2025-09-08T13:44:34,583 Created temporary directory: /tmp/pip-build-tracker-sz_nugkp 2025-09-08T13:44:34,584 Initialized build tracking at /tmp/pip-build-tracker-sz_nugkp 2025-09-08T13:44:34,584 Created build tracker: /tmp/pip-build-tracker-sz_nugkp 2025-09-08T13:44:34,584 Entered build tracker: /tmp/pip-build-tracker-sz_nugkp 2025-09-08T13:44:34,585 Created temporary directory: /tmp/pip-wheel-evwydass 2025-09-08T13:44:34,588 Created temporary directory: /tmp/pip-ephem-wheel-cache-r9hiad2h 2025-09-08T13:44:34,645 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T13:44:34,647 2 location(s) to search for versions of sciencebeam-alignment: 2025-09-08T13:44:34,647 * https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,647 * https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,647 Fetching project page and analyzing links: https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,648 Getting page https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,649 Found index url https://pypi.org/simple/ 2025-09-08T13:44:34,718 Fetched page https://pypi.org/simple/sciencebeam-alignment/ as application/vnd.pypi.simple.v1+json 2025-09-08T13:44:34,720 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 2025-09-08T13:44:34,720 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 2025-09-08T13:44:34,720 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 2025-09-08T13:44:34,720 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 2025-09-08T13:44:34,721 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 2025-09-08T13:44:34,721 Fetching project page and analyzing links: https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,721 Getting page https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,722 Found index url https://www.piwheels.org/simple/ 2025-09-08T13:44:34,811 Fetched page https://www.piwheels.org/simple/sciencebeam-alignment/ as text/html 2025-09-08T13:44:34,818 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/) 2025-09-08T13:44:34,819 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/) 2025-09-08T13:44:34,819 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/) 2025-09-08T13:44:34,819 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/) 2025-09-08T13:44:34,820 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/) 2025-09-08T13:44:34,820 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/) 2025-09-08T13:44:34,820 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/) 2025-09-08T13:44:34,820 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,821 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,822 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/) 2025-09-08T13:44:34,823 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/) 2025-09-08T13:44:34,823 Skipping link: not a file: https://www.piwheels.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,823 Skipping link: not a file: https://pypi.org/simple/sciencebeam-alignment/ 2025-09-08T13:44:34,846 Given no hashes to check 1 links for project 'sciencebeam-alignment': discarding no candidates 2025-09-08T13:44:34,848 Collecting sciencebeam-alignment==0.0.2 2025-09-08T13:44:34,849 Created temporary directory: /tmp/pip-unpack-sel6b83q 2025-09-08T13:44:35,194 Downloading sciencebeam_alignment-0.0.2.tar.gz (6.9 kB) 2025-09-08T13:44:35,222 Added sciencebeam-alignment==0.0.2 from https://files.pythonhosted.org/packages/5c/1f/1ac79237e5fae7cd3f3b832544c6b1bfb365c153916f63843fb789da1f5d/sciencebeam_alignment-0.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-sz_nugkp' 2025-09-08T13:44:35,223 Running setup.py (path:/tmp/pip-wheel-evwydass/sciencebeam-alignment_ad2245c1ece8461d9f1e588724a78c0f/setup.py) egg_info for package sciencebeam-alignment 2025-09-08T13:44:35,223 Created temporary directory: /tmp/pip-pip-egg-info-tn9g5_3n 2025-09-08T13:44:35,223 Preparing metadata (setup.py): started 2025-09-08T13:44:35,224 Running command python setup.py egg_info 2025-09-08T13:44:36,082 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T13:44:36,082 !! 2025-09-08T13:44:36,082 ******************************************************************************** 2025-09-08T13:44:36,082 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T13:44:36,082 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T13:44:36,083 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T13:44:36,083 or your builds will no longer be supported. 2025-09-08T13:44:36,083 ******************************************************************************** 2025-09-08T13:44:36,083 !! 2025-09-08T13:44:36,083 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T13:44:36,721 running egg_info 2025-09-08T13:44:36,796 creating /tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info 2025-09-08T13:44:36,796 writing /tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info/PKG-INFO 2025-09-08T13:44:36,797 writing dependency_links to /tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info/dependency_links.txt 2025-09-08T13:44:36,798 writing requirements to /tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info/requires.txt 2025-09-08T13:44:36,798 writing top-level names to /tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info/top_level.txt 2025-09-08T13:44:36,798 writing manifest file '/tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T13:44:37,101 reading manifest file '/tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T13:44:37,101 reading manifest template 'MANIFEST.in' 2025-09-08T13:44:37,105 writing manifest file '/tmp/pip-pip-egg-info-tn9g5_3n/sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T13:44:37,241 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T13:44:37,246 Source in /tmp/pip-wheel-evwydass/sciencebeam-alignment_ad2245c1ece8461d9f1e588724a78c0f has version 0.0.2, which satisfies requirement sciencebeam-alignment==0.0.2 from https://files.pythonhosted.org/packages/5c/1f/1ac79237e5fae7cd3f3b832544c6b1bfb365c153916f63843fb789da1f5d/sciencebeam_alignment-0.0.2.tar.gz 2025-09-08T13:44:37,246 Removed sciencebeam-alignment==0.0.2 from https://files.pythonhosted.org/packages/5c/1f/1ac79237e5fae7cd3f3b832544c6b1bfb365c153916f63843fb789da1f5d/sciencebeam_alignment-0.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-sz_nugkp' 2025-09-08T13:44:37,250 Created temporary directory: /tmp/pip-unpack-8e0wnhch 2025-09-08T13:44:37,250 Created temporary directory: /tmp/pip-unpack-any6c6w7 2025-09-08T13:44:37,250 Building wheels for collected packages: sciencebeam-alignment 2025-09-08T13:44:37,252 Created temporary directory: /tmp/pip-wheel-n3qwixtw 2025-09-08T13:44:37,252 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 2025-09-08T13:44:37,253 Building wheel for sciencebeam-alignment (setup.py): started 2025-09-08T13:44:37,254 Destination directory: /tmp/pip-wheel-n3qwixtw 2025-09-08T13:44:37,254 Running command python setup.py bdist_wheel 2025-09-08T13:44:38,114 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T13:44:38,115 !! 2025-09-08T13:44:38,115 ******************************************************************************** 2025-09-08T13:44:38,115 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T13:44:38,115 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T13:44:38,115 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T13:44:38,115 or your builds will no longer be supported. 2025-09-08T13:44:38,115 ******************************************************************************** 2025-09-08T13:44:38,116 !! 2025-09-08T13:44:38,116 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T13:44:38,676 running bdist_wheel 2025-09-08T13:44:39,048 running build 2025-09-08T13:44:39,048 running build_py 2025-09-08T13:44:39,124 creating build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,125 copying sciencebeam_alignment/align.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,126 copying sciencebeam_alignment/word_sequence_matcher.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,126 copying sciencebeam_alignment/align_test.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,127 copying sciencebeam_alignment/word_sequence_matcher_test.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,127 copying sciencebeam_alignment/__init__.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,128 copying sciencebeam_alignment/align_performance.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,128 copying sciencebeam_alignment/conftest.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,129 copying sciencebeam_alignment/sequence_matcher.py -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,129 running egg_info 2025-09-08T13:44:39,202 writing sciencebeam_alignment.egg-info/PKG-INFO 2025-09-08T13:44:39,203 writing dependency_links to sciencebeam_alignment.egg-info/dependency_links.txt 2025-09-08T13:44:39,204 writing requirements to sciencebeam_alignment.egg-info/requires.txt 2025-09-08T13:44:39,204 writing top-level names to sciencebeam_alignment.egg-info/top_level.txt 2025-09-08T13:44:39,279 reading manifest file 'sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T13:44:39,281 reading manifest template 'MANIFEST.in' 2025-09-08T13:44:39,284 writing manifest file 'sciencebeam_alignment.egg-info/SOURCES.txt' 2025-09-08T13:44:39,285 copying sciencebeam_alignment/align_fast_utils.pyx -> build/lib.linux-armv7l-cpython-313/sciencebeam_alignment 2025-09-08T13:44:39,286 running build_ext 2025-09-08T13:44:39,918 Compiling sciencebeam_alignment/align_fast_utils.pyx because it changed. 2025-09-08T13:44:39,918 [1/1] Cythonizing sciencebeam_alignment/align_fast_utils.pyx 2025-09-08T13:44:42,135 Error compiling Cython file: 2025-09-08T13:44:42,135 ------------------------------------------------------------ 2025-09-08T13:44:42,135 ... 2025-09-08T13:44:42,135 DEF MIN_INT = -2147483647 2025-09-08T13:44:42,135 ctypedef np.int_t int_t 2025-09-08T13:44:42,135 ^ 2025-09-08T13:44:42,135 ------------------------------------------------------------ 2025-09-08T13:44:42,136 sciencebeam_alignment/align_fast_utils.pyx:11:9: 'int_t' is not a type identifier 2025-09-08T13:44:42,632 Error compiling Cython file: 2025-09-08T13:44:42,632 ------------------------------------------------------------ 2025-09-08T13:44:42,632 ... 2025-09-08T13:44:42,632 for j in range(1, n): 2025-09-08T13:44:42,632 scoring_matrix[i, j] = imax4( 2025-09-08T13:44:42,632 min_score, 2025-09-08T13:44:42,632 # Match elements. 2025-09-08T13:44:42,633 scoring_matrix[i - 1, j - 1] + 2025-09-08T13:44:42,633 ^ 2025-09-08T13:44:42,633 ------------------------------------------------------------ 2025-09-08T13:44:42,633 sciencebeam_alignment/align_fast_utils.pyx:52:33: Compiler crash in OptimizeBuiltinCalls 2025-09-08T13:44:42,633 ModuleNode.body = StatListNode(align_fast_utils.pyx:1:0) 2025-09-08T13:44:42,633 StatListNode.stats[10] = StatListNode(align_fast_utils.pyx:37:0) 2025-09-08T13:44:42,633 StatListNode.stats[0] = DefNode(align_fast_utils.pyx:37:0, 2025-09-08T13:44:42,633 is_cyfunction = True, 2025-09-08T13:44:42,633 modifiers = [...]/0, 2025-09-08T13:44:42,634 name = 'native_compute_inner_alignment_matrix_simple_scoring_int', 2025-09-08T13:44:42,634 node_positions = [...]/70, 2025-09-08T13:44:42,634 np_args_idx = [...]/0, 2025-09-08T13:44:42,634 num_required_args = 7, 2025-09-08T13:44:42,634 outer_attrs = [...]/2, 2025-09-08T13:44:42,634 py_wrapper_required = True, 2025-09-08T13:44:42,634 reqd_kw_flags_cname = '0', 2025-09-08T13:44:42,634 used = True) 2025-09-08T13:44:42,634 DefNode.body = StatListNode(align_fast_utils.pyx:42:4) 2025-09-08T13:44:42,634 StatListNode.stats[2] = LetNode(align_fast_utils.pyx:46:4) 2025-09-08T13:44:42,634 LetNode.body = ForFromStatNode(align_fast_utils.pyx:46:4, 2025-09-08T13:44:42,634 from_range = True, 2025-09-08T13:44:42,635 relation1 = '<=', 2025-09-08T13:44:42,635 relation2 = '<') 2025-09-08T13:44:42,635 ForFromStatNode.body = StatListNode(align_fast_utils.pyx:47:8) 2025-09-08T13:44:42,635 StatListNode.stats[0] = LetNode(align_fast_utils.pyx:47:8) 2025-09-08T13:44:42,635 LetNode.body = ForFromStatNode(align_fast_utils.pyx:47:8, 2025-09-08T13:44:42,635 from_range = True, 2025-09-08T13:44:42,635 relation1 = '<=', 2025-09-08T13:44:42,635 relation2 = '<') 2025-09-08T13:44:42,635 ForFromStatNode.body = StatListNode(align_fast_utils.pyx:48:40) 2025-09-08T13:44:42,635 StatListNode.stats[0] = SingleAssignmentNode(align_fast_utils.pyx:48:40) 2025-09-08T13:44:42,635 SingleAssignmentNode.rhs = SimpleCallNode(align_fast_utils.pyx:48:40, 2025-09-08T13:44:42,636 analysed = True, 2025-09-08T13:44:42,636 is_temp = 1, 2025-09-08T13:44:42,636 result_is_used = True, 2025-09-08T13:44:42,636 use_managed_ref = True) 2025-09-08T13:44:42,636 SimpleCallNode.args[1] = AddNode(align_fast_utils.pyx:52:45, 2025-09-08T13:44:42,636 infix = True, 2025-09-08T13:44:42,636 operator = '+', 2025-09-08T13:44:42,636 result_is_used = True, 2025-09-08T13:44:42,636 use_managed_ref = True) 2025-09-08T13:44:42,636 AddNode.operand1 = IndexNode(align_fast_utils.pyx:52:30, 2025-09-08T13:44:42,636 is_subscript = True, 2025-09-08T13:44:42,637 result_is_used = True, 2025-09-08T13:44:42,637 use_managed_ref = True) 2025-09-08T13:44:42,637 IndexNode.index = TupleNode(align_fast_utils.pyx:52:30, 2025-09-08T13:44:42,637 is_sequence_constructor = 1, 2025-09-08T13:44:42,637 result_is_used = True, 2025-09-08T13:44:42,637 use_managed_ref = True) 2025-09-08T13:44:42,637 TupleNode.args[0] = SubNode(align_fast_utils.pyx:52:33, 2025-09-08T13:44:42,637 infix = True, 2025-09-08T13:44:42,637 operator = '-', 2025-09-08T13:44:42,637 result_is_used = True, 2025-09-08T13:44:42,637 use_managed_ref = True) 2025-09-08T13:44:42,638 Compiler crash traceback from this point on: 2025-09-08T13:44:42,638 File "Cython/Compiler/Visitor.py", line 174, in Cython.Compiler.Visitor.TreeVisitor._visit 2025-09-08T13:44:42,638 File "Cython/Compiler/Visitor.py", line 538, in Cython.Compiler.Visitor.MethodDispatcherTransform.visit_BinopNode 2025-09-08T13:44:42,638 File "Cython/Compiler/Visitor.py", line 552, in Cython.Compiler.Visitor.MethodDispatcherTransform._visit_binop_node 2025-09-08T13:44:42,638 AttributeError: 'NoneType' object has no attribute 'is_builtin_type' 2025-09-08T13:44:42,643 Traceback (most recent call last): 2025-09-08T13:44:42,651 File "", line 2, in 2025-09-08T13:44:42,651 exec(compile(''' 2025-09-08T13:44:42,651 ~~~~^^^^^^^^^^^^ 2025-09-08T13:44:42,651 # This is -- a caller that pip uses to run setup.py 2025-09-08T13:44:42,651 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T13:44:42,651 ...<32 lines>... 2025-09-08T13:44:42,651 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T13:44:42,651 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T13:44:42,651 ''' % ('/tmp/pip-wheel-evwydass/sciencebeam-alignment_ad2245c1ece8461d9f1e588724a78c0f/setup.py',), "", "exec")) 2025-09-08T13:44:42,652 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T13:44:42,652 File "", line 35, in 2025-09-08T13:44:42,652 File "/tmp/pip-wheel-evwydass/sciencebeam-alignment_ad2245c1ece8461d9f1e588724a78c0f/setup.py", line 33, in 2025-09-08T13:44:42,652 setup( 2025-09-08T13:44:42,652 ~~~~~^ 2025-09-08T13:44:42,652 name='sciencebeam_alignment', 2025-09-08T13:44:42,652 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T13:44:42,653 ...<16 lines>... 2025-09-08T13:44:42,653 include_dirs=[get_numpy_include_dir()] 2025-09-08T13:44:42,653 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T13:44:42,653 ) 2025-09-08T13:44:42,653 ^ 2025-09-08T13:44:42,653 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T13:44:42,653 return distutils.core.setup(**attrs) 2025-09-08T13:44:42,653 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T13:44:42,654 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T13:44:42,654 return run_commands(dist) 2025-09-08T13:44:42,654 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T13:44:42,654 dist.run_commands() 2025-09-08T13:44:42,654 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T13:44:42,654 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T13:44:42,654 self.run_command(cmd) 2025-09-08T13:44:42,654 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T13:44:42,654 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T13:44:42,655 super().run_command(command) 2025-09-08T13:44:42,655 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T13:44:42,655 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T13:44:42,655 cmd_obj.run() 2025-09-08T13:44:42,655 ~~~~~~~~~~~^^ 2025-09-08T13:44:42,655 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T13:44:42,655 self.run_command("build") 2025-09-08T13:44:42,655 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T13:44:42,655 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T13:44:42,656 self.distribution.run_command(command) 2025-09-08T13:44:42,656 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T13:44:42,656 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T13:44:42,656 super().run_command(command) 2025-09-08T13:44:42,656 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T13:44:42,656 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T13:44:42,656 cmd_obj.run() 2025-09-08T13:44:42,656 ~~~~~~~~~~~^^ 2025-09-08T13:44:42,657 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T13:44:42,657 self.run_command(cmd_name) 2025-09-08T13:44:42,657 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T13:44:42,657 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T13:44:42,657 self.distribution.run_command(command) 2025-09-08T13:44:42,657 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T13:44:42,657 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T13:44:42,657 super().run_command(command) 2025-09-08T13:44:42,657 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T13:44:42,658 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T13:44:42,658 cmd_obj.run() 2025-09-08T13:44:42,658 ~~~~~~~~~~~^^ 2025-09-08T13:44:42,658 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/build_ext.py", line 96, in run 2025-09-08T13:44:42,658 _build_ext.run(self) 2025-09-08T13:44:42,658 ~~~~~~~~~~~~~~^^^^^^ 2025-09-08T13:44:42,658 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-08T13:44:42,658 self.build_extensions() 2025-09-08T13:44:42,658 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T13:44:42,659 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-08T13:44:42,659 self._build_extensions_serial() 2025-09-08T13:44:42,659 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T13:44:42,659 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-08T13:44:42,659 self.build_extension(ext) 2025-09-08T13:44:42,659 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T13:44:42,659 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/build_ext.py", line 261, in build_extension 2025-09-08T13:44:42,659 _build_ext.build_extension(self, ext) 2025-09-08T13:44:42,660 ~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ 2025-09-08T13:44:42,660 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-08T13:44:42,660 new_ext = cythonize( 2025-09-08T13:44:42,660 ~~~~~~~~~^ 2025-09-08T13:44:42,660 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-08T13:44:42,660 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T13:44:42,660 )[0] 2025-09-08T13:44:42,660 ^ 2025-09-08T13:44:42,660 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-08T13:44:42,660 cythonize_one(*args) 2025-09-08T13:44:42,661 ~~~~~~~~~~~~~^^^^^^^ 2025-09-08T13:44:42,661 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-08T13:44:42,661 raise CompileError(None, pyx_file) 2025-09-08T13:44:42,661 Cython.Compiler.Errors.CompileError: sciencebeam_alignment/align_fast_utils.pyx 2025-09-08T13:44:43,154 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T13:44:43,165 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T13:44:43,165 exec(compile('"'"''"'"''"'"' 2025-09-08T13:44:43,165 # This is -- a caller that pip uses to run setup.py 2025-09-08T13:44:43,165 # 2025-09-08T13:44:43,165 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T13:44:43,165 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T13:44:43,165 # - It provides a clear error message when setuptools is not installed. 2025-09-08T13:44:43,165 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T13:44:43,165 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T13:44:43,165 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T13:44:43,165 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T13:44:43,165 import os, sys, tokenize, traceback 2025-09-08T13:44:43,165 2025-09-08T13:44:43,165 try: 2025-09-08T13:44:43,165 import setuptools 2025-09-08T13:44:43,165 except ImportError: 2025-09-08T13:44:43,165 print( 2025-09-08T13:44:43,165 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T13:44:43,165 "the build environment with exception:", 2025-09-08T13:44:43,165 file=sys.stderr, 2025-09-08T13:44:43,165 ) 2025-09-08T13:44:43,165 traceback.print_exc() 2025-09-08T13:44:43,165 sys.exit(1) 2025-09-08T13:44:43,165 2025-09-08T13:44:43,165 __file__ = %r 2025-09-08T13:44:43,165 sys.argv[0] = __file__ 2025-09-08T13:44:43,165 2025-09-08T13:44:43,165 if os.path.exists(__file__): 2025-09-08T13:44:43,165 filename = __file__ 2025-09-08T13:44:43,165 with tokenize.open(__file__) as f: 2025-09-08T13:44:43,165 setup_py_code = f.read() 2025-09-08T13:44:43,165 else: 2025-09-08T13:44:43,165 filename = "" 2025-09-08T13:44:43,165 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T13:44:43,165 2025-09-08T13:44:43,165 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T13:44:43,165 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-evwydass/sciencebeam-alignment_ad2245c1ece8461d9f1e588724a78c0f/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-n3qwixtw[/] 2025-09-08T13:44:43,166 [bold magenta]cwd[/]: /tmp/pip-wheel-evwydass/sciencebeam-alignment_ad2245c1ece8461d9f1e588724a78c0f/ 2025-09-08T13:44:43,166 Building wheel for sciencebeam-alignment (setup.py): finished with status 'error' 2025-09-08T13:44:43,166 ERROR: Failed building wheel for sciencebeam-alignment 2025-09-08T13:44:43,167 Running setup.py clean for sciencebeam-alignment 2025-09-08T13:44:43,168 Running command python setup.py clean 2025-09-08T13:44:44,010 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T13:44:44,010 !! 2025-09-08T13:44:44,011 ******************************************************************************** 2025-09-08T13:44:44,011 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T13:44:44,011 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T13:44:44,011 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T13:44:44,011 or your builds will no longer be supported. 2025-09-08T13:44:44,011 ******************************************************************************** 2025-09-08T13:44:44,011 !! 2025-09-08T13:44:44,011 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T13:44:44,658 running clean 2025-09-08T13:44:44,807 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T13:44:44,807 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T13:44:44,807 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T13:44:44,807 removing 'build' 2025-09-08T13:44:44,943 Failed to build sciencebeam-alignment 2025-09-08T13:44:44,944 ERROR: Failed to build one or more wheels 2025-09-08T13:44:44,945 Exception information: 2025-09-08T13:44:44,945 Traceback (most recent call last): 2025-09-08T13:44:44,945 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T13:44:44,945 status = _inner_run() 2025-09-08T13:44:44,945 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T13:44:44,945 return self.run(options, args) 2025-09-08T13:44:44,945 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T13:44:44,945 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T13:44:44,945 return func(self, options, args) 2025-09-08T13:44:44,945 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T13:44:44,945 raise CommandError("Failed to build one or more wheels") 2025-09-08T13:44:44,945 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T13:44:44,949 Removed build tracker: '/tmp/pip-build-tracker-sz_nugkp'