2025-09-08T21:38:05,912 Created temporary directory: /tmp/pip-build-tracker-z63mb88i 2025-09-08T21:38:05,913 Initialized build tracking at /tmp/pip-build-tracker-z63mb88i 2025-09-08T21:38:05,913 Created build tracker: /tmp/pip-build-tracker-z63mb88i 2025-09-08T21:38:05,913 Entered build tracker: /tmp/pip-build-tracker-z63mb88i 2025-09-08T21:38:05,914 Created temporary directory: /tmp/pip-wheel-oqyjw9ya 2025-09-08T21:38:05,917 Created temporary directory: /tmp/pip-ephem-wheel-cache-riq6zdpv 2025-09-08T21:38:05,979 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T21:38:05,981 2 location(s) to search for versions of cogent3: 2025-09-08T21:38:05,981 * https://pypi.org/simple/cogent3/ 2025-09-08T21:38:05,981 * https://www.piwheels.org/simple/cogent3/ 2025-09-08T21:38:05,982 Fetching project page and analyzing links: https://pypi.org/simple/cogent3/ 2025-09-08T21:38:05,982 Getting page https://pypi.org/simple/cogent3/ 2025-09-08T21:38:05,983 Found index 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No binaries permitted for cogent3: https://files.pythonhosted.org/packages/d2/1a/6ed8f843c35e64c3b0d28ec9f22467d7d91c8b2e8ec81e29a1ad8ee85f04/cogent3-2019.11.15a0-cp36-cp36m-manylinux2010_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,160 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/c9/fa/62141d1dbe1b86ae7a9642e9417299c9e0364cb99b697f57d0ee833a3c48/cogent3-2019.11.15a0-cp36-cp36m-manylinux2010_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,160 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/10/f5/49f15f6c5d3bbed1591be36e58367067e442de4f83c1edf590b1c143f0f9/cogent3-2019.11.15a0-cp36-cp36m-win32.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,160 Skipping link: No binaries permitted for cogent3: 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https://files.pythonhosted.org/packages/19/83/ecb3070dd10705656ef4a84d8d83b397a3461033cc633b21c8f8182e49e7/cogent3-2019.11.15a0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,163 Found link https://files.pythonhosted.org/packages/30/82/391489edb8eec7f7b9ee557abb13be7b8484e73fc3276b43ca9cfb00ccf7/cogent3-2019.11.15a0.tar.gz (from https://pypi.org/simple/cogent3/), version: 2019.11.15a0 2025-09-08T21:38:06,163 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/98/ad/e4ed445b52baab16df84ccf3694f6e82a620fb67e8d157b11a20f20e9bb5/cogent3-2019.12.6a0-cp36-cp36m-macosx_10_6_intel.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,163 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/09/79/760c5042271bd0ab53d4a9bfc99b545ba3881026c29fda24923b6621b1e6/cogent3-2019.12.6a0-cp36-cp36m-manylinux1_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,164 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/ca/de/cb62c3f50bcc7c083ad4f58f9ac1f0a5811eb2ff578d8e0bddd9e338ccc1/cogent3-2019.12.6a0-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,164 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/4a/3d/9b868d7567e07c278e1a846bc13d6daa7f89bd6617bd56fce8a70845bd17/cogent3-2019.12.6a0-cp36-cp36m-manylinux2010_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,164 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/4b/ac/2c11882d570cd6bfd5a7fbc51d61241932f9714b928087cdb039fa732402/cogent3-2019.12.6a0-cp36-cp36m-manylinux2010_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,164 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/d0/b5/6f2febcad6b2688808e7e35f0d1d5892774550275d648fd8f80a6e41a470/cogent3-2019.12.6a0-cp36-cp36m-win32.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,164 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/ad/1a/3e956d06f8e5ac2eb0700978a0ae9b43aeeb6ba38b63792d64fb370b6c53/cogent3-2019.12.6a0-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,165 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/f4/42/4c373aae14f4c894933795ff11fd8ebe8614534c76363d46006f04deff9a/cogent3-2019.12.6a0-cp37-cp37m-macosx_10_6_intel.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,165 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/f4/f9/8d8e6e5a4a441eaa82e045c7fb1f11b22ab99ce0aa4fb35354da9459bc7d/cogent3-2019.12.6a0-cp37-cp37m-manylinux1_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,165 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/69/82/9a0228b7051650fb56039a291bf1291ecd763fbe8633153a8f8c466e15a9/cogent3-2019.12.6a0-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,165 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/28/eb/eaf1ea03f638bc0a1aff895c9d849ce977f4d9aea80471a359efa7bab0b0/cogent3-2019.12.6a0-cp37-cp37m-manylinux2010_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,165 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/4b/c9/e154b307615b24c5c91681f9db2853bb4ae8927cff891ece9df7862b3b8d/cogent3-2019.12.6a0-cp37-cp37m-manylinux2010_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,165 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/f7/97/b3598090549898fe8ce13faf05822589c8aefd0ee2d3cb3e2cc2d20f78b9/cogent3-2019.12.6a0-cp37-cp37m-win32.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,166 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/a8/e6/93b4cd4f7b6e0f46b88575259ed0d868c0e5cafb632942642b726003ae65/cogent3-2019.12.6a0-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,166 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/de/13/0a833021985c8bece2bf71366a2832d57b2a1ece94791cea2cb1dba07bd3/cogent3-2019.12.6a0-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,166 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/dc/68/8c5addab163b8bbc9928d8ab56688676f11df980b7d2c3fd10bd4ff66c26/cogent3-2019.12.6a0-cp38-cp38-manylinux1_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,166 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/8e/31/9b20128162f1a6ba1e85499e09cdf66003ab19ced0b71d8ee761914f0e20/cogent3-2019.12.6a0-cp38-cp38-manylinux1_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,166 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/b6/6a/90fe0ade4fb3c8f9e5f9aa7e0410ad7ba6a9fe2d537ed3498dfa13c49403/cogent3-2019.12.6a0-cp38-cp38-manylinux2010_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,166 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/fd/5d/01289b185ab8bc8e33fc0e86305fa57074b6f8e83acf96bb5df4e7f62ac0/cogent3-2019.12.6a0-cp38-cp38-manylinux2010_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,166 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/23/a2/84c00d040b15c247ea1a74d2ff07ccabb27a8b51f51f5ac2a0986fdd2519/cogent3-2019.12.6a0-cp38-cp38-win32.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,167 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/b4/cf/64e4e9c5d51b35192585faa9633021c84e818d92dd3a2b9dff40763eab44/cogent3-2019.12.6a0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,167 Found link https://files.pythonhosted.org/packages/f6/bd/8647fa2e52c5b34012964509ce74bfa0f9ecf65e430fcad1eeda3c556b74/cogent3-2019.12.6a0.tar.gz (from https://pypi.org/simple/cogent3/), version: 2019.12.6a0 2025-09-08T21:38:06,167 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/f5/2a/7eaab88f3af7ee490f14fac2c5908465a28e4f502f580392d46692eae886/cogent3-2020.2.7a0-cp36-cp36m-macosx_10_6_intel.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,167 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/18/91/474a65dae272c018b40f64937fcb65128f25cc8d790f9a41d733047a75ab/cogent3-2020.2.7a0-cp36-cp36m-manylinux1_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,167 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/5f/c5/45c950e2f3751bc62d16170f10f15297524e08fe0ac45e9f9257a5245424/cogent3-2020.2.7a0-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,167 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/91/e8/43e89e08fb23321a05e66cd0c36020fa4ead12fb19224bde069cde874fcb/cogent3-2020.2.7a0-cp36-cp36m-manylinux2010_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,168 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/ad/e4/cdeb6ec7effc04c5ae138babcb8d0f8db8f477e09128cc73d5f73f038130/cogent3-2020.2.7a0-cp36-cp36m-manylinux2010_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,168 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/f7/d2/206333e62da24ae451834805ef48315f1aae12fd8bb45be4937109a88728/cogent3-2020.2.7a0-cp36-cp36m-win32.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,168 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/ad/ee/60cf2cac696c8b33ab954fb42af5e3e8e54ea90580836768dc4e78f3ab07/cogent3-2020.2.7a0-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,168 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/48/63/ba31718f75c9c2404b84e0200239ee9a7891177121ffcccfdd4cea741b12/cogent3-2020.2.7a0-cp37-cp37m-macosx_10_6_intel.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,168 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/60/42/5f2a5dfd1751f73d1787a95469c8cc1286c6dfd952ba144de2e83fd8fc5c/cogent3-2020.2.7a0-cp37-cp37m-manylinux1_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,168 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/f9/46/c1d38bff0dfdfee7030173593926817e31fc9848c459fea24ea6b1905147/cogent3-2020.2.7a0-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,168 Skipping link: No binaries permitted for cogent3: https://files.pythonhosted.org/packages/f6/cc/6e4c7695538cccafe5935229987078e136b94c8e6ee8c6f1d2e68892909c/cogent3-2020.2.7a0-cp37-cp37m-manylinux2010_i686.whl (from https://pypi.org/simple/cogent3/) 2025-09-08T21:38:06,169 Skipping link: No binaries permitted for cogent3: 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https://archive1.piwheels.org/simple/cogent3/cogent3-2019.11.15a0-cp37-cp37m-linux_armv7l.whl#sha256=a499ee06c1c3e32b53143deac33048e168ab4842312601fdafa47d8c1a76b2d3 (from https://www.piwheels.org/simple/cogent3/) 2025-09-08T21:38:06,307 Skipping link: not a file: https://www.piwheels.org/simple/cogent3/ 2025-09-08T21:38:06,307 Skipping link: not a file: https://pypi.org/simple/cogent3/ 2025-09-08T21:38:06,337 Given no hashes to check 1 links for project 'cogent3': discarding no candidates 2025-09-08T21:38:06,339 Collecting cogent3==2019.11.15a0 2025-09-08T21:38:06,340 Created temporary directory: /tmp/pip-unpack-nxlwaqab 2025-09-08T21:38:06,487 Downloading cogent3-2019.11.15a0.tar.gz (1.1 MB) 2025-09-08T21:38:06,897 Added cogent3==2019.11.15a0 from https://files.pythonhosted.org/packages/30/82/391489edb8eec7f7b9ee557abb13be7b8484e73fc3276b43ca9cfb00ccf7/cogent3-2019.11.15a0.tar.gz to build tracker '/tmp/pip-build-tracker-z63mb88i' 2025-09-08T21:38:06,898 Running setup.py (path:/tmp/pip-wheel-oqyjw9ya/cogent3_361a2974708840259572d1f8cf5274c3/setup.py) egg_info for package cogent3 2025-09-08T21:38:06,899 Created temporary directory: /tmp/pip-pip-egg-info-fctexbtp 2025-09-08T21:38:06,899 Preparing metadata (setup.py): started 2025-09-08T21:38:06,899 Running command python setup.py egg_info 2025-09-08T21:38:07,427 /tmp/pip-wheel-oqyjw9ya/cogent3_361a2974708840259572d1f8cf5274c3/setup.py:44: SyntaxWarning: invalid escape sequence '\d' 2025-09-08T21:38:07,427 numpy_version = re.split("[^\d]", numpy.__version__) 2025-09-08T21:38:07,428 /tmp/pip-wheel-oqyjw9ya/cogent3_361a2974708840259572d1f8cf5274c3/setup.py:106: SyntaxWarning: invalid escape sequence '\d' 2025-09-08T21:38:07,428 version = tuple([int(v) for v in re.split("[^\d]", version) if v.isdigit()]) 2025-09-08T21:38:16,930 warning: src/cogent3/evolve/_solved_models.pyx:17:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2025-09-08T21:38:16,930 warning: src/cogent3/evolve/_solved_models.pyx:17:33: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2025-09-08T21:38:16,930 warning: src/cogent3/evolve/_solved_models.pyx:17:40: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2025-09-08T21:38:16,930 warning: src/cogent3/evolve/_solved_models.pyx:17:51: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2025-09-08T21:38:16,930 warning: src/cogent3/evolve/_solved_models.pyx:18:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2025-09-08T21:38:18,777 Compiling src/cogent3/align/_compare.pyx because it changed. 2025-09-08T21:38:18,777 Compiling src/cogent3/align/_pairwise_seqs.pyx because it changed. 2025-09-08T21:38:18,777 Compiling src/cogent3/align/_pairwise_pogs.pyx because it changed. 2025-09-08T21:38:18,778 Compiling src/cogent3/evolve/_solved_models.pyx because it changed. 2025-09-08T21:38:18,778 Compiling src/cogent3/evolve/_likelihood_tree.pyx because it changed. 2025-09-08T21:38:18,778 Compiling src/cogent3/evolve/_pairwise_distance.pyx because it changed. 2025-09-08T21:38:18,778 Compiling src/cogent3/maths/_period.pyx because it changed. 2025-09-08T21:38:18,778 [1/7] Cythonizing src/cogent3/align/_compare.pyx 2025-09-08T21:38:18,778 [2/7] Cythonizing src/cogent3/align/_pairwise_pogs.pyx 2025-09-08T21:38:18,778 [3/7] Cythonizing src/cogent3/align/_pairwise_seqs.pyx 2025-09-08T21:38:18,778 [4/7] Cythonizing src/cogent3/evolve/_likelihood_tree.pyx 2025-09-08T21:38:18,778 [5/7] Cythonizing src/cogent3/evolve/_pairwise_distance.pyx 2025-09-08T21:38:18,778 [6/7] Cythonizing src/cogent3/evolve/_solved_models.pyx 2025-09-08T21:38:18,779 [7/7] Cythonizing src/cogent3/maths/_period.pyx 2025-09-08T21:38:19,072 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:332: InformationOnly: Normalizing '2019.11.15.a' to '2019.11.15a0' 2025-09-08T21:38:19,072 self.metadata.version = self._normalize_version(self.metadata.version) 2025-09-08T21:38:19,075 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T21:38:19,075 !! 2025-09-08T21:38:19,075 ******************************************************************************** 2025-09-08T21:38:19,075 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T21:38:19,076 License :: OSI Approved :: GNU General Public License (GPL) 2025-09-08T21:38:19,076 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T21:38:19,076 ******************************************************************************** 2025-09-08T21:38:19,076 !! 2025-09-08T21:38:19,076 self._finalize_license_expression() 2025-09-08T21:38:19,160 running egg_info 2025-09-08T21:38:19,229 creating /tmp/pip-pip-egg-info-fctexbtp/cogent3.egg-info 2025-09-08T21:38:19,229 writing /tmp/pip-pip-egg-info-fctexbtp/cogent3.egg-info/PKG-INFO 2025-09-08T21:38:19,236 Traceback (most recent call last): 2025-09-08T21:38:19,242 File "", line 2, in 2025-09-08T21:38:19,242 exec(compile(''' 2025-09-08T21:38:19,242 ~~~~^^^^^^^^^^^^ 2025-09-08T21:38:19,242 # This is -- a caller that pip uses to run setup.py 2025-09-08T21:38:19,243 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:19,243 ...<32 lines>... 2025-09-08T21:38:19,243 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T21:38:19,243 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:19,243 ''' % ('/tmp/pip-wheel-oqyjw9ya/cogent3_361a2974708840259572d1f8cf5274c3/setup.py',), "", "exec")) 2025-09-08T21:38:19,243 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:19,243 File "", line 35, in 2025-09-08T21:38:19,243 File "/tmp/pip-wheel-oqyjw9ya/cogent3_361a2974708840259572d1f8cf5274c3/setup.py", line 140, in 2025-09-08T21:38:19,244 setup( 2025-09-08T21:38:19,244 ~~~~~^ 2025-09-08T21:38:19,244 name="cogent3", 2025-09-08T21:38:19,244 ^^^^^^^^^^^^^^^ 2025-09-08T21:38:19,244 ...<69 lines>... 2025-09-08T21:38:19,244 cmdclass=extra_commands, 2025-09-08T21:38:19,244 ^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:19,244 ) 2025-09-08T21:38:19,245 ^ 2025-09-08T21:38:19,245 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T21:38:19,245 return distutils.core.setup(**attrs) 2025-09-08T21:38:19,245 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T21:38:19,245 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T21:38:19,245 return run_commands(dist) 2025-09-08T21:38:19,245 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T21:38:19,245 dist.run_commands() 2025-09-08T21:38:19,245 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T21:38:19,246 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T21:38:19,246 self.run_command(cmd) 2025-09-08T21:38:19,246 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T21:38:19,246 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T21:38:19,246 super().run_command(command) 2025-09-08T21:38:19,246 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T21:38:19,246 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T21:38:19,246 cmd_obj.run() 2025-09-08T21:38:19,246 ~~~~~~~~~~~^^ 2025-09-08T21:38:19,247 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/egg_info.py", line 305, in run 2025-09-08T21:38:19,247 writer(self, ep.name, os.path.join(self.egg_info, ep.name)) 2025-09-08T21:38:19,247 ~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:19,247 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/egg_info.py", line 658, in write_pkg_info 2025-09-08T21:38:19,247 metadata.write_pkg_info(cmd.egg_info) 2025-09-08T21:38:19,247 ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^ 2025-09-08T21:38:19,247 File "/usr/local/lib/python3.13/dist-packages/setuptools/_core_metadata.py", line 140, in write_pkg_info 2025-09-08T21:38:19,247 self.write_pkg_file(f) 2025-09-08T21:38:19,247 ~~~~~~~~~~~~~~~~~~~^^^ 2025-09-08T21:38:19,247 File "/usr/local/lib/python3.13/dist-packages/setuptools/_core_metadata.py", line 182, in write_pkg_file 2025-09-08T21:38:19,248 write_field('License', rfc822_escape(license)) 2025-09-08T21:38:19,248 ~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T21:38:19,248 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/util.py", line 497, in rfc822_escape 2025-09-08T21:38:19,248 lines = header.splitlines(keepends=True) 2025-09-08T21:38:19,248 ^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:19,248 AttributeError: 'list' object has no attribute 'splitlines' 2025-09-08T21:38:20,125 ERROR: python setup.py egg_info exited with 1 2025-09-08T21:38:20,137 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c ' 2025-09-08T21:38:20,137 exec(compile('"'"''"'"''"'"' 2025-09-08T21:38:20,137 # This is -- a caller that pip uses to run setup.py 2025-09-08T21:38:20,137 # 2025-09-08T21:38:20,137 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T21:38:20,137 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T21:38:20,137 # - It provides a clear error message when setuptools is not installed. 2025-09-08T21:38:20,137 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T21:38:20,137 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T21:38:20,137 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T21:38:20,137 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T21:38:20,137 import os, sys, tokenize, traceback 2025-09-08T21:38:20,137 2025-09-08T21:38:20,137 try: 2025-09-08T21:38:20,137 import setuptools 2025-09-08T21:38:20,137 except ImportError: 2025-09-08T21:38:20,137 print( 2025-09-08T21:38:20,137 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T21:38:20,137 "the build environment with exception:", 2025-09-08T21:38:20,137 file=sys.stderr, 2025-09-08T21:38:20,137 ) 2025-09-08T21:38:20,137 traceback.print_exc() 2025-09-08T21:38:20,137 sys.exit(1) 2025-09-08T21:38:20,137 2025-09-08T21:38:20,137 __file__ = %r 2025-09-08T21:38:20,137 sys.argv[0] = __file__ 2025-09-08T21:38:20,137 2025-09-08T21:38:20,137 if os.path.exists(__file__): 2025-09-08T21:38:20,137 filename = __file__ 2025-09-08T21:38:20,137 with tokenize.open(__file__) as f: 2025-09-08T21:38:20,137 setup_py_code = f.read() 2025-09-08T21:38:20,137 else: 2025-09-08T21:38:20,137 filename = "" 2025-09-08T21:38:20,137 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T21:38:20,137 2025-09-08T21:38:20,137 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T21:38:20,137 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-oqyjw9ya/cogent3_361a2974708840259572d1f8cf5274c3/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-fctexbtp[/] 2025-09-08T21:38:20,137 [bold magenta]cwd[/]: /tmp/pip-wheel-oqyjw9ya/cogent3_361a2974708840259572d1f8cf5274c3/ 2025-09-08T21:38:20,138 Preparing metadata (setup.py): finished with status 'error' 2025-09-08T21:38:20,139 ERROR: metadata generation failed 2025-09-08T21:38:20,145 Exception information: 2025-09-08T21:38:20,145 Traceback (most recent call last): 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 63, in generate_metadata 2025-09-08T21:38:20,145 call_subprocess( 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~^ 2025-09-08T21:38:20,145 args, 2025-09-08T21:38:20,145 ^^^^^ 2025-09-08T21:38:20,145 ...<2 lines>... 2025-09-08T21:38:20,145 spinner=spinner, 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 ^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess 2025-09-08T21:38:20,145 raise error 2025-09-08T21:38:20,145 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 2025-09-08T21:38:20,145 2025-09-08T21:38:20,145 The above exception was the direct cause of the following exception: 2025-09-08T21:38:20,145 2025-09-08T21:38:20,145 Traceback (most recent call last): 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T21:38:20,145 status = _inner_run() 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T21:38:20,145 return self.run(options, args) 2025-09-08T21:38:20,145 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T21:38:20,145 return func(self, options, args) 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2025-09-08T21:38:20,145 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve 2025-09-08T21:38:20,145 result = self._result = resolver.resolve( 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~^ 2025-09-08T21:38:20,145 collected.requirements, max_rounds=limit_how_complex_resolution_can_be 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 ^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 515, in resolve 2025-09-08T21:38:20,145 state = resolution.resolve(requirements, max_rounds=max_rounds) 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 388, in resolve 2025-09-08T21:38:20,145 self._add_to_criteria(self.state.criteria, r, parent=None) 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 141, in _add_to_criteria 2025-09-08T21:38:20,145 if not criterion.candidates: 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/structs.py", line 194, in __bool__ 2025-09-08T21:38:20,145 return bool(self._sequence) 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 163, in __bool__ 2025-09-08T21:38:20,145 self._bool = any(self) 2025-09-08T21:38:20,145 ~~~^^^^^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 147, in 2025-09-08T21:38:20,145 return (c for c in iterator if id(c) not in self._incompatible_ids) 2025-09-08T21:38:20,145 ^^^^^^^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 37, in _iter_built 2025-09-08T21:38:20,145 candidate = func() 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 187, in _make_candidate_from_link 2025-09-08T21:38:20,145 base: Optional[BaseCandidate] = self._make_base_candidate_from_link( 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T21:38:20,145 link, template, name, version 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 ^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link 2025-09-08T21:38:20,145 self._link_candidate_cache[link] = LinkCandidate( 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~^ 2025-09-08T21:38:20,145 link, 2025-09-08T21:38:20,145 ^^^^^ 2025-09-08T21:38:20,145 ...<3 lines>... 2025-09-08T21:38:20,145 version=version, 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 ^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__ 2025-09-08T21:38:20,145 super().__init__( 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~^ 2025-09-08T21:38:20,145 link=link, 2025-09-08T21:38:20,145 ^^^^^^^^^^ 2025-09-08T21:38:20,145 ...<4 lines>... 2025-09-08T21:38:20,145 version=version, 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 ^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ 2025-09-08T21:38:20,145 self.dist = self._prepare() 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare 2025-09-08T21:38:20,145 dist = self._prepare_distribution() 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution 2025-09-08T21:38:20,145 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement 2025-09-08T21:38:20,145 return self._prepare_linked_requirement(req, parallel_builds) 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement 2025-09-08T21:38:20,145 dist = _get_prepared_distribution( 2025-09-08T21:38:20,145 req, 2025-09-08T21:38:20,145 ...<3 lines>... 2025-09-08T21:38:20,145 self.check_build_deps, 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution 2025-09-08T21:38:20,145 abstract_dist.prepare_distribution_metadata( 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T21:38:20,145 finder, build_isolation, check_build_deps 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 ^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata 2025-09-08T21:38:20,145 self.req.prepare_metadata() 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata 2025-09-08T21:38:20,145 self.metadata_directory = generate_metadata_legacy( 2025-09-08T21:38:20,145 ~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T21:38:20,145 build_env=self.build_env, 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ...<3 lines>... 2025-09-08T21:38:20,145 details=details, 2025-09-08T21:38:20,145 ^^^^^^^^^^^^^^^^ 2025-09-08T21:38:20,145 ) 2025-09-08T21:38:20,145 ^ 2025-09-08T21:38:20,145 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 70, in generate_metadata 2025-09-08T21:38:20,145 raise MetadataGenerationFailed(package_details=details) from error 2025-09-08T21:38:20,145 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2025-09-08T21:38:20,168 Removed cogent3==2019.11.15a0 from https://files.pythonhosted.org/packages/30/82/391489edb8eec7f7b9ee557abb13be7b8484e73fc3276b43ca9cfb00ccf7/cogent3-2019.11.15a0.tar.gz from build tracker '/tmp/pip-build-tracker-z63mb88i' 2025-09-08T21:38:20,169 Removed build tracker: '/tmp/pip-build-tracker-z63mb88i'