2025-09-08T19:51:20,873 Created temporary directory: /tmp/pip-build-tracker-6a0y9qmv 2025-09-08T19:51:20,873 Initialized build tracking at /tmp/pip-build-tracker-6a0y9qmv 2025-09-08T19:51:20,873 Created build tracker: /tmp/pip-build-tracker-6a0y9qmv 2025-09-08T19:51:20,873 Entered build tracker: /tmp/pip-build-tracker-6a0y9qmv 2025-09-08T19:51:20,874 Created temporary directory: /tmp/pip-wheel-vypohppu 2025-09-08T19:51:20,877 Created temporary directory: /tmp/pip-ephem-wheel-cache-uk166b58 2025-09-08T19:51:20,943 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T19:51:20,945 2 location(s) to search for versions of sciencebeam-alignment: 2025-09-08T19:51:20,945 * https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:20,945 * https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:20,945 Fetching project page and analyzing links: https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:20,946 Getting page https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:20,947 Found index url https://pypi.org/simple/ 2025-09-08T19:51:21,020 Fetched page https://pypi.org/simple/sciencebeam-alignment/ as application/vnd.pypi.simple.v1+json 2025-09-08T19:51:21,021 Found link https://files.pythonhosted.org/packages/ba/b3/25ff1592c9178a52b8482b9155b9f4d6a8a4540c9ee697ac3b47d317dbef/sciencebeam_alignment-0.0.1.tar.gz (from https://pypi.org/simple/sciencebeam-alignment/), version: 0.0.1 2025-09-08T19:51:21,021 Found link https://files.pythonhosted.org/packages/5c/1f/1ac79237e5fae7cd3f3b832544c6b1bfb365c153916f63843fb789da1f5d/sciencebeam_alignment-0.0.2.tar.gz (from https://pypi.org/simple/sciencebeam-alignment/), version: 0.0.2 2025-09-08T19:51:21,022 Found link https://files.pythonhosted.org/packages/3e/3e/b8d8496426dc0dad1e9221b117fd9154ae68301bf8622d21f6808354f9eb/sciencebeam_alignment-0.0.3.tar.gz (from https://pypi.org/simple/sciencebeam-alignment/), version: 0.0.3 2025-09-08T19:51:21,022 Found link https://files.pythonhosted.org/packages/2d/ca/991716febd8eda0f5c1460764ab846c2ac9058352727d4644add2b98bfc9/sciencebeam_alignment-0.0.4.tar.gz (from https://pypi.org/simple/sciencebeam-alignment/), version: 0.0.4 2025-09-08T19:51:21,022 Found link https://files.pythonhosted.org/packages/58/4b/053c438c812662abdb38c2287872dbe1610abe6c186c57ed1145fa60b800/sciencebeam_alignment-0.0.5.tar.gz (from https://pypi.org/simple/sciencebeam-alignment/), version: 0.0.5 2025-09-08T19:51:21,023 Fetching project page and analyzing links: https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:21,023 Getting page https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:21,024 Found index url https://www.piwheels.org/simple/ 2025-09-08T19:51:21,128 Fetched page https://www.piwheels.org/simple/sciencebeam-alignment/ as text/html 2025-09-08T19:51:21,134 Skipping link: No binaries permitted for sciencebeam-alignment: 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sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.5-cp37-cp37m-linux_armv7l.whl#sha256=b35538a374be0b882ad62a93319c4ea5fb02a0c84cf60789abcec69ed9790476 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,135 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.5-cp39-cp39-linux_armv6l.whl#sha256=bd65676962a4c16e42bb7ffa3f4ad4f42918b02049a9c0978c4fbd54a5ec41ae (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,135 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.5-cp39-cp39-linux_armv7l.whl#sha256=bd65676962a4c16e42bb7ffa3f4ad4f42918b02049a9c0978c4fbd54a5ec41ae (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,135 Skipping link: No binaries 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Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.3-cp39-cp39-linux_armv6l.whl#sha256=0501a81869a611b21299046d7bf3818145cbbd5dfdcfb585c09892653fe9db5c (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,136 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.3-cp39-cp39-linux_armv7l.whl#sha256=0501a81869a611b21299046d7bf3818145cbbd5dfdcfb585c09892653fe9db5c (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,136 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.3-cp35-cp35m-linux_armv7l.whl#sha256=da088e47ab99ef79a684f39cc95b3add908929ead82f7eff717321d2f1aef74f (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,136 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.3-cp35-cp35m-linux_armv6l.whl#sha256=da088e47ab99ef79a684f39cc95b3add908929ead82f7eff717321d2f1aef74f (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,136 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.3-cp37-cp37m-linux_armv7l.whl#sha256=f3bef5781f0c4ae80e3042e44f293a559d54cc16b21e0668515b12f8fbb60fd4 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,136 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.3-cp37-cp37m-linux_armv6l.whl#sha256=f3bef5781f0c4ae80e3042e44f293a559d54cc16b21e0668515b12f8fbb60fd4 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,136 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp39-cp39-linux_armv6l.whl#sha256=ae8e3b140956b24bb81d02fe5ab92b7e57435f23111c5fb0205d91468db1f817 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,136 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp39-cp39-linux_armv7l.whl#sha256=ae8e3b140956b24bb81d02fe5ab92b7e57435f23111c5fb0205d91468db1f817 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp37-cp37m-linux_armv6l.whl#sha256=35220b86167215c8cacd0d0ec455977589a0bf60f7a758b8be270bba6fd558b2 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp37-cp37m-linux_armv7l.whl#sha256=35220b86167215c8cacd0d0ec455977589a0bf60f7a758b8be270bba6fd558b2 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp35-cp35m-linux_armv6l.whl#sha256=fd7816e9289021865c68d3482d3c77c08185712f3a56233f452c23dc3ec77438 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp35-cp35m-linux_armv7l.whl#sha256=fd7816e9289021865c68d3482d3c77c08185712f3a56233f452c23dc3ec77438 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp34-cp34m-linux_armv6l.whl#sha256=e22ce1ed14280ae843333bc34a0c28ef4c924828cf24dc1d9f93a0dbbc95e743 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.2-cp34-cp34m-linux_armv7l.whl#sha256=e22ce1ed14280ae843333bc34a0c28ef4c924828cf24dc1d9f93a0dbbc95e743 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp39-cp39-linux_armv6l.whl#sha256=589c61f3e67c3759243877493600bf9eb7cce822b5c18075abb6787bf812d31d (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp39-cp39-linux_armv7l.whl#sha256=589c61f3e67c3759243877493600bf9eb7cce822b5c18075abb6787bf812d31d (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,137 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp37-cp37m-linux_armv6l.whl#sha256=f2180e90387f02e4b9d84af0ba4839a792551217894c9899a14244ac35a2df7e (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,138 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp37-cp37m-linux_armv7l.whl#sha256=f2180e90387f02e4b9d84af0ba4839a792551217894c9899a14244ac35a2df7e (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,138 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp34-cp34m-linux_armv6l.whl#sha256=8d21029ea3d4c1b92b1aee026d3746bbc094d3172b334619add4e393deae2c08 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,138 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp34-cp34m-linux_armv7l.whl#sha256=8d21029ea3d4c1b92b1aee026d3746bbc094d3172b334619add4e393deae2c08 (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,138 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp35-cp35m-linux_armv6l.whl#sha256=2c173d2c8c37f66a4ea7d4c26960a8460a5a5a85f0479cd42bfa206284f6c01e (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,138 Skipping link: No binaries permitted for sciencebeam-alignment: https://archive1.piwheels.org/simple/sciencebeam-alignment/sciencebeam_alignment-0.0.1-cp35-cp35m-linux_armv7l.whl#sha256=2c173d2c8c37f66a4ea7d4c26960a8460a5a5a85f0479cd42bfa206284f6c01e (from https://www.piwheels.org/simple/sciencebeam-alignment/) 2025-09-08T19:51:21,138 Skipping link: not a file: https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:21,138 Skipping link: not a file: https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T19:51:21,166 Given no hashes to check 1 links for project 'sciencebeam-alignment': discarding no candidates 2025-09-08T19:51:21,167 Collecting sciencebeam-alignment==0.0.3 2025-09-08T19:51:21,168 Created temporary directory: /tmp/pip-unpack-xfwflc54 2025-09-08T19:51:21,731 Downloading sciencebeam_alignment-0.0.3.tar.gz (8.8 kB) 2025-09-08T19:51:21,762 Added sciencebeam-alignment==0.0.3 from https://files.pythonhosted.org/packages/3e/3e/b8d8496426dc0dad1e9221b117fd9154ae68301bf8622d21f6808354f9eb/sciencebeam_alignment-0.0.3.tar.gz to build tracker '/tmp/pip-build-tracker-6a0y9qmv' 2025-09-08T19:51:21,763 Running setup.py (path:/tmp/pip-wheel-vypohppu/sciencebeam-alignment_6eaaab616ccf438aa7ed04dc385d9f27/setup.py) egg_info for package sciencebeam-alignment 2025-09-08T19:51:21,763 Created temporary directory: /tmp/pip-pip-egg-info-b7r640y9 2025-09-08T19:51:21,763 Preparing metadata (setup.py): started 2025-09-08T19:51:21,764 Running command python setup.py egg_info 2025-09-08T19:51:22,596 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T19:51:22,597 !! 2025-09-08T19:51:22,597 ******************************************************************************** 2025-09-08T19:51:22,597 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T19:51:22,597 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T19:51:22,597 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T19:51:22,597 or your builds will no longer be supported. 2025-09-08T19:51:22,597 ******************************************************************************** 2025-09-08T19:51:22,598 !! 2025-09-08T19:51:22,598 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T19:51:23,177 running egg_info 2025-09-08T19:51:23,252 creating /tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info 2025-09-08T19:51:23,252 writing /tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info/PKG-INFO 2025-09-08T19:51:23,253 writing dependency_links to /tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info/dependency_links.txt 2025-09-08T19:51:23,254 writing requirements to /tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info/requires.txt 2025-09-08T19:51:23,254 writing top-level names to /tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info/top_level.txt 2025-09-08T19:51:23,254 writing manifest file '/tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T19:51:23,557 reading manifest file '/tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T19:51:23,558 reading manifest template 'MANIFEST.in' 2025-09-08T19:51:23,561 writing manifest file '/tmp/pip-pip-egg-info-b7r640y9/sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T19:51:23,698 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T19:51:23,703 Source in /tmp/pip-wheel-vypohppu/sciencebeam-alignment_6eaaab616ccf438aa7ed04dc385d9f27 has version 0.0.3, which satisfies requirement sciencebeam-alignment==0.0.3 from https://files.pythonhosted.org/packages/3e/3e/b8d8496426dc0dad1e9221b117fd9154ae68301bf8622d21f6808354f9eb/sciencebeam_alignment-0.0.3.tar.gz 2025-09-08T19:51:23,703 Removed sciencebeam-alignment==0.0.3 from https://files.pythonhosted.org/packages/3e/3e/b8d8496426dc0dad1e9221b117fd9154ae68301bf8622d21f6808354f9eb/sciencebeam_alignment-0.0.3.tar.gz from build tracker '/tmp/pip-build-tracker-6a0y9qmv' 2025-09-08T19:51:23,707 Created temporary directory: /tmp/pip-unpack-zaxg8mqa 2025-09-08T19:51:23,707 Created temporary directory: /tmp/pip-unpack-qgn4sds5 2025-09-08T19:51:23,707 Building wheels for collected packages: sciencebeam-alignment 2025-09-08T19:51:23,709 Created temporary directory: /tmp/pip-wheel-9mettb2l 2025-09-08T19:51:23,709 DEPRECATION: Building 'sciencebeam-alignment' 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 'sciencebeam-alignment'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T19:51:23,710 Building wheel for sciencebeam-alignment (setup.py): started 2025-09-08T19:51:23,711 Destination directory: /tmp/pip-wheel-9mettb2l 2025-09-08T19:51:23,711 Running command python setup.py bdist_wheel 2025-09-08T19:51:24,539 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T19:51:24,539 !! 2025-09-08T19:51:24,540 ******************************************************************************** 2025-09-08T19:51:24,540 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T19:51:24,540 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T19:51:24,540 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T19:51:24,540 or your builds will no longer be supported. 2025-09-08T19:51:24,540 ******************************************************************************** 2025-09-08T19:51:24,540 !! 2025-09-08T19:51:24,541 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T19:51:25,041 running bdist_wheel 2025-09-08T19:51:25,411 running build 2025-09-08T19:51:25,411 running build_py 2025-09-08T19:51:25,490 creating build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T19:51:25,490 copying sciencebeam_alignment/align.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T19:51:25,491 copying sciencebeam_alignment/word_sequence_matcher.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T19:51:25,492 copying sciencebeam_alignment/__init__.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T19:51:25,492 copying sciencebeam_alignment/align_performance.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T19:51:25,493 copying sciencebeam_alignment/sequence_matcher.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T19:51:25,493 creating build/lib.linux-armv7l-cpython-313/tests 2025-09-08T19:51:25,494 copying tests/align_test.py -> build/lib.linux-armv7l-cpython-313/tests 2025-09-08T19:51:25,494 copying tests/word_sequence_matcher_test.py -> build/lib.linux-armv7l-cpython-313/tests 2025-09-08T19:51:25,495 copying tests/__init__.py -> build/lib.linux-armv7l-cpython-313/tests 2025-09-08T19:51:25,495 copying tests/conftest.py -> build/lib.linux-armv7l-cpython-313/tests 2025-09-08T19:51:25,496 running egg_info 2025-09-08T19:51:25,568 writing sciencebeam_alignment.egg-info/PKG-INFO 2025-09-08T19:51:25,570 writing dependency_links to sciencebeam_alignment.egg-info/dependency_links.txt 2025-09-08T19:51:25,570 writing requirements to sciencebeam_alignment.egg-info/requires.txt 2025-09-08T19:51:25,571 writing top-level names to sciencebeam_alignment.egg-info/top_level.txt 2025-09-08T19:51:25,647 reading manifest file 'sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T19:51:25,649 reading manifest template 'MANIFEST.in' 2025-09-08T19:51:25,652 writing manifest file 'sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T19:51:25,653 copying sciencebeam_alignment/align_fast_utils.pyx -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T19:51:25,654 running build_ext 2025-09-08T19:51:26,278 Compiling sciencebeam_alignment/align_fast_utils.pyx because it changed. 2025-09-08T19:51:26,278 [1/1] Cythonizing sciencebeam_alignment/align_fast_utils.pyx 2025-09-08T19:51:28,498 Error compiling Cython file: 2025-09-08T19:51:28,498 ------------------------------------------------------------ 2025-09-08T19:51:28,498 ... 2025-09-08T19:51:28,499 DEF MIN_INT = -2147483647 2025-09-08T19:51:28,499 ctypedef np.int_t int_t 2025-09-08T19:51:28,499 ^ 2025-09-08T19:51:28,499 ------------------------------------------------------------ 2025-09-08T19:51:28,499 sciencebeam_alignment/align_fast_utils.pyx:11:9: 'int_t' is not a type identifier 2025-09-08T19:51:29,003 Error compiling Cython file: 2025-09-08T19:51:29,003 ------------------------------------------------------------ 2025-09-08T19:51:29,003 ... 2025-09-08T19:51:29,003 for j in range(1, n): 2025-09-08T19:51:29,003 scoring_matrix[i, j] = imax4( 2025-09-08T19:51:29,003 min_score, 2025-09-08T19:51:29,003 # Match elements. 2025-09-08T19:51:29,003 scoring_matrix[i - 1, j - 1] + 2025-09-08T19:51:29,003 ^ 2025-09-08T19:51:29,003 ------------------------------------------------------------ 2025-09-08T19:51:29,004 sciencebeam_alignment/align_fast_utils.pyx:52:33: Compiler crash in OptimizeBuiltinCalls 2025-09-08T19:51:29,004 ModuleNode.body = StatListNode(align_fast_utils.pyx:1:0) 2025-09-08T19:51:29,004 StatListNode.stats[10] = StatListNode(align_fast_utils.pyx:37:0) 2025-09-08T19:51:29,004 StatListNode.stats[0] = DefNode(align_fast_utils.pyx:37:0, 2025-09-08T19:51:29,004 is_cyfunction = True, 2025-09-08T19:51:29,004 modifiers = [...]/0, 2025-09-08T19:51:29,004 name = 'native_compute_inner_alignment_matrix_simple_scoring_int', 2025-09-08T19:51:29,004 node_positions = [...]/70, 2025-09-08T19:51:29,004 np_args_idx = [...]/0, 2025-09-08T19:51:29,004 num_required_args = 7, 2025-09-08T19:51:29,004 outer_attrs = [...]/2, 2025-09-08T19:51:29,005 py_wrapper_required = True, 2025-09-08T19:51:29,005 reqd_kw_flags_cname = '0', 2025-09-08T19:51:29,005 used = True) 2025-09-08T19:51:29,005 DefNode.body = StatListNode(align_fast_utils.pyx:42:4) 2025-09-08T19:51:29,005 StatListNode.stats[2] = LetNode(align_fast_utils.pyx:46:4) 2025-09-08T19:51:29,005 LetNode.body = ForFromStatNode(align_fast_utils.pyx:46:4, 2025-09-08T19:51:29,005 from_range = True, 2025-09-08T19:51:29,005 relation1 = '<=', 2025-09-08T19:51:29,005 relation2 = '<') 2025-09-08T19:51:29,005 ForFromStatNode.body = StatListNode(align_fast_utils.pyx:47:8) 2025-09-08T19:51:29,005 StatListNode.stats[0] = LetNode(align_fast_utils.pyx:47:8) 2025-09-08T19:51:29,005 LetNode.body = ForFromStatNode(align_fast_utils.pyx:47:8, 2025-09-08T19:51:29,006 from_range = True, 2025-09-08T19:51:29,006 relation1 = '<=', 2025-09-08T19:51:29,006 relation2 = '<') 2025-09-08T19:51:29,006 ForFromStatNode.body = StatListNode(align_fast_utils.pyx:48:40) 2025-09-08T19:51:29,006 StatListNode.stats[0] = SingleAssignmentNode(align_fast_utils.pyx:48:40) 2025-09-08T19:51:29,006 SingleAssignmentNode.rhs = SimpleCallNode(align_fast_utils.pyx:48:40, 2025-09-08T19:51:29,006 analysed = True, 2025-09-08T19:51:29,006 is_temp = 1, 2025-09-08T19:51:29,006 result_is_used = True, 2025-09-08T19:51:29,007 use_managed_ref = True) 2025-09-08T19:51:29,007 SimpleCallNode.args[1] = AddNode(align_fast_utils.pyx:52:45, 2025-09-08T19:51:29,007 infix = True, 2025-09-08T19:51:29,007 operator = '+', 2025-09-08T19:51:29,007 result_is_used = True, 2025-09-08T19:51:29,007 use_managed_ref = True) 2025-09-08T19:51:29,007 AddNode.operand1 = IndexNode(align_fast_utils.pyx:52:30, 2025-09-08T19:51:29,007 is_subscript = True, 2025-09-08T19:51:29,007 result_is_used = True, 2025-09-08T19:51:29,007 use_managed_ref = True) 2025-09-08T19:51:29,007 IndexNode.index = TupleNode(align_fast_utils.pyx:52:30, 2025-09-08T19:51:29,007 is_sequence_constructor = 1, 2025-09-08T19:51:29,008 result_is_used = True, 2025-09-08T19:51:29,008 use_managed_ref = True) 2025-09-08T19:51:29,008 TupleNode.args[0] = SubNode(align_fast_utils.pyx:52:33, 2025-09-08T19:51:29,008 infix = True, 2025-09-08T19:51:29,008 operator = '-', 2025-09-08T19:51:29,008 result_is_used = True, 2025-09-08T19:51:29,008 use_managed_ref = True) 2025-09-08T19:51:29,008 Compiler crash traceback from this point on: 2025-09-08T19:51:29,008 File "Cython/Compiler/Visitor.py", line 174, in Cython.Compiler.Visitor.TreeVisitor._visit 2025-09-08T19:51:29,008 File "Cython/Compiler/Visitor.py", line 538, in Cython.Compiler.Visitor.MethodDispatcherTransform.visit_BinopNode 2025-09-08T19:51:29,009 File "Cython/Compiler/Visitor.py", line 552, in Cython.Compiler.Visitor.MethodDispatcherTransform._visit_binop_node 2025-09-08T19:51:29,009 AttributeError: 'NoneType' object has no attribute 'is_builtin_type' 2025-09-08T19:51:29,013 Traceback (most recent call last): 2025-09-08T19:51:29,022 File "", line 2, in 2025-09-08T19:51:29,022 exec(compile(''' 2025-09-08T19:51:29,022 ~~~~^^^^^^^^^^^^ 2025-09-08T19:51:29,022 # This is -- a caller that pip uses to run setup.py 2025-09-08T19:51:29,022 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T19:51:29,022 ...<32 lines>... 2025-09-08T19:51:29,023 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T19:51:29,023 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T19:51:29,023 ''' % ('/tmp/pip-wheel-vypohppu/sciencebeam-alignment_6eaaab616ccf438aa7ed04dc385d9f27/setup.py',), "", "exec")) 2025-09-08T19:51:29,023 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T19:51:29,023 File "", line 35, in 2025-09-08T19:51:29,023 File "/tmp/pip-wheel-vypohppu/sciencebeam-alignment_6eaaab616ccf438aa7ed04dc385d9f27/setup.py", line 38, in 2025-09-08T19:51:29,023 setup( 2025-09-08T19:51:29,024 ~~~~~^ 2025-09-08T19:51:29,024 name='sciencebeam_alignment', 2025-09-08T19:51:29,024 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T19:51:29,024 ...<18 lines>... 2025-09-08T19:51:29,024 long_description_content_type='text/markdown' 2025-09-08T19:51:29,024 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T19:51:29,024 ) 2025-09-08T19:51:29,024 ^ 2025-09-08T19:51:29,025 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T19:51:29,025 return distutils.core.setup(**attrs) 2025-09-08T19:51:29,025 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T19:51:29,025 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T19:51:29,025 return run_commands(dist) 2025-09-08T19:51:29,025 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T19:51:29,025 dist.run_commands() 2025-09-08T19:51:29,025 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T19:51:29,026 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T19:51:29,026 self.run_command(cmd) 2025-09-08T19:51:29,026 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T19:51:29,026 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T19:51:29,026 super().run_command(command) 2025-09-08T19:51:29,026 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T19:51:29,026 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T19:51:29,026 cmd_obj.run() 2025-09-08T19:51:29,026 ~~~~~~~~~~~^^ 2025-09-08T19:51:29,026 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T19:51:29,027 self.run_command("build") 2025-09-08T19:51:29,027 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T19:51:29,027 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T19:51:29,027 self.distribution.run_command(command) 2025-09-08T19:51:29,027 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T19:51:29,027 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T19:51:29,027 super().run_command(command) 2025-09-08T19:51:29,027 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T19:51:29,028 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T19:51:29,028 cmd_obj.run() 2025-09-08T19:51:29,028 ~~~~~~~~~~~^^ 2025-09-08T19:51:29,028 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T19:51:29,028 self.run_command(cmd_name) 2025-09-08T19:51:29,028 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T19:51:29,028 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T19:51:29,028 self.distribution.run_command(command) 2025-09-08T19:51:29,029 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T19:51:29,029 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T19:51:29,029 super().run_command(command) 2025-09-08T19:51:29,029 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T19:51:29,029 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T19:51:29,029 cmd_obj.run() 2025-09-08T19:51:29,029 ~~~~~~~~~~~^^ 2025-09-08T19:51:29,029 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/build_ext.py", line 96, in run 2025-09-08T19:51:29,029 _build_ext.run(self) 2025-09-08T19:51:29,030 ~~~~~~~~~~~~~~^^^^^^ 2025-09-08T19:51:29,030 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-08T19:51:29,030 self.build_extensions() 2025-09-08T19:51:29,030 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T19:51:29,030 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-08T19:51:29,030 self._build_extensions_serial() 2025-09-08T19:51:29,030 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T19:51:29,031 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-08T19:51:29,031 self.build_extension(ext) 2025-09-08T19:51:29,031 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T19:51:29,031 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/build_ext.py", line 261, in build_extension 2025-09-08T19:51:29,031 _build_ext.build_extension(self, ext) 2025-09-08T19:51:29,031 ~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 2025-09-08T19:51:29,031 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-08T19:51:29,031 new_ext = cythonize( 2025-09-08T19:51:29,031 ~~~~~~~~~^ 2025-09-08T19:51:29,032 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-08T19:51:29,032 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T19:51:29,032 )[0] 2025-09-08T19:51:29,032 ^ 2025-09-08T19:51:29,032 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-08T19:51:29,032 cythonize_one(*args) 2025-09-08T19:51:29,032 ~~~~~~~~~~~~~^^^^^^^ 2025-09-08T19:51:29,032 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-08T19:51:29,032 raise CompileError(None, pyx_file) 2025-09-08T19:51:29,033 Cython.Compiler.Errors.CompileError: sciencebeam_alignment/align_fast_utils.pyx 2025-09-08T19:51:29,528 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T19:51:29,540 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T19:51:29,540 exec(compile('"'"''"'"''"'"' 2025-09-08T19:51:29,540 # This is -- a caller that pip uses to run setup.py 2025-09-08T19:51:29,540 # 2025-09-08T19:51:29,540 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T19:51:29,540 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T19:51:29,540 # - It provides a clear error message when setuptools is not installed. 2025-09-08T19:51:29,540 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T19:51:29,540 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T19:51:29,540 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T19:51:29,540 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T19:51:29,540 import os, sys, tokenize, traceback 2025-09-08T19:51:29,540 2025-09-08T19:51:29,540 try: 2025-09-08T19:51:29,540 import setuptools 2025-09-08T19:51:29,540 except ImportError: 2025-09-08T19:51:29,540 print( 2025-09-08T19:51:29,540 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T19:51:29,540 "the build environment with exception:", 2025-09-08T19:51:29,540 file=sys.stderr, 2025-09-08T19:51:29,540 ) 2025-09-08T19:51:29,540 traceback.print_exc() 2025-09-08T19:51:29,540 sys.exit(1) 2025-09-08T19:51:29,540 2025-09-08T19:51:29,540 __file__ = %r 2025-09-08T19:51:29,540 sys.argv[0] = __file__ 2025-09-08T19:51:29,540 2025-09-08T19:51:29,540 if os.path.exists(__file__): 2025-09-08T19:51:29,540 filename = __file__ 2025-09-08T19:51:29,540 with tokenize.open(__file__) as f: 2025-09-08T19:51:29,540 setup_py_code = f.read() 2025-09-08T19:51:29,540 else: 2025-09-08T19:51:29,540 filename = "" 2025-09-08T19:51:29,540 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T19:51:29,540 2025-09-08T19:51:29,540 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T19:51:29,540 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-vypohppu/sciencebeam-alignment_6eaaab616ccf438aa7ed04dc385d9f27/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-9mettb2l[/] 2025-09-08T19:51:29,540 [bold magenta]cwd[/]: /tmp/pip-wheel-vypohppu/sciencebeam-alignment_6eaaab616ccf438aa7ed04dc385d9f27/ 2025-09-08T19:51:29,540 Building wheel for sciencebeam-alignment (setup.py): finished with status 'error' 2025-09-08T19:51:29,541 ERROR: Failed building wheel for sciencebeam-alignment 2025-09-08T19:51:29,542 Running setup.py clean for sciencebeam-alignment 2025-09-08T19:51:29,543 Running command python setup.py clean 2025-09-08T19:51:30,373 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T19:51:30,373 !! 2025-09-08T19:51:30,374 ******************************************************************************** 2025-09-08T19:51:30,374 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T19:51:30,374 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T19:51:30,374 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T19:51:30,374 or your builds will no longer be supported. 2025-09-08T19:51:30,374 ******************************************************************************** 2025-09-08T19:51:30,374 !! 2025-09-08T19:51:30,375 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T19:51:30,950 running clean 2025-09-08T19:51:31,095 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T19:51:31,096 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T19:51:31,096 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T19:51:31,096 removing 'build' 2025-09-08T19:51:31,232 Failed to build sciencebeam-alignment 2025-09-08T19:51:31,233 ERROR: Failed to build one or more wheels 2025-09-08T19:51:31,234 Exception information: 2025-09-08T19:51:31,234 Traceback (most recent call last): 2025-09-08T19:51:31,234 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T19:51:31,234 status = _inner_run() 2025-09-08T19:51:31,234 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T19:51:31,234 return self.run(options, args) 2025-09-08T19:51:31,234 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T19:51:31,234 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T19:51:31,234 return func(self, options, args) 2025-09-08T19:51:31,234 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T19:51:31,234 raise CommandError("Failed to build one or more wheels") 2025-09-08T19:51:31,234 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T19:51:31,238 Removed build tracker: '/tmp/pip-build-tracker-6a0y9qmv'