16068 | if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { 2025-09-10T05:17:03,791 | ^~~~~~~~~~~~~~~ 2025-09-10T05:17:03,840 pybedtools/cbedtools.cpp: In function ‘void __pyx_tp_dealloc_10pybedtools_9cbedtools_IntervalFile(PyObject*)’: 2025-09-10T05:17:03,840 pybedtools/cbedtools.cpp:16201:134: error: ‘_PyGC_FINALIZED’ was not declared in this scope 2025-09-10T05:17:03,840 16201 | if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { 2025-09-10T05:17:03,841 | ^~~~~~~~~~~~~~~ 2025-09-10T05:17:03,919 pybedtools/cbedtools.cpp: In function ‘int __pyx_pymod_exec_cbedtools(PyObject*)’: 2025-09-10T05:17:03,919 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,919 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,919 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,919 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,919 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,919 | ^ 2025-09-10T05:17:03,920 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,920 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,920 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,920 pybedtools/cbedtools.cpp:17588:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,920 17588 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_kdict); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 63, __pyx_L1_error) 2025-09-10T05:17:03,920 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,920 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,920 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,920 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,922 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,922 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,922 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,922 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,922 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,922 | ^ 2025-09-10T05:17:03,923 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,923 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,923 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,923 pybedtools/cbedtools.cpp:17588:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,923 17588 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_kdict); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 63, __pyx_L1_error) 2025-09-10T05:17:03,923 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,923 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,923 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,923 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,925 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,925 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,925 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,925 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,925 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,925 | ^ 2025-09-10T05:17:03,926 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,926 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,926 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,926 pybedtools/cbedtools.cpp:17588:5: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,926 17588 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_kdict); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 63, __pyx_L1_error) 2025-09-10T05:17:03,926 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,926 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,926 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,927 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,935 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,936 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,936 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,936 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,936 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,936 | ^ 2025-09-10T05:17:03,936 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,936 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,936 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,936 pybedtools/cbedtools.cpp:17679:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,936 17679 | __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_k); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,937 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,937 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,937 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,937 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,938 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,938 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,938 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,939 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,939 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,939 | ^ 2025-09-10T05:17:03,939 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,939 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,939 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,939 pybedtools/cbedtools.cpp:17679:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,939 17679 | __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_k); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,939 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,940 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,940 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,940 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,941 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,941 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,941 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,941 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,942 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,942 | ^ 2025-09-10T05:17:03,942 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,942 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,942 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,942 pybedtools/cbedtools.cpp:17679:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,942 17679 | __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_k); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,942 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,943 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,943 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,943 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,945 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,945 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,945 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,945 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,946 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,946 | ^ 2025-09-10T05:17:03,946 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,946 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,946 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,946 pybedtools/cbedtools.cpp:17681:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,946 17681 | __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_kdict); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,946 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,946 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,947 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,947 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,948 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,948 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,948 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,948 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,948 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,948 | ^ 2025-09-10T05:17:03,949 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,949 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,949 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,949 pybedtools/cbedtools.cpp:17681:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,949 17681 | __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_kdict); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,949 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,949 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,949 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,949 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,951 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,951 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,951 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,951 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,951 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,951 | ^ 2025-09-10T05:17:03,951 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,952 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,952 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,952 pybedtools/cbedtools.cpp:17681:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,952 17681 | __Pyx_GetModuleGlobalName(__pyx_t_7, __pyx_n_s_kdict); if (unlikely(!__pyx_t_7)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,952 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,952 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,952 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,952 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,955 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,955 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,955 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,955 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,955 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,955 | ^ 2025-09-10T05:17:03,955 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,955 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,956 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,956 pybedtools/cbedtools.cpp:17683:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,956 17683 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_v); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,956 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,956 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,956 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,957 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,958 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,958 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,958 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,958 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,958 | ^ 2025-09-10T05:17:03,958 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,958 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,958 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,958 pybedtools/cbedtools.cpp:17683:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,959 17683 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_v); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,959 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,959 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,959 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,959 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,960 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:03,960 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:03,961 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:03,961 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:03,961 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:03,961 | ^ 2025-09-10T05:17:03,961 pybedtools/cbedtools.cpp:1527:43: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:03,961 1527 | (var) = (likely(__pyx_dict_version == __PYX_GET_DICT_VERSION(__pyx_d))) ?\ 2025-09-10T05:17:03,961 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,961 pybedtools/cbedtools.cpp:17683:7: note: in expansion of macro ‘__Pyx_GetModuleGlobalName’ 2025-09-10T05:17:03,962 17683 | __Pyx_GetModuleGlobalName(__pyx_t_6, __pyx_n_s_v); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 64, __pyx_L1_error) 2025-09-10T05:17:03,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:03,962 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:03,962 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:03,962 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,020 pybedtools/cbedtools.cpp:1724:38: error: ‘_PyDict_SetItem_KnownHash’ was not declared in this scope; did you mean ‘_PyDict_GetItem_KnownHash’? 2025-09-10T05:17:04,020 1724 | (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value)) 2025-09-10T05:17:04,020 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,021 pybedtools/cbedtools.cpp:17939:7: note: in expansion of macro ‘__Pyx_SetNameInClass’ 2025-09-10T05:17:04,021 17939 | if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_init, __pyx_t_6) < 0) __PYX_ERR(0, 149, __pyx_L1_error) 2025-09-10T05:17:04,021 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,070 pybedtools/cbedtools.cpp:1724:38: error: ‘_PyDict_SetItem_KnownHash’ was not declared in this scope; did you mean ‘_PyDict_GetItem_KnownHash’? 2025-09-10T05:17:04,070 1724 | (likely(PyDict_CheckExact(ns)) ? _PyDict_SetItem_KnownHash(ns, name, value, ((PyASCIIObject *) name)->hash) : PyObject_SetItem(ns, name, value)) 2025-09-10T05:17:04,070 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,070 pybedtools/cbedtools.cpp:17951:7: note: in expansion of macro ‘__Pyx_SetNameInClass’ 2025-09-10T05:17:04,070 17951 | if (__Pyx_SetNameInClass(__pyx_t_5, __pyx_n_s_str, __pyx_t_6) < 0) __PYX_ERR(0, 185, __pyx_L1_error) 2025-09-10T05:17:04,070 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,097 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx_PyInt_SubtractObjC(PyObject*, PyObject*, long int, int, int)’: 2025-09-10T05:17:04,097 pybedtools/cbedtools.cpp:18559:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,097 18559 | const digit* digits = ((PyLongObject*)op1)->ob_digit; 2025-09-10T05:17:04,098 | ^~~~~~~~ 2025-09-10T05:17:04,105 pybedtools/cbedtools.cpp: In function ‘int __Pyx_PyBytes_Equals(PyObject*, PyObject*, int)’: 2025-09-10T05:17:04,105 pybedtools/cbedtools.cpp:18681:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,105 18681 | hash1 = ((PyBytesObject*)s1)->ob_shash; 2025-09-10T05:17:04,106 | ^~~~~~~~ 2025-09-10T05:17:04,106 In file included from /usr/include/python3.13/bytesobject.h:59, 2025-09-10T05:17:04,106 from /usr/include/python3.13/Python.h:78: 2025-09-10T05:17:04,106 /usr/include/python3.13/cpython/bytesobject.h:7:35: note: declared here 2025-09-10T05:17:04,106 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2025-09-10T05:17:04,106 | ^~~~~~~~ 2025-09-10T05:17:04,106 pybedtools/cbedtools.cpp:18681:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,106 18681 | hash1 = ((PyBytesObject*)s1)->ob_shash; 2025-09-10T05:17:04,106 | ^~~~~~~~ 2025-09-10T05:17:04,106 /usr/include/python3.13/cpython/bytesobject.h:7:35: note: declared here 2025-09-10T05:17:04,107 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2025-09-10T05:17:04,107 | ^~~~~~~~ 2025-09-10T05:17:04,107 pybedtools/cbedtools.cpp:18681:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,107 18681 | hash1 = ((PyBytesObject*)s1)->ob_shash; 2025-09-10T05:17:04,107 | ^~~~~~~~ 2025-09-10T05:17:04,107 /usr/include/python3.13/cpython/bytesobject.h:7:35: note: declared here 2025-09-10T05:17:04,107 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2025-09-10T05:17:04,107 | ^~~~~~~~ 2025-09-10T05:17:04,108 pybedtools/cbedtools.cpp:18682:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,108 18682 | hash2 = ((PyBytesObject*)s2)->ob_shash; 2025-09-10T05:17:04,108 | ^~~~~~~~ 2025-09-10T05:17:04,108 /usr/include/python3.13/cpython/bytesobject.h:7:35: note: declared here 2025-09-10T05:17:04,108 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2025-09-10T05:17:04,108 | ^~~~~~~~ 2025-09-10T05:17:04,108 pybedtools/cbedtools.cpp:18682:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,108 18682 | hash2 = ((PyBytesObject*)s2)->ob_shash; 2025-09-10T05:17:04,108 | ^~~~~~~~ 2025-09-10T05:17:04,109 /usr/include/python3.13/cpython/bytesobject.h:7:35: note: declared here 2025-09-10T05:17:04,109 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2025-09-10T05:17:04,109 | ^~~~~~~~ 2025-09-10T05:17:04,109 pybedtools/cbedtools.cpp:18682:43: warning: ‘PyBytesObject::ob_shash’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,109 18682 | hash2 = ((PyBytesObject*)s2)->ob_shash; 2025-09-10T05:17:04,109 | ^~~~~~~~ 2025-09-10T05:17:04,109 /usr/include/python3.13/cpython/bytesobject.h:7:35: note: declared here 2025-09-10T05:17:04,109 7 | Py_DEPRECATED(3.11) Py_hash_t ob_shash; 2025-09-10T05:17:04,110 | ^~~~~~~~ 2025-09-10T05:17:04,154 pybedtools/cbedtools.cpp: In function ‘int __Pyx_PyUnicode_Equals(PyObject*, PyObject*, int)’: 2025-09-10T05:17:04,154 pybedtools/cbedtools.cpp:537:51: error: ‘_PyUnicode_Ready’ was not declared in this scope; did you mean ‘PyUnicode_READY’? 2025-09-10T05:17:04,154 537 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-10T05:17:04,154 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,155 pybedtools/cbedtools.cpp:920:43: note: in definition of macro ‘unlikely’ 2025-09-10T05:17:04,155 920 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-10T05:17:04,155 | ^ 2025-09-10T05:17:04,155 pybedtools/cbedtools.cpp:18741:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-10T05:17:04,155 18741 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-10T05:17:04,155 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,159 pybedtools/cbedtools.cpp: In function ‘int __Pyx_IterFinish()’: 2025-09-10T05:17:04,160 pybedtools/cbedtools.cpp:18847:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,160 18847 | PyObject* exc_type = tstate->curexc_type; 2025-09-10T05:17:04,160 | ^~~~~~~~~~~ 2025-09-10T05:17:04,160 pybedtools/cbedtools.cpp:18851:33: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,160 18851 | exc_value = tstate->curexc_value; 2025-09-10T05:17:04,160 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,160 pybedtools/cbedtools.cpp:18852:30: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,161 18852 | exc_tb = tstate->curexc_traceback; 2025-09-10T05:17:04,161 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,161 pybedtools/cbedtools.cpp:18853:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,161 18853 | tstate->curexc_type = 0; 2025-09-10T05:17:04,161 | ^~~~~~~~~~~ 2025-09-10T05:17:04,161 pybedtools/cbedtools.cpp:18854:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,161 18854 | tstate->curexc_value = 0; 2025-09-10T05:17:04,161 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,162 pybedtools/cbedtools.cpp:18855:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,162 18855 | tstate->curexc_traceback = 0; 2025-09-10T05:17:04,162 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,163 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx_PyInt_EqObjC(PyObject*, PyObject*, long int, long int)’: 2025-09-10T05:17:04,163 pybedtools/cbedtools.cpp:18907:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,164 18907 | const digit* digits = ((PyLongObject*)op1)->ob_digit; 2025-09-10T05:17:04,164 | ^~~~~~~~ 2025-09-10T05:17:04,183 pybedtools/cbedtools.cpp: In function ‘_PyErr_StackItem* __Pyx_PyErr_GetTopmostException(PyThreadState*)’: 2025-09-10T05:17:04,183 pybedtools/cbedtools.cpp:19126:23: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,183 19126 | while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && 2025-09-10T05:17:04,183 | ^~~~~~~~ 2025-09-10T05:17:04,184 pybedtools/cbedtools.cpp:19126:53: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,184 19126 | while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) && 2025-09-10T05:17:04,184 | ^~~~~~~~ 2025-09-10T05:17:04,184 pybedtools/cbedtools.cpp: In function ‘void __Pyx__ExceptionSave(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2025-09-10T05:17:04,184 pybedtools/cbedtools.cpp:19140:23: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,184 19140 | *type = exc_info->exc_type; 2025-09-10T05:17:04,184 | ^~~~~~~~ 2025-09-10T05:17:04,185 pybedtools/cbedtools.cpp:19142:21: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2025-09-10T05:17:04,185 19142 | *tb = exc_info->exc_traceback; 2025-09-10T05:17:04,185 | ^~~~~~~~~~~~~ 2025-09-10T05:17:04,185 pybedtools/cbedtools.cpp: In function ‘void __Pyx__ExceptionReset(PyThreadState*, PyObject*, PyObject*, PyObject*)’: 2025-09-10T05:17:04,185 pybedtools/cbedtools.cpp:19156:26: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,185 19156 | tmp_type = exc_info->exc_type; 2025-09-10T05:17:04,186 | ^~~~~~~~ 2025-09-10T05:17:04,186 pybedtools/cbedtools.cpp:19158:24: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2025-09-10T05:17:04,186 19158 | tmp_tb = exc_info->exc_traceback; 2025-09-10T05:17:04,186 | ^~~~~~~~~~~~~ 2025-09-10T05:17:04,186 pybedtools/cbedtools.cpp:19159:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,186 19159 | exc_info->exc_type = type; 2025-09-10T05:17:04,186 | ^~~~~~~~ 2025-09-10T05:17:04,186 pybedtools/cbedtools.cpp:19161:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2025-09-10T05:17:04,187 19161 | exc_info->exc_traceback = tb; 2025-09-10T05:17:04,187 | ^~~~~~~~~~~~~ 2025-09-10T05:17:04,188 pybedtools/cbedtools.cpp: In function ‘int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState*, PyObject*)’: 2025-09-10T05:17:04,188 pybedtools/cbedtools.cpp:19192:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,188 19192 | PyObject *exc_type = tstate->curexc_type; 2025-09-10T05:17:04,188 | ^~~~~~~~~~~ 2025-09-10T05:17:04,189 pybedtools/cbedtools.cpp: In function ‘void __Pyx_ErrRestoreInState(PyThreadState*, PyObject*, PyObject*, PyObject*)’: 2025-09-10T05:17:04,190 pybedtools/cbedtools.cpp:19205:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,190 19205 | tmp_type = tstate->curexc_type; 2025-09-10T05:17:04,190 | ^~~~~~~~~~~ 2025-09-10T05:17:04,190 pybedtools/cbedtools.cpp:19206:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,190 19206 | tmp_value = tstate->curexc_value; 2025-09-10T05:17:04,190 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,190 pybedtools/cbedtools.cpp:19207:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,190 19207 | tmp_tb = tstate->curexc_traceback; 2025-09-10T05:17:04,190 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,191 pybedtools/cbedtools.cpp:19208:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,191 19208 | tstate->curexc_type = type; 2025-09-10T05:17:04,191 | ^~~~~~~~~~~ 2025-09-10T05:17:04,191 pybedtools/cbedtools.cpp:19209:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,191 19209 | tstate->curexc_value = value; 2025-09-10T05:17:04,191 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,191 pybedtools/cbedtools.cpp:19210:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,191 19210 | tstate->curexc_traceback = tb; 2025-09-10T05:17:04,192 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,192 pybedtools/cbedtools.cpp: In function ‘void __Pyx_ErrFetchInState(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2025-09-10T05:17:04,192 pybedtools/cbedtools.cpp:19216:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,192 19216 | *type = tstate->curexc_type; 2025-09-10T05:17:04,193 | ^~~~~~~~~~~ 2025-09-10T05:17:04,193 pybedtools/cbedtools.cpp:19217:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,193 19217 | *value = tstate->curexc_value; 2025-09-10T05:17:04,193 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,193 pybedtools/cbedtools.cpp:19218:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,193 19218 | *tb = tstate->curexc_traceback; 2025-09-10T05:17:04,193 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,193 pybedtools/cbedtools.cpp:19219:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,194 19219 | tstate->curexc_type = 0; 2025-09-10T05:17:04,194 | ^~~~~~~~~~~ 2025-09-10T05:17:04,194 pybedtools/cbedtools.cpp:19220:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,194 19220 | tstate->curexc_value = 0; 2025-09-10T05:17:04,194 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,194 pybedtools/cbedtools.cpp:19221:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,194 19221 | tstate->curexc_traceback = 0; 2025-09-10T05:17:04,194 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,234 pybedtools/cbedtools.cpp: In function ‘uint64_t __Pyx_get_tp_dict_version(PyObject*)’: 2025-09-10T05:17:04,234 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,234 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,234 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,234 pybedtools/cbedtools.cpp:19920:27: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,235 19920 | return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; 2025-09-10T05:17:04,235 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,235 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,235 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,235 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,237 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,237 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,237 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,237 pybedtools/cbedtools.cpp:19920:27: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,237 19920 | return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; 2025-09-10T05:17:04,237 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,238 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,238 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,238 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,240 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,240 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,240 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,240 pybedtools/cbedtools.cpp:19920:27: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,240 19920 | return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0; 2025-09-10T05:17:04,240 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,241 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,241 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,241 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,244 pybedtools/cbedtools.cpp: In function ‘uint64_t __Pyx_get_object_dict_version(PyObject*)’: 2025-09-10T05:17:04,244 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,244 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,244 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,244 pybedtools/cbedtools.cpp:19932:36: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,244 19932 | return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; 2025-09-10T05:17:04,244 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,245 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,245 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,245 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,247 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,247 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,247 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,247 pybedtools/cbedtools.cpp:19932:36: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,247 19932 | return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; 2025-09-10T05:17:04,247 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,247 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,248 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,248 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,250 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,250 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,250 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,250 pybedtools/cbedtools.cpp:19932:36: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,250 19932 | return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0; 2025-09-10T05:17:04,250 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,251 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,251 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,251 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,254 pybedtools/cbedtools.cpp: In function ‘int __Pyx_object_dict_version_matches(PyObject*, uint64_t, uint64_t)’: 2025-09-10T05:17:04,254 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,254 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,254 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,254 pybedtools/cbedtools.cpp:920:43: note: in definition of macro ‘unlikely’ 2025-09-10T05:17:04,254 920 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-10T05:17:04,254 | ^ 2025-09-10T05:17:04,254 pybedtools/cbedtools.cpp:19936:56: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,254 19936 | if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) 2025-09-10T05:17:04,255 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,255 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,255 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,255 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,257 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,257 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,257 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,257 pybedtools/cbedtools.cpp:920:43: note: in definition of macro ‘unlikely’ 2025-09-10T05:17:04,257 920 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-10T05:17:04,257 | ^ 2025-09-10T05:17:04,257 pybedtools/cbedtools.cpp:19936:56: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,257 19936 | if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) 2025-09-10T05:17:04,257 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,258 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,258 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,258 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,260 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,260 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,260 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,260 pybedtools/cbedtools.cpp:920:43: note: in definition of macro ‘unlikely’ 2025-09-10T05:17:04,260 920 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-10T05:17:04,260 | ^ 2025-09-10T05:17:04,260 pybedtools/cbedtools.cpp:19936:56: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,261 19936 | if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict))) 2025-09-10T05:17:04,261 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,261 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,261 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,261 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,264 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx__GetModuleGlobalName(PyObject*, uint64_t*, PyObject**)’: 2025-09-10T05:17:04,264 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,264 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,264 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,264 pybedtools/cbedtools.cpp:1501:21: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,264 1501 | (version_var) = __PYX_GET_DICT_VERSION(dict);\ 2025-09-10T05:17:04,264 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,264 pybedtools/cbedtools.cpp:19953:5: note: in expansion of macro ‘__PYX_UPDATE_DICT_CACHE’ 2025-09-10T05:17:04,264 19953 | __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) 2025-09-10T05:17:04,264 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,265 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,265 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,265 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,266 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,267 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,267 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,267 pybedtools/cbedtools.cpp:1501:21: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,267 1501 | (version_var) = __PYX_GET_DICT_VERSION(dict);\ 2025-09-10T05:17:04,267 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,267 pybedtools/cbedtools.cpp:19953:5: note: in expansion of macro ‘__PYX_UPDATE_DICT_CACHE’ 2025-09-10T05:17:04,267 19953 | __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) 2025-09-10T05:17:04,267 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,267 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,268 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,268 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,269 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,269 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,270 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,270 pybedtools/cbedtools.cpp:1501:21: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,270 1501 | (version_var) = __PYX_GET_DICT_VERSION(dict);\ 2025-09-10T05:17:04,270 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,270 pybedtools/cbedtools.cpp:19953:5: note: in expansion of macro ‘__PYX_UPDATE_DICT_CACHE’ 2025-09-10T05:17:04,270 19953 | __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version) 2025-09-10T05:17:04,270 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,271 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,271 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,271 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,275 pybedtools/cbedtools.cpp: In function ‘void __Pyx_Raise(PyObject*, PyObject*, PyObject*, PyObject*)’: 2025-09-10T05:17:04,275 pybedtools/cbedtools.cpp:20122:36: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,275 20122 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-10T05:17:04,275 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,276 pybedtools/cbedtools.cpp:20125:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,276 20125 | tstate->curexc_traceback = tb; 2025-09-10T05:17:04,276 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,277 pybedtools/cbedtools.cpp: In function ‘int __Pyx__GetException(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2025-09-10T05:17:04,277 pybedtools/cbedtools.cpp:20146:26: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,277 20146 | local_type = tstate->curexc_type; 2025-09-10T05:17:04,277 | ^~~~~~~~~~~ 2025-09-10T05:17:04,278 pybedtools/cbedtools.cpp:20147:27: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,278 20147 | local_value = tstate->curexc_value; 2025-09-10T05:17:04,278 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,278 pybedtools/cbedtools.cpp:20148:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,278 20148 | local_tb = tstate->curexc_traceback; 2025-09-10T05:17:04,278 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,278 pybedtools/cbedtools.cpp:20149:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,278 20149 | tstate->curexc_type = 0; 2025-09-10T05:17:04,278 | ^~~~~~~~~~~ 2025-09-10T05:17:04,279 pybedtools/cbedtools.cpp:20150:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-10T05:17:04,279 20150 | tstate->curexc_value = 0; 2025-09-10T05:17:04,279 | ^~~~~~~~~~~~ 2025-09-10T05:17:04,279 pybedtools/cbedtools.cpp:20151:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-10T05:17:04,279 20151 | tstate->curexc_traceback = 0; 2025-09-10T05:17:04,279 | ^~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,280 pybedtools/cbedtools.cpp:20157:26: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,280 20157 | if (unlikely(tstate->curexc_type)) 2025-09-10T05:17:04,280 | ^~~~~~~~~~~ 2025-09-10T05:17:04,280 pybedtools/cbedtools.cpp:920:43: note: in definition of macro ‘unlikely’ 2025-09-10T05:17:04,280 920 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-10T05:17:04,280 | ^ 2025-09-10T05:17:04,283 pybedtools/cbedtools.cpp:20178:30: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,283 20178 | tmp_type = exc_info->exc_type; 2025-09-10T05:17:04,283 | ^~~~~~~~ 2025-09-10T05:17:04,284 pybedtools/cbedtools.cpp:20180:28: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2025-09-10T05:17:04,284 20180 | tmp_tb = exc_info->exc_traceback; 2025-09-10T05:17:04,284 | ^~~~~~~~~~~~~ 2025-09-10T05:17:04,284 pybedtools/cbedtools.cpp:20181:19: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,284 20181 | exc_info->exc_type = local_type; 2025-09-10T05:17:04,284 | ^~~~~~~~ 2025-09-10T05:17:04,284 pybedtools/cbedtools.cpp:20183:19: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2025-09-10T05:17:04,284 20183 | exc_info->exc_traceback = local_tb; 2025-09-10T05:17:04,284 | ^~~~~~~~~~~~~ 2025-09-10T05:17:04,289 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx_PyInt_AndObjC(PyObject*, PyObject*, long int, int, int)’: 2025-09-10T05:17:04,289 pybedtools/cbedtools.cpp:20302:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,289 20302 | const digit* digits = ((PyLongObject*)op1)->ob_digit; 2025-09-10T05:17:04,289 | ^~~~~~~~ 2025-09-10T05:17:04,296 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx_PyInt_AddObjC(PyObject*, PyObject*, long int, int, int)’: 2025-09-10T05:17:04,296 pybedtools/cbedtools.cpp:20417:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,296 20417 | const digit* digits = ((PyLongObject*)op1)->ob_digit; 2025-09-10T05:17:04,297 | ^~~~~~~~ 2025-09-10T05:17:04,312 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx_PyIter_Next2Default(PyObject*)’: 2025-09-10T05:17:04,312 pybedtools/cbedtools.cpp:1323:47: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-10T05:17:04,313 1323 | #define __Pyx_PyErr_Occurred() __pyx_tstate->curexc_type 2025-09-10T05:17:04,313 | ^~~~~~~~~~~ 2025-09-10T05:17:04,313 pybedtools/cbedtools.cpp:20652:16: note: in expansion of macro ‘__Pyx_PyErr_Occurred’ 2025-09-10T05:17:04,313 20652 | exc_type = __Pyx_PyErr_Occurred(); 2025-09-10T05:17:04,313 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,373 pybedtools/cbedtools.cpp: In function ‘PyObject* __Pyx_PyIter_Next2(PyObject*, PyObject*)’: 2025-09-10T05:17:04,373 pybedtools/cbedtools.cpp:20680:35: error: ‘_PyObject_NextNotImplemented’ was not declared in this scope; did you mean ‘PyObject_HashNotImplemented’? 2025-09-10T05:17:04,373 20680 | if (unlikely(iternext == &_PyObject_NextNotImplemented)) 2025-09-10T05:17:04,374 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,374 pybedtools/cbedtools.cpp:920:43: note: in definition of macro ‘unlikely’ 2025-09-10T05:17:04,374 920 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-10T05:17:04,374 | ^ 2025-09-10T05:17:04,385 pybedtools/cbedtools.cpp: In function ‘void __Pyx__ExceptionSwap(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2025-09-10T05:17:04,385 pybedtools/cbedtools.cpp:20828:26: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,385 20828 | tmp_type = exc_info->exc_type; 2025-09-10T05:17:04,385 | ^~~~~~~~ 2025-09-10T05:17:04,385 pybedtools/cbedtools.cpp:20830:24: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2025-09-10T05:17:04,385 20830 | tmp_tb = exc_info->exc_traceback; 2025-09-10T05:17:04,385 | ^~~~~~~~~~~~~ 2025-09-10T05:17:04,386 pybedtools/cbedtools.cpp:20831:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_type’ 2025-09-10T05:17:04,386 20831 | exc_info->exc_type = *type; 2025-09-10T05:17:04,386 | ^~~~~~~~ 2025-09-10T05:17:04,386 pybedtools/cbedtools.cpp:20833:15: error: ‘_PyErr_StackItem’ {aka ‘struct _err_stackitem’} has no member named ‘exc_traceback’ 2025-09-10T05:17:04,386 20833 | exc_info->exc_traceback = *tb; 2025-09-10T05:17:04,386 | ^~~~~~~~~~~~~ 2025-09-10T05:17:04,411 pybedtools/cbedtools.cpp: In function ‘int __Pyx_CLineForTraceback(PyThreadState*, int)’: 2025-09-10T05:17:04,411 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,411 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,411 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,412 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:04,412 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:04,412 | ^ 2025-09-10T05:17:04,412 pybedtools/cbedtools.cpp:1506:16: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,412 1506 | if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ 2025-09-10T05:17:04,412 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,412 pybedtools/cbedtools.cpp:21320:9: note: in expansion of macro ‘__PYX_PY_DICT_LOOKUP_IF_MODIFIED’ 2025-09-10T05:17:04,412 21320 | __PYX_PY_DICT_LOOKUP_IF_MODIFIED( 2025-09-10T05:17:04,412 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,412 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,413 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,413 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,414 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,414 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,414 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,415 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:04,415 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:04,415 | ^ 2025-09-10T05:17:04,415 pybedtools/cbedtools.cpp:1506:16: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,415 1506 | if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ 2025-09-10T05:17:04,415 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,415 pybedtools/cbedtools.cpp:21320:9: note: in expansion of macro ‘__PYX_PY_DICT_LOOKUP_IF_MODIFIED’ 2025-09-10T05:17:04,415 21320 | __PYX_PY_DICT_LOOKUP_IF_MODIFIED( 2025-09-10T05:17:04,415 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,415 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,416 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,416 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,417 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,418 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,418 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,418 pybedtools/cbedtools.cpp:919:43: note: in definition of macro ‘likely’ 2025-09-10T05:17:04,418 919 | #define likely(x) __builtin_expect(!!(x), 1) 2025-09-10T05:17:04,418 | ^ 2025-09-10T05:17:04,418 pybedtools/cbedtools.cpp:1506:16: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,418 1506 | if (likely(__PYX_GET_DICT_VERSION(DICT) == __pyx_dict_version)) {\ 2025-09-10T05:17:04,418 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,418 pybedtools/cbedtools.cpp:21320:9: note: in expansion of macro ‘__PYX_PY_DICT_LOOKUP_IF_MODIFIED’ 2025-09-10T05:17:04,419 21320 | __PYX_PY_DICT_LOOKUP_IF_MODIFIED( 2025-09-10T05:17:04,419 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,419 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,419 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,419 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,421 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,421 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,421 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,421 pybedtools/cbedtools.cpp:1510:30: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,421 1510 | __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ 2025-09-10T05:17:04,421 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,422 pybedtools/cbedtools.cpp:21320:9: note: in expansion of macro ‘__PYX_PY_DICT_LOOKUP_IF_MODIFIED’ 2025-09-10T05:17:04,422 21320 | __PYX_PY_DICT_LOOKUP_IF_MODIFIED( 2025-09-10T05:17:04,422 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,422 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,422 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,422 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,424 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,424 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,424 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,424 pybedtools/cbedtools.cpp:1510:30: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,424 1510 | __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ 2025-09-10T05:17:04,425 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,425 pybedtools/cbedtools.cpp:21320:9: note: in expansion of macro ‘__PYX_PY_DICT_LOOKUP_IF_MODIFIED’ 2025-09-10T05:17:04,425 21320 | __PYX_PY_DICT_LOOKUP_IF_MODIFIED( 2025-09-10T05:17:04,425 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,425 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,425 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,425 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,427 pybedtools/cbedtools.cpp:1499:65: warning: ‘PyDictObject::ma_version_tag’ is deprecated [-Wdeprecated-declarations] 2025-09-10T05:17:04,427 1499 | #define __PYX_GET_DICT_VERSION(dict) (((PyDictObject*)(dict))->ma_version_tag) 2025-09-10T05:17:04,427 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,428 pybedtools/cbedtools.cpp:1510:30: note: in expansion of macro ‘__PYX_GET_DICT_VERSION’ 2025-09-10T05:17:04,428 1510 | __pyx_dict_version = __PYX_GET_DICT_VERSION(DICT);\ 2025-09-10T05:17:04,428 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,428 pybedtools/cbedtools.cpp:21320:9: note: in expansion of macro ‘__PYX_PY_DICT_LOOKUP_IF_MODIFIED’ 2025-09-10T05:17:04,428 21320 | __PYX_PY_DICT_LOOKUP_IF_MODIFIED( 2025-09-10T05:17:04,428 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,428 /usr/include/python3.13/cpython/dictobject.h:25:34: note: declared here 2025-09-10T05:17:04,428 25 | Py_DEPRECATED(3.12) uint64_t ma_version_tag; 2025-09-10T05:17:04,429 | ^~~~~~~~~~~~~~ 2025-09-10T05:17:04,439 pybedtools/cbedtools.cpp: In function ‘void __Pyx_AddTraceback(const char*, int, int, const char*)’: 2025-09-10T05:17:04,439 pybedtools/cbedtools.cpp:475:62: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-10T05:17:04,439 475 | #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) 2025-09-10T05:17:04,440 | ^~ 2025-09-10T05:17:04,440 pybedtools/cbedtools.cpp:21511:5: note: in expansion of macro ‘__Pyx_PyFrame_SetLineNumber’ 2025-09-10T05:17:04,440 21511 | __Pyx_PyFrame_SetLineNumber(py_frame, py_line); 2025-09-10T05:17:04,440 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,440 In file included from /usr/include/python3.13/Python.h:67: 2025-09-10T05:17:04,440 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-10T05:17:04,440 22 | typedef struct _frame PyFrameObject; 2025-09-10T05:17:04,440 | ^~~~~~ 2025-09-10T05:17:04,442 pybedtools/cbedtools.cpp: In function ‘int __Pyx_PyInt_As_int(PyObject*)’: 2025-09-10T05:17:04,442 pybedtools/cbedtools.cpp:21605:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,442 21605 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,443 | ^~~~~~~~ 2025-09-10T05:17:04,450 pybedtools/cbedtools.cpp:21660:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,450 21660 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,451 | ^~~~~~~~ 2025-09-10T05:17:04,464 pybedtools/cbedtools.cpp:21746:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-10T05:17:04,464 21746 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-10T05:17:04,464 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,464 21747 | bytes, sizeof(val), 2025-09-10T05:17:04,465 | ~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,465 21748 | is_little, !is_unsigned); 2025-09-10T05:17:04,465 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,465 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-10T05:17:04,465 from /usr/include/python3.13/Python.h:81: 2025-09-10T05:17:04,465 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-10T05:17:04,465 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-10T05:17:04,465 | ^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,469 pybedtools/cbedtools.cpp: In function ‘long int __Pyx_PyInt_As_long(PyObject*)’: 2025-09-10T05:17:04,470 pybedtools/cbedtools.cpp:21801:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,470 21801 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,470 | ^~~~~~~~ 2025-09-10T05:17:04,477 pybedtools/cbedtools.cpp:21856:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,478 21856 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,478 | ^~~~~~~~ 2025-09-10T05:17:04,491 pybedtools/cbedtools.cpp:21942:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-10T05:17:04,491 21942 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-10T05:17:04,492 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,492 21943 | bytes, sizeof(val), 2025-09-10T05:17:04,492 | ~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,492 21944 | is_little, !is_unsigned); 2025-09-10T05:17:04,492 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,492 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-10T05:17:04,492 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-10T05:17:04,493 | ^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,497 pybedtools/cbedtools.cpp: In function ‘CHRPOS __Pyx_PyInt_As_CHRPOS(PyObject*)’: 2025-09-10T05:17:04,497 pybedtools/cbedtools.cpp:21997:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,497 21997 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,497 | ^~~~~~~~ 2025-09-10T05:17:04,505 pybedtools/cbedtools.cpp:22052:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,505 22052 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,505 | ^~~~~~~~ 2025-09-10T05:17:04,519 pybedtools/cbedtools.cpp:22138:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-10T05:17:04,519 22138 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-10T05:17:04,519 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,520 22139 | bytes, sizeof(val), 2025-09-10T05:17:04,520 | ~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,520 22140 | is_little, !is_unsigned); 2025-09-10T05:17:04,520 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,520 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-10T05:17:04,520 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-10T05:17:04,520 | ^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,525 pybedtools/cbedtools.cpp: In function ‘size_t __Pyx_PyInt_As_size_t(PyObject*)’: 2025-09-10T05:17:04,525 pybedtools/cbedtools.cpp:22193:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,525 22193 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,525 | ^~~~~~~~ 2025-09-10T05:17:04,533 pybedtools/cbedtools.cpp:22248:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,533 22248 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,533 | ^~~~~~~~ 2025-09-10T05:17:04,547 pybedtools/cbedtools.cpp:22334:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-10T05:17:04,548 22334 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-10T05:17:04,548 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,548 22335 | bytes, sizeof(val), 2025-09-10T05:17:04,548 | ~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,548 22336 | is_little, !is_unsigned); 2025-09-10T05:17:04,548 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,548 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-10T05:17:04,549 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-10T05:17:04,549 | ^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,555 pybedtools/cbedtools.cpp: In function ‘long unsigned int __Pyx_PyInt_As_unsigned_long(PyObject*)’: 2025-09-10T05:17:04,555 pybedtools/cbedtools.cpp:22465:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,555 22465 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,555 | ^~~~~~~~ 2025-09-10T05:17:04,563 pybedtools/cbedtools.cpp:22520:55: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,563 22520 | const digit* digits = ((PyLongObject*)x)->ob_digit; 2025-09-10T05:17:04,564 | ^~~~~~~~ 2025-09-10T05:17:04,595 pybedtools/cbedtools.cpp:22606:46: error: too few arguments to function ‘int _PyLong_AsByteArray(PyLongObject*, unsigned char*, size_t, int, int, int)’ 2025-09-10T05:17:04,595 22606 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-10T05:17:04,596 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,596 22607 | bytes, sizeof(val), 2025-09-10T05:17:04,596 | ~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,596 22608 | is_little, !is_unsigned); 2025-09-10T05:17:04,596 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,596 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-10T05:17:04,596 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-10T05:17:04,596 | ^~~~~~~~~~~~~~~~~~~ 2025-09-10T05:17:04,607 pybedtools/cbedtools.cpp: In function ‘Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*)’: 2025-09-10T05:17:04,608 pybedtools/cbedtools.cpp:22849:47: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’ 2025-09-10T05:17:04,608 22849 | const digit* digits = ((PyLongObject*)b)->ob_digit; 2025-09-10T05:17:04,608 | ^~~~~~~~ 2025-09-10T05:17:05,428 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-10T05:17:05,582 ERROR: python setup.py bdist_wheel exited with 1 2025-09-10T05:17:05,597 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-10T05:17:05,597 exec(compile('"'"''"'"''"'"' 2025-09-10T05:17:05,597 # This is -- a caller that pip uses to run setup.py 2025-09-10T05:17:05,597 # 2025-09-10T05:17:05,597 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-10T05:17:05,597 # import from `distutils.core` to work with newer packaging standards. 2025-09-10T05:17:05,597 # - It provides a clear error message when setuptools is not installed. 2025-09-10T05:17:05,597 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-10T05:17:05,597 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-10T05:17:05,597 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-10T05:17:05,597 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-10T05:17:05,597 import os, sys, tokenize, traceback 2025-09-10T05:17:05,597 2025-09-10T05:17:05,597 try: 2025-09-10T05:17:05,597 import setuptools 2025-09-10T05:17:05,597 except ImportError: 2025-09-10T05:17:05,597 print( 2025-09-10T05:17:05,597 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-10T05:17:05,597 "the build environment with exception:", 2025-09-10T05:17:05,597 file=sys.stderr, 2025-09-10T05:17:05,597 ) 2025-09-10T05:17:05,597 traceback.print_exc() 2025-09-10T05:17:05,597 sys.exit(1) 2025-09-10T05:17:05,597 2025-09-10T05:17:05,597 __file__ = %r 2025-09-10T05:17:05,597 sys.argv[0] = __file__ 2025-09-10T05:17:05,597 2025-09-10T05:17:05,597 if os.path.exists(__file__): 2025-09-10T05:17:05,597 filename = __file__ 2025-09-10T05:17:05,597 with tokenize.open(__file__) as f: 2025-09-10T05:17:05,597 setup_py_code = f.read() 2025-09-10T05:17:05,597 else: 2025-09-10T05:17:05,597 filename = "" 2025-09-10T05:17:05,597 setup_py_code = "from setuptools import setup; setup()" 2025-09-10T05:17:05,597 2025-09-10T05:17:05,597 exec(compile(setup_py_code, filename, "exec")) 2025-09-10T05:17:05,597 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-6zutxrxu[/] 2025-09-10T05:17:05,597 [bold magenta]cwd[/]: /tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e/ 2025-09-10T05:17:05,597 Building wheel for pybedtools (setup.py): finished with status 'error' 2025-09-10T05:17:05,598 ERROR: Failed building wheel for pybedtools 2025-09-10T05:17:05,599 Running setup.py clean for pybedtools 2025-09-10T05:17:05,600 Running command python setup.py clean 2025-09-10T05:17:06,422 /tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e/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. 2025-09-10T05:17:06,422 import pkg_resources 2025-09-10T05:17:07,276 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-10T05:17:07,277 !! 2025-09-10T05:17:07,277 ******************************************************************************** 2025-09-10T05:17:07,277 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-10T05:17:07,277 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-10T05:17:07,277 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-10T05:17:07,277 ******************************************************************************** 2025-09-10T05:17:07,278 !! 2025-09-10T05:17:07,278 self._finalize_license_expression() 2025-09-10T05:17:07,278 usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] 2025-09-10T05:17:07,278 or: setup.py --help [cmd1 cmd2 ...] 2025-09-10T05:17:07,278 or: setup.py --help-commands 2025-09-10T05:17:07,278 or: setup.py cmd --help 2025-09-10T05:17:07,279 error: option --all not recognized 2025-09-10T05:17:07,420 ERROR: python setup.py clean exited with 1 2025-09-10T05:17:07,426 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-10T05:17:07,426 exec(compile('"'"''"'"''"'"' 2025-09-10T05:17:07,426 # This is -- a caller that pip uses to run setup.py 2025-09-10T05:17:07,426 # 2025-09-10T05:17:07,426 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-10T05:17:07,426 # import from `distutils.core` to work with newer packaging standards. 2025-09-10T05:17:07,426 # - It provides a clear error message when setuptools is not installed. 2025-09-10T05:17:07,426 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-10T05:17:07,426 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-10T05:17:07,426 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-10T05:17:07,426 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-10T05:17:07,426 import os, sys, tokenize, traceback 2025-09-10T05:17:07,426 2025-09-10T05:17:07,426 try: 2025-09-10T05:17:07,426 import setuptools 2025-09-10T05:17:07,426 except ImportError: 2025-09-10T05:17:07,426 print( 2025-09-10T05:17:07,426 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-10T05:17:07,426 "the build environment with exception:", 2025-09-10T05:17:07,426 file=sys.stderr, 2025-09-10T05:17:07,426 ) 2025-09-10T05:17:07,426 traceback.print_exc() 2025-09-10T05:17:07,426 sys.exit(1) 2025-09-10T05:17:07,426 2025-09-10T05:17:07,426 __file__ = %r 2025-09-10T05:17:07,426 sys.argv[0] = __file__ 2025-09-10T05:17:07,426 2025-09-10T05:17:07,426 if os.path.exists(__file__): 2025-09-10T05:17:07,426 filename = __file__ 2025-09-10T05:17:07,426 with tokenize.open(__file__) as f: 2025-09-10T05:17:07,426 setup_py_code = f.read() 2025-09-10T05:17:07,426 else: 2025-09-10T05:17:07,426 filename = "" 2025-09-10T05:17:07,426 setup_py_code = "from setuptools import setup; setup()" 2025-09-10T05:17:07,426 2025-09-10T05:17:07,426 exec(compile(setup_py_code, filename, "exec")) 2025-09-10T05:17:07,426 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e/setup.py'"'"',), "", "exec"))' clean --all[/] 2025-09-10T05:17:07,426 [bold magenta]cwd[/]: /tmp/pip-wheel-q54nh1kg/pybedtools_f4f2e45f5db5485aa907747ea9ee858e 2025-09-10T05:17:07,426 ERROR: Failed cleaning build dir for pybedtools 2025-09-10T05:17:07,427 Failed to build pybedtools 2025-09-10T05:17:07,428 ERROR: Failed to build one or more wheels 2025-09-10T05:17:07,429 Exception information: 2025-09-10T05:17:07,429 Traceback (most recent call last): 2025-09-10T05:17:07,429 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-10T05:17:07,429 status = _inner_run() 2025-09-10T05:17:07,429 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-10T05:17:07,429 return self.run(options, args) 2025-09-10T05:17:07,429 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-10T05:17:07,429 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-10T05:17:07,429 return func(self, options, args) 2025-09-10T05:17:07,429 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-10T05:17:07,429 raise CommandError("Failed to build one or more wheels") 2025-09-10T05:17:07,429 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-10T05:17:07,434 Removed build tracker: '/tmp/pip-build-tracker-zwo802pp'