2025-09-08T03:41:02,034 Created temporary directory: /tmp/pip-build-tracker-6qk7hls2 2025-09-08T03:41:02,034 Initialized build tracking at /tmp/pip-build-tracker-6qk7hls2 2025-09-08T03:41:02,034 Created build tracker: /tmp/pip-build-tracker-6qk7hls2 2025-09-08T03:41:02,035 Entered build tracker: /tmp/pip-build-tracker-6qk7hls2 2025-09-08T03:41:02,035 Created temporary directory: /tmp/pip-wheel-a1ddv1y_ 2025-09-08T03:41:02,038 Created temporary directory: /tmp/pip-ephem-wheel-cache-3wba_hbr 2025-09-08T03:41:02,095 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T03:41:02,097 2 location(s) to search for versions of coral: 2025-09-08T03:41:02,097 * https://pypi.org/simple/coral/ 2025-09-08T03:41:02,097 * https://www.piwheels.org/simple/coral/ 2025-09-08T03:41:02,097 Fetching project page and analyzing links: https://pypi.org/simple/coral/ 2025-09-08T03:41:02,098 Getting page https://pypi.org/simple/coral/ 2025-09-08T03:41:02,099 Found index url https://pypi.org/simple/ 2025-09-08T03:41:02,168 Fetched page https://pypi.org/simple/coral/ as application/vnd.pypi.simple.v1+json 2025-09-08T03:41:02,170 Found link https://files.pythonhosted.org/packages/44/48/4d4128d36f48447200db44d95130825a167676ad8961c5f20d96e2e253c7/coral-0.1.0.tar.gz (from https://pypi.org/simple/coral/), version: 0.1.0 2025-09-08T03:41:02,170 Found link https://files.pythonhosted.org/packages/5e/32/a978f786759decac49a3c01bc90b0ee0ca3d7057f144a8c34bcf8a04fcfa/coral-0.2.1.tar.gz (from https://pypi.org/simple/coral/), version: 0.2.1 2025-09-08T03:41:02,170 Found link https://files.pythonhosted.org/packages/2e/93/013c15b7a8f45cf10db8407bcd093a36509c5d8e5401d549b3d9dd56188e/coral-0.3.0.tar.gz (from https://pypi.org/simple/coral/), version: 0.3.0 2025-09-08T03:41:02,170 Found link https://files.pythonhosted.org/packages/0d/f0/fae5d6f962af4feca22ead719f30b8bffe9c72b39fc31c7ed784d367a4e5/coral-0.3.1.tar.gz (from https://pypi.org/simple/coral/), version: 0.3.1 2025-09-08T03:41:02,171 Found link https://files.pythonhosted.org/packages/93/9c/b1b04b1b899d4bbfa1ec0253d64fa314eb23d23a34a0e07cee70b9f2ae35/coral-0.3.2.tar.gz (from https://pypi.org/simple/coral/), version: 0.3.2 2025-09-08T03:41:02,171 Found link https://files.pythonhosted.org/packages/dd/eb/cab2e724fe9df60cea55d5df16a12999cb302e628f4069623cf4b3022b96/coral-0.3.3.tar.gz (from https://pypi.org/simple/coral/), version: 0.3.3 2025-09-08T03:41:02,171 Found link https://files.pythonhosted.org/packages/e0/98/e39408ac64c87765767caa582aff07b66d2f31329cb1647712c44fa99f1c/coral-0.3.4.tar.gz (from https://pypi.org/simple/coral/), version: 0.3.4 2025-09-08T03:41:02,171 Found link https://files.pythonhosted.org/packages/4c/3e/c067cd40b343c9f28f73a9601295d7ccca025ce4013d881d955a5ce7dfdc/coral-0.4.0.tar.gz (from https://pypi.org/simple/coral/), version: 0.4.0 2025-09-08T03:41:02,171 Found link https://files.pythonhosted.org/packages/81/3d/26bb52490da33b7045eafb6b130ae68bc05b65fbc2d17e2ea57f57f98291/coral-0.4.1.tar.gz (from https://pypi.org/simple/coral/), version: 0.4.1 2025-09-08T03:41:02,172 Found link https://files.pythonhosted.org/packages/d0/36/89f1f3a35c9dc240f7ec72b157c7937a50fd4a884ff81470ecfa21f7d3f6/coral-0.4.2.tar.gz (from https://pypi.org/simple/coral/), version: 0.4.2 2025-09-08T03:41:02,172 Found link https://files.pythonhosted.org/packages/55/bb/dc671afad82512788ef48ac860bd0cacff56a7f168fe2dfa0135af8a14de/coral-0.4.3.tar.gz (from https://pypi.org/simple/coral/), version: 0.4.3 2025-09-08T03:41:02,172 Found link https://files.pythonhosted.org/packages/ef/3a/f46fe8052c0de4303554be16f07e9dc12c3fec80ed7672ec0a27e87ae04f/coral-0.5.0.tar.gz (from https://pypi.org/simple/coral/), version: 0.5.0 2025-09-08T03:41:02,172 Fetching project page and analyzing links: https://www.piwheels.org/simple/coral/ 2025-09-08T03:41:02,172 Getting page https://www.piwheels.org/simple/coral/ 2025-09-08T03:41:02,173 Found index url https://www.piwheels.org/simple/ 2025-09-08T03:41:02,265 Fetched page https://www.piwheels.org/simple/coral/ as text/html 2025-09-08T03:41:02,270 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp37-cp37m-linux_armv7l.whl#sha256=9ef02e4abf98773e98284e893fba6ab45cda3acbdfe33190287535a7e00b7290 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,270 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp37-cp37m-linux_armv6l.whl#sha256=9ef02e4abf98773e98284e893fba6ab45cda3acbdfe33190287535a7e00b7290 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,271 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp35-cp35m-linux_armv7l.whl#sha256=397e8acd329e11f130cc62fbc6a2558e4c0fc4bfe9ee2d932168f140dd702432 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,271 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp35-cp35m-linux_armv6l.whl#sha256=397e8acd329e11f130cc62fbc6a2558e4c0fc4bfe9ee2d932168f140dd702432 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,271 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp34-cp34m-linux_armv6l.whl#sha256=e731f7b3759a083fe31deb621572bb89164ff7b1c34305670417085f44657cc8 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,271 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp34-cp34m-linux_armv7l.whl#sha256=e731f7b3759a083fe31deb621572bb89164ff7b1c34305670417085f44657cc8 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,271 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp39-cp39-linux_armv6l.whl#sha256=f145a6d11106366d1aa813a8eb0826bc45502a632bdb06bfa30d84037ff37e6d (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,271 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.2-cp39-cp39-linux_armv7l.whl#sha256=f145a6d11106366d1aa813a8eb0826bc45502a632bdb06bfa30d84037ff37e6d (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,271 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.1-cp34-cp34m-linux_armv6l.whl#sha256=52249524520db9c39b5f19306b2de79b2175aa79ac703948bb3be4a64c127ec1 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.1-cp34-cp34m-linux_armv7l.whl#sha256=52249524520db9c39b5f19306b2de79b2175aa79ac703948bb3be4a64c127ec1 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.0-cp34-cp34m-linux_armv6l.whl#sha256=ca69c6f12d12daeb60e3106b13c770ddd42cb3b185c65893943624a19e200ab8 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.3.0-cp34-cp34m-linux_armv7l.whl#sha256=ca69c6f12d12daeb60e3106b13c770ddd42cb3b185c65893943624a19e200ab8 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.2.1-cp34-cp34m-linux_armv6l.whl#sha256=32f5aa1fb4110309a08f978b5ffce36b6e2d1c3081a7903e50d97024d4426326 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.2.1-cp34-cp34m-linux_armv7l.whl#sha256=32f5aa1fb4110309a08f978b5ffce36b6e2d1c3081a7903e50d97024d4426326 (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp37-cp37m-linux_armv6l.whl#sha256=c6d2fdd9aa054c756578e0b37592c4c484c8546a28f544e4203db044c4bd8f6d (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp37-cp37m-linux_armv7l.whl#sha256=c6d2fdd9aa054c756578e0b37592c4c484c8546a28f544e4203db044c4bd8f6d (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,272 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp35-cp35m-linux_armv6l.whl#sha256=0a8394fe5c1f4d0f6c9b19e8d8476363beb2f948cc2d614565ce1677e10e53da (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,273 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp35-cp35m-linux_armv7l.whl#sha256=0a8394fe5c1f4d0f6c9b19e8d8476363beb2f948cc2d614565ce1677e10e53da (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,273 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp34-cp34m-linux_armv6l.whl#sha256=97368028a2d5849299ae3200f4f6eb75db2c53d8587c421b374358d13d12321a (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,273 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp34-cp34m-linux_armv7l.whl#sha256=97368028a2d5849299ae3200f4f6eb75db2c53d8587c421b374358d13d12321a (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,273 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp39-cp39-linux_armv6l.whl#sha256=82dc4faaa5c1c265273e8a32e3d51d3b3299be7cf67ea664b53ffa9ef54f4ece (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,273 Skipping link: No binaries permitted for coral: https://archive1.piwheels.org/simple/coral/coral-0.1.0-cp39-cp39-linux_armv7l.whl#sha256=82dc4faaa5c1c265273e8a32e3d51d3b3299be7cf67ea664b53ffa9ef54f4ece (from https://www.piwheels.org/simple/coral/) 2025-09-08T03:41:02,273 Skipping link: not a file: https://www.piwheels.org/simple/coral/ 2025-09-08T03:41:02,274 Skipping link: not a file: https://pypi.org/simple/coral/ 2025-09-08T03:41:02,530 Given no hashes to check 1 links for project 'coral': discarding no candidates 2025-09-08T03:41:02,531 Collecting coral==0.3.2 2025-09-08T03:41:02,532 Created temporary directory: /tmp/pip-unpack-n2_5nvym 2025-09-08T03:41:02,674 Downloading coral-0.3.2.tar.gz (128 kB) 2025-09-08T03:41:02,761 Added coral==0.3.2 from https://files.pythonhosted.org/packages/93/9c/b1b04b1b899d4bbfa1ec0253d64fa314eb23d23a34a0e07cee70b9f2ae35/coral-0.3.2.tar.gz to build tracker '/tmp/pip-build-tracker-6qk7hls2' 2025-09-08T03:41:02,762 Running setup.py (path:/tmp/pip-wheel-a1ddv1y_/coral_01eea8da4eee443fbaaa4fa1d9b1cdb9/setup.py) egg_info for package coral 2025-09-08T03:41:02,762 Created temporary directory: /tmp/pip-pip-egg-info-18cxz039 2025-09-08T03:41:02,762 Preparing metadata (setup.py): started 2025-09-08T03:41:02,763 Running command python setup.py egg_info 2025-09-08T03:41:03,936 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T03:41:03,937 warnings.warn(msg) 2025-09-08T03:41:04,396 running egg_info 2025-09-08T03:41:04,472 creating /tmp/pip-pip-egg-info-18cxz039/coral.egg-info 2025-09-08T03:41:04,472 writing /tmp/pip-pip-egg-info-18cxz039/coral.egg-info/PKG-INFO 2025-09-08T03:41:04,475 writing dependency_links to /tmp/pip-pip-egg-info-18cxz039/coral.egg-info/dependency_links.txt 2025-09-08T03:41:04,476 writing requirements to /tmp/pip-pip-egg-info-18cxz039/coral.egg-info/requires.txt 2025-09-08T03:41:04,476 writing top-level names to /tmp/pip-pip-egg-info-18cxz039/coral.egg-info/top_level.txt 2025-09-08T03:41:04,477 writing manifest file '/tmp/pip-pip-egg-info-18cxz039/coral.egg-info/SOURCES.txt' 2025-09-08T03:41:04,784 reading manifest file '/tmp/pip-pip-egg-info-18cxz039/coral.egg-info/SOURCES.txt' 2025-09-08T03:41:04,784 reading manifest template 'MANIFEST.in' 2025-09-08T03:41:04,788 writing manifest file '/tmp/pip-pip-egg-info-18cxz039/coral.egg-info/SOURCES.txt' 2025-09-08T03:41:04,924 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T03:41:04,928 Source in /tmp/pip-wheel-a1ddv1y_/coral_01eea8da4eee443fbaaa4fa1d9b1cdb9 has version 0.3.2, which satisfies requirement coral==0.3.2 from https://files.pythonhosted.org/packages/93/9c/b1b04b1b899d4bbfa1ec0253d64fa314eb23d23a34a0e07cee70b9f2ae35/coral-0.3.2.tar.gz 2025-09-08T03:41:04,929 Removed coral==0.3.2 from https://files.pythonhosted.org/packages/93/9c/b1b04b1b899d4bbfa1ec0253d64fa314eb23d23a34a0e07cee70b9f2ae35/coral-0.3.2.tar.gz from build tracker '/tmp/pip-build-tracker-6qk7hls2' 2025-09-08T03:41:04,933 Created temporary directory: /tmp/pip-unpack-elw5j7he 2025-09-08T03:41:04,934 Created temporary directory: /tmp/pip-unpack-fpaceio_ 2025-09-08T03:41:04,934 Building wheels for collected packages: coral 2025-09-08T03:41:04,935 Created temporary directory: /tmp/pip-wheel-wvxbgegy 2025-09-08T03:41:04,936 DEPRECATION: Building 'coral' 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 'coral'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T03:41:04,937 Building wheel for coral (setup.py): started 2025-09-08T03:41:04,937 Destination directory: /tmp/pip-wheel-wvxbgegy 2025-09-08T03:41:04,937 Running command python setup.py bdist_wheel 2025-09-08T03:41:05,836 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T03:41:05,836 warnings.warn(msg) 2025-09-08T03:41:06,232 running bdist_wheel 2025-09-08T03:41:06,606 running build 2025-09-08T03:41:06,606 running build_py 2025-09-08T03:41:06,686 creating build/lib.linux-armv7l-cpython-313/coral 2025-09-08T03:41:06,686 copying coral/__init__.py -> build/lib.linux-armv7l-cpython-313/coral 2025-09-08T03:41:06,687 creating build/lib.linux-armv7l-cpython-313/coral/analysis 2025-09-08T03:41:06,687 copying coral/analysis/utils.py -> build/lib.linux-armv7l-cpython-313/coral/analysis 2025-09-08T03:41:06,688 copying coral/analysis/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/analysis 2025-09-08T03:41:06,689 creating build/lib.linux-armv7l-cpython-313/coral/analysis/_sequence 2025-09-08T03:41:06,689 copying coral/analysis/_sequence/anneal.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequence 2025-09-08T03:41:06,689 copying coral/analysis/_sequence/tm_params.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequence 2025-09-08T03:41:06,690 copying coral/analysis/_sequence/repeats.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequence 2025-09-08T03:41:06,690 copying coral/analysis/_sequence/melting_temp.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequence 2025-09-08T03:41:06,691 copying coral/analysis/_sequence/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequence 2025-09-08T03:41:06,692 creating build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing 2025-09-08T03:41:06,692 copying coral/analysis/_sequencing/needle.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing 2025-09-08T03:41:06,693 copying coral/analysis/_sequencing/sanger.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing 2025-09-08T03:41:06,693 copying coral/analysis/_sequencing/align.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing 2025-09-08T03:41:06,694 copying coral/analysis/_sequencing/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing 2025-09-08T03:41:06,695 creating build/lib.linux-armv7l-cpython-313/coral/analysis/_structure 2025-09-08T03:41:06,695 copying coral/analysis/_structure/vienna.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_structure 2025-09-08T03:41:06,695 copying coral/analysis/_structure/dimers.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_structure 2025-09-08T03:41:06,696 copying coral/analysis/_structure/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_structure 2025-09-08T03:41:06,696 copying coral/analysis/_structure/nupack.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_structure 2025-09-08T03:41:06,697 copying coral/analysis/_structure/structure_windows.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_structure 2025-09-08T03:41:06,698 creating build/lib.linux-armv7l-cpython-313/coral/constants 2025-09-08T03:41:06,698 copying coral/constants/molecular_bio.py -> build/lib.linux-armv7l-cpython-313/coral/constants 2025-09-08T03:41:06,698 copying coral/constants/restriction_sites.py -> build/lib.linux-armv7l-cpython-313/coral/constants 2025-09-08T03:41:06,699 copying coral/constants/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/constants 2025-09-08T03:41:06,699 copying coral/constants/genbank.py -> build/lib.linux-armv7l-cpython-313/coral/constants 2025-09-08T03:41:06,700 creating build/lib.linux-armv7l-cpython-313/coral/database 2025-09-08T03:41:06,700 copying coral/database/_rebase.py -> build/lib.linux-armv7l-cpython-313/coral/database 2025-09-08T03:41:06,701 copying coral/database/_yeast.py -> build/lib.linux-armv7l-cpython-313/coral/database 2025-09-08T03:41:06,701 copying coral/database/_entrez.py -> build/lib.linux-armv7l-cpython-313/coral/database 2025-09-08T03:41:06,702 copying coral/database/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/database 2025-09-08T03:41:06,703 creating build/lib.linux-armv7l-cpython-313/coral/design 2025-09-08T03:41:06,703 copying coral/design/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/design 2025-09-08T03:41:06,704 copying coral/design/_gibson.py -> build/lib.linux-armv7l-cpython-313/coral/design 2025-09-08T03:41:06,704 copying coral/design/_primers.py -> build/lib.linux-armv7l-cpython-313/coral/design 2025-09-08T03:41:06,705 creating build/lib.linux-armv7l-cpython-313/coral/design/_oligo_synthesis 2025-09-08T03:41:06,705 copying coral/design/_oligo_synthesis/oligo_assembly.py -> build/lib.linux-armv7l-cpython-313/coral/design/_oligo_synthesis 2025-09-08T03:41:06,706 copying coral/design/_oligo_synthesis/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/design/_oligo_synthesis 2025-09-08T03:41:06,706 creating build/lib.linux-armv7l-cpython-313/coral/design/_sequence_generation 2025-09-08T03:41:06,707 copying coral/design/_sequence_generation/random_sequences.py -> build/lib.linux-armv7l-cpython-313/coral/design/_sequence_generation 2025-09-08T03:41:06,707 copying coral/design/_sequence_generation/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/design/_sequence_generation 2025-09-08T03:41:06,708 creating build/lib.linux-armv7l-cpython-313/coral/seqio 2025-09-08T03:41:06,708 copying coral/seqio/_dna.py -> build/lib.linux-armv7l-cpython-313/coral/seqio 2025-09-08T03:41:06,709 copying coral/seqio/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/seqio 2025-09-08T03:41:06,710 creating build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,710 copying coral/reaction/_resect.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,710 copying coral/reaction/_pcr.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,711 copying coral/reaction/utils.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,711 copying coral/reaction/_oligo_assembly.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,712 copying coral/reaction/_central_dogma.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,712 copying coral/reaction/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,713 copying coral/reaction/_gibson.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,713 copying coral/reaction/_restriction.py -> build/lib.linux-armv7l-cpython-313/coral/reaction 2025-09-08T03:41:06,714 creating build/lib.linux-armv7l-cpython-313/coral/sequence 2025-09-08T03:41:06,714 copying coral/sequence/_sequence.py -> build/lib.linux-armv7l-cpython-313/coral/sequence 2025-09-08T03:41:06,715 copying coral/sequence/_dna.py -> build/lib.linux-armv7l-cpython-313/coral/sequence 2025-09-08T03:41:06,716 copying coral/sequence/_rna.py -> build/lib.linux-armv7l-cpython-313/coral/sequence 2025-09-08T03:41:06,716 copying coral/sequence/_peptide.py -> build/lib.linux-armv7l-cpython-313/coral/sequence 2025-09-08T03:41:06,717 copying coral/sequence/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/sequence 2025-09-08T03:41:06,717 running egg_info 2025-09-08T03:41:06,793 writing coral.egg-info/PKG-INFO 2025-09-08T03:41:06,796 writing dependency_links to coral.egg-info/dependency_links.txt 2025-09-08T03:41:06,798 writing requirements to coral.egg-info/requires.txt 2025-09-08T03:41:06,798 writing top-level names to coral.egg-info/top_level.txt 2025-09-08T03:41:06,880 reading manifest file 'coral.egg-info/SOURCES.txt' 2025-09-08T03:41:06,884 reading manifest template 'MANIFEST.in' 2025-09-08T03:41:06,889 writing manifest file 'coral.egg-info/SOURCES.txt' 2025-09-08T03:41:06,890 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'coral.analysis._sequencing.data' is absent from the `packages` configuration. 2025-09-08T03:41:06,891 !! 2025-09-08T03:41:06,891 ******************************************************************************** 2025-09-08T03:41:06,891 ############################ 2025-09-08T03:41:06,891 # Package would be ignored # 2025-09-08T03:41:06,891 ############################ 2025-09-08T03:41:06,891 Python recognizes 'coral.analysis._sequencing.data' as an importable package[^1], 2025-09-08T03:41:06,891 but it is absent from setuptools' `packages` configuration. 2025-09-08T03:41:06,891 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T03:41:06,892 package, please make sure that 'coral.analysis._sequencing.data' is explicitly added 2025-09-08T03:41:06,892 to the `packages` configuration field. 2025-09-08T03:41:06,892 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T03:41:06,892 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T03:41:06,892 instead of `find_packages(...)`/`find:`). 2025-09-08T03:41:06,892 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T03:41:06,892 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T03:41:06,893 If you don't want 'coral.analysis._sequencing.data' to be distributed and are 2025-09-08T03:41:06,893 already explicitly excluding 'coral.analysis._sequencing.data' via 2025-09-08T03:41:06,893 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T03:41:06,893 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T03:41:06,893 combination with a more fine grained `package-data` configuration. 2025-09-08T03:41:06,893 You can read more about "package data files" on setuptools documentation page: 2025-09-08T03:41:06,893 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T03:41:06,894 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T03:41:06,894 even if it does not contain any `.py` files. 2025-09-08T03:41:06,894 On the other hand, currently there is no concept of package data 2025-09-08T03:41:06,894 directory, all directories are treated like packages. 2025-09-08T03:41:06,894 ******************************************************************************** 2025-09-08T03:41:06,894 !! 2025-09-08T03:41:06,894 check.warn(importable) 2025-09-08T03:41:06,895 copying coral/analysis/_sequencing/calign.c -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing 2025-09-08T03:41:06,898 creating build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing/data 2025-09-08T03:41:06,898 copying coral/analysis/_sequencing/data/BLOSUM62 -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing/data 2025-09-08T03:41:06,899 copying coral/analysis/_sequencing/data/DNA -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing/data 2025-09-08T03:41:06,899 copying coral/analysis/_sequencing/data/DNA_simple -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing/data 2025-09-08T03:41:06,900 copying coral/analysis/_sequencing/data/__init__.py -> build/lib.linux-armv7l-cpython-313/coral/analysis/_sequencing/data 2025-09-08T03:41:06,903 running build_ext 2025-09-08T03:41:07,236 building 'coral.analysis._sequencing.calign' extension 2025-09-08T03:41:07,236 creating build/temp.linux-armv7l-cpython-313/coral/analysis/_sequencing 2025-09-08T03:41:07,237 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c coral/analysis/_sequencing/calign.c -o build/temp.linux-armv7l-cpython-313/coral/analysis/_sequencing/calign.o 2025-09-08T03:41:07,880 coral/analysis/_sequencing/calign.c: In function ‘__Pyx_ListComp_Append’: 2025-09-08T03:41:07,881 coral/analysis/_sequencing/calign.c:945:23: error: lvalue required as left operand of assignment 2025-09-08T03:41:07,881 945 | Py_SIZE(list) = len+1; 2025-09-08T03:41:07,881 | ^ 2025-09-08T03:41:07,931 coral/analysis/_sequencing/calign.c: In function ‘__pyx_pf_5coral_8analysis_11_sequencing_6calign_2aligner’: 2025-09-08T03:41:07,934 coral/analysis/_sequencing/calign.c:3346:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T03:41:07,935 3346 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T03:41:07,935 | ^~ 2025-09-08T03:41:07,935 In file included from /usr/include/python3.13/Python.h:76, 2025-09-08T03:41:07,935 from coral/analysis/_sequencing/calign.c:12: 2025-09-08T03:41:07,935 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T03:41:07,936 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T03:41:07,936 | ^~~~~~~~~~~~~~~ 2025-09-08T03:41:07,939 coral/analysis/_sequencing/calign.c:3362:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T03:41:07,939 3362 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T03:41:07,939 | ^~ 2025-09-08T03:41:07,939 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T03:41:07,939 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T03:41:07,940 | ^~~~~~~~~~~~~~~ 2025-09-08T03:41:07,964 coral/analysis/_sequencing/calign.c:3989:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-08T03:41:07,964 3989 | for (__pyx_t_19 = 1; __pyx_t_19 < __pyx_t_6; __pyx_t_19+=1) { 2025-09-08T03:41:07,964 | ^ 2025-09-08T03:41:07,968 coral/analysis/_sequencing/calign.c:4009:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-08T03:41:07,968 4009 | for (__pyx_t_20 = 1; __pyx_t_20 < __pyx_t_5; __pyx_t_20+=1) { 2025-09-08T03:41:07,969 | ^ 2025-09-08T03:41:08,079 coral/analysis/_sequencing/calign.c:4857:16: error: implicit declaration of function ‘PyString_FromStringAndSize’; did you mean ‘PyBytes_FromStringAndSize’? [-Wimplicit-function-declaration] 2025-09-08T03:41:08,079 4857 | __pyx_v_ai = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2025-09-08T03:41:08,079 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,079 | PyBytes_FromStringAndSize 2025-09-08T03:41:08,085 coral/analysis/_sequencing/calign.c:4857:14: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T03:41:08,085 4857 | __pyx_v_ai = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2025-09-08T03:41:08,085 | ^ 2025-09-08T03:41:08,090 coral/analysis/_sequencing/calign.c:4866:14: error: assignment to ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T03:41:08,090 4866 | __pyx_v_aj = PyString_FromStringAndSize(NULL, __pyx_v_seqlen); 2025-09-08T03:41:08,090 | ^ 2025-09-08T03:41:08,117 coral/analysis/_sequencing/calign.c:4875:21: error: implicit declaration of function ‘PyString_AS_STRING’; did you mean ‘PyBytes_AS_STRING’? [-Wimplicit-function-declaration] 2025-09-08T03:41:08,117 4875 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2025-09-08T03:41:08,117 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,117 | PyBytes_AS_STRING 2025-09-08T03:41:08,123 coral/analysis/_sequencing/calign.c:4875:19: error: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T03:41:08,123 4875 | __pyx_v_align_j = PyString_AS_STRING(__pyx_v_aj); 2025-09-08T03:41:08,123 | ^ 2025-09-08T03:41:08,128 coral/analysis/_sequencing/calign.c:4884:19: error: assignment to ‘char *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T03:41:08,128 4884 | __pyx_v_align_i = PyString_AS_STRING(__pyx_v_ai); 2025-09-08T03:41:08,128 | ^ 2025-09-08T03:41:08,176 coral/analysis/_sequencing/calign.c:5163:3: error: implicit declaration of function ‘_PyString_Resize’ [-Wimplicit-function-declaration] 2025-09-08T03:41:08,176 5163 | _PyString_Resize((&__pyx_v_aj), __pyx_v_align_counter); 2025-09-08T03:41:08,176 | ^~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,187 coral/analysis/_sequencing/calign.c: In function ‘__pyx_pf_5coral_8analysis_11_sequencing_6calign_4score_alignment’: 2025-09-08T03:41:08,192 coral/analysis/_sequencing/calign.c:5475:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T03:41:08,193 5475 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T03:41:08,193 | ^~ 2025-09-08T03:41:08,193 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T03:41:08,193 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T03:41:08,193 | ^~~~~~~~~~~~~~~ 2025-09-08T03:41:08,222 coral/analysis/_sequencing/calign.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-08T03:41:08,231 coral/analysis/_sequencing/calign.c:5812:50: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-08T03:41:08,231 5812 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-08T03:41:08,231 | ^~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,231 | PyBUF_C_CONTIGUOUS 2025-09-08T03:41:08,232 coral/analysis/_sequencing/calign.c:5812:50: note: each undeclared identifier is reported only once for each function it appears in 2025-09-08T03:41:08,262 coral/analysis/_sequencing/calign.c:5868:50: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-08T03:41:08,262 5868 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-08T03:41:08,262 | ^~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,262 | PyBUF_F_CONTIGUOUS 2025-09-08T03:41:08,270 coral/analysis/_sequencing/calign.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-08T03:41:08,277 coral/analysis/_sequencing/calign.c:6934:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T03:41:08,278 6934 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-08T03:41:08,278 | ^~ 2025-09-08T03:41:08,278 coral/analysis/_sequencing/calign.c:442:43: note: in definition of macro ‘unlikely’ 2025-09-08T03:41:08,278 442 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T03:41:08,278 | ^ 2025-09-08T03:41:08,286 coral/analysis/_sequencing/calign.c:6938:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T03:41:08,286 6938 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-08T03:41:08,287 | ^~ 2025-09-08T03:41:08,296 coral/analysis/_sequencing/calign.c:6957:31: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T03:41:08,296 6957 | if (unlikely(__pyx_v_descr->fields == Py_None)) { 2025-09-08T03:41:08,296 | ^~ 2025-09-08T03:41:08,296 coral/analysis/_sequencing/calign.c:442:43: note: in definition of macro ‘unlikely’ 2025-09-08T03:41:08,296 442 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T03:41:08,296 | ^ 2025-09-08T03:41:08,305 coral/analysis/_sequencing/calign.c:6961:51: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T03:41:08,305 6961 | __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; 2025-09-08T03:41:08,305 | ^~ 2025-09-08T03:41:08,321 coral/analysis/_sequencing/calign.c:7166:79: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-08T03:41:08,321 7166 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); 2025-09-08T03:41:08,321 | ^~ 2025-09-08T03:41:08,340 coral/analysis/_sequencing/calign.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-08T03:41:08,349 coral/analysis/_sequencing/calign.c:8246:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T03:41:08,349 8246 | __pyx_codeobj__43 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__42, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_max_index, 96, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,349 | ^~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,350 In file included from /usr/include/python3.13/Python.h:101: 2025-09-08T03:41:08,350 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T03:41:08,350 213 | PyCode_New( 2025-09-08T03:41:08,350 | ^~~~~~~~~~ 2025-09-08T03:41:08,360 coral/analysis/_sequencing/calign.c:8246:243: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T03:41:08,360 8246 | __pyx_codeobj__43 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__42, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_max_index, 96, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,361 | ^~ 2025-09-08T03:41:08,361 | | 2025-09-08T03:41:08,361 | int 2025-09-08T03:41:08,361 coral/analysis/_sequencing/calign.c:69:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,361 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,361 | ^~~~~ 2025-09-08T03:41:08,361 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T03:41:08,361 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T03:41:08,362 | ~~~~~~~~~~^ 2025-09-08T03:41:08,371 coral/analysis/_sequencing/calign.c:8246:247: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T03:41:08,372 8246 | __pyx_codeobj__43 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__42, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_max_index, 96, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,372 | ^~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,372 | | 2025-09-08T03:41:08,372 | PyObject * {aka struct _object *} 2025-09-08T03:41:08,372 coral/analysis/_sequencing/calign.c:69:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,372 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,372 | ^~~~ 2025-09-08T03:41:08,372 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T03:41:08,372 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T03:41:08,373 | ~~~~^ 2025-09-08T03:41:08,382 coral/analysis/_sequencing/calign.c:69:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T03:41:08,382 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,382 | ^~~~~~~~~~ 2025-09-08T03:41:08,383 coral/analysis/_sequencing/calign.c:8246:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,383 8246 | __pyx_codeobj__43 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__42, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_max_index, 96, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 96; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,383 | ^~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,383 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T03:41:08,383 213 | PyCode_New( 2025-09-08T03:41:08,383 | ^~~~~~~~~~ 2025-09-08T03:41:08,394 coral/analysis/_sequencing/calign.c:8258:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T03:41:08,394 8258 | __pyx_codeobj__45 = (PyObject*)__Pyx_PyCode_New(7, 0, 41, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__44, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_aligner, 107, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,394 | ^~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,394 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T03:41:08,394 213 | PyCode_New( 2025-09-08T03:41:08,394 | ^~~~~~~~~~ 2025-09-08T03:41:08,403 coral/analysis/_sequencing/calign.c:8258:242: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T03:41:08,403 8258 | __pyx_codeobj__45 = (PyObject*)__Pyx_PyCode_New(7, 0, 41, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__44, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_aligner, 107, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,404 | ^~~ 2025-09-08T03:41:08,404 | | 2025-09-08T03:41:08,404 | int 2025-09-08T03:41:08,404 coral/analysis/_sequencing/calign.c:69:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,404 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,404 | ^~~~~ 2025-09-08T03:41:08,404 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T03:41:08,404 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T03:41:08,404 | ~~~~~~~~~~^ 2025-09-08T03:41:08,413 coral/analysis/_sequencing/calign.c:8258:247: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T03:41:08,413 8258 | __pyx_codeobj__45 = (PyObject*)__Pyx_PyCode_New(7, 0, 41, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__44, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_aligner, 107, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,414 | ^~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,414 | | 2025-09-08T03:41:08,414 | PyObject * {aka struct _object *} 2025-09-08T03:41:08,414 coral/analysis/_sequencing/calign.c:69:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,414 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,414 | ^~~~ 2025-09-08T03:41:08,414 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T03:41:08,414 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T03:41:08,414 | ~~~~^ 2025-09-08T03:41:08,423 coral/analysis/_sequencing/calign.c:69:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T03:41:08,423 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,423 | ^~~~~~~~~~ 2025-09-08T03:41:08,423 coral/analysis/_sequencing/calign.c:8258:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,423 8258 | __pyx_codeobj__45 = (PyObject*)__Pyx_PyCode_New(7, 0, 41, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__44, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_aligner, 107, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 107; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,424 | ^~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,424 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T03:41:08,424 213 | PyCode_New( 2025-09-08T03:41:08,424 | ^~~~~~~~~~ 2025-09-08T03:41:08,432 coral/analysis/_sequencing/calign.c:8270:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T03:41:08,432 8270 | __pyx_codeobj__47 = (PyObject*)__Pyx_PyCode_New(5, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__46, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_score_alignment, 281, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,432 | ^~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,432 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T03:41:08,433 213 | PyCode_New( 2025-09-08T03:41:08,433 | ^~~~~~~~~~ 2025-09-08T03:41:08,442 coral/analysis/_sequencing/calign.c:8270:250: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T03:41:08,442 8270 | __pyx_codeobj__47 = (PyObject*)__Pyx_PyCode_New(5, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__46, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_score_alignment, 281, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,442 | ^~~ 2025-09-08T03:41:08,442 | | 2025-09-08T03:41:08,442 | int 2025-09-08T03:41:08,442 coral/analysis/_sequencing/calign.c:69:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,443 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,443 | ^~~~~ 2025-09-08T03:41:08,443 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T03:41:08,443 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T03:41:08,443 | ~~~~~~~~~~^ 2025-09-08T03:41:08,452 coral/analysis/_sequencing/calign.c:8270:255: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T03:41:08,452 8270 | __pyx_codeobj__47 = (PyObject*)__Pyx_PyCode_New(5, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__46, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_score_alignment, 281, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,452 | ^~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,452 | | 2025-09-08T03:41:08,452 | PyObject * {aka struct _object *} 2025-09-08T03:41:08,452 coral/analysis/_sequencing/calign.c:69:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,452 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,452 | ^~~~ 2025-09-08T03:41:08,453 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T03:41:08,453 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T03:41:08,453 | ~~~~^ 2025-09-08T03:41:08,462 coral/analysis/_sequencing/calign.c:69:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T03:41:08,462 69 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T03:41:08,462 | ^~~~~~~~~~ 2025-09-08T03:41:08,462 coral/analysis/_sequencing/calign.c:8270:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T03:41:08,462 8270 | __pyx_codeobj__47 = (PyObject*)__Pyx_PyCode_New(5, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__46, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_nick_projects_python_coral, __pyx_n_s_score_alignment, 281, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T03:41:08,462 | ^~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,462 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T03:41:08,462 213 | PyCode_New( 2025-09-08T03:41:08,462 | ^~~~~~~~~~ 2025-09-08T03:41:08,479 coral/analysis/_sequencing/calign.c: In function ‘__Pyx_ErrRestore’: 2025-09-08T03:41:08,488 coral/analysis/_sequencing/calign.c:8611:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T03:41:08,488 8611 | tmp_type = tstate->curexc_type; 2025-09-08T03:41:08,488 | ^~ 2025-09-08T03:41:08,498 coral/analysis/_sequencing/calign.c:8612:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T03:41:08,498 8612 | tmp_value = tstate->curexc_value; 2025-09-08T03:41:08,498 | ^~ 2025-09-08T03:41:08,507 coral/analysis/_sequencing/calign.c:8613:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T03:41:08,507 8613 | tmp_tb = tstate->curexc_traceback; 2025-09-08T03:41:08,507 | ^~ 2025-09-08T03:41:08,516 coral/analysis/_sequencing/calign.c:8614:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T03:41:08,516 8614 | tstate->curexc_type = type; 2025-09-08T03:41:08,517 | ^~ 2025-09-08T03:41:08,526 coral/analysis/_sequencing/calign.c:8615:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T03:41:08,526 8615 | tstate->curexc_value = value; 2025-09-08T03:41:08,526 | ^~ 2025-09-08T03:41:08,535 coral/analysis/_sequencing/calign.c:8616:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T03:41:08,535 8616 | tstate->curexc_traceback = tb; 2025-09-08T03:41:08,535 | ^~ 2025-09-08T03:41:08,535 coral/analysis/_sequencing/calign.c: In function ‘__Pyx_ErrFetch’: 2025-09-08T03:41:08,544 coral/analysis/_sequencing/calign.c:8627:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T03:41:08,545 8627 | *type = tstate->curexc_type; 2025-09-08T03:41:08,545 | ^~ 2025-09-08T03:41:08,554 coral/analysis/_sequencing/calign.c:8628:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T03:41:08,554 8628 | *value = tstate->curexc_value; 2025-09-08T03:41:08,554 | ^~ 2025-09-08T03:41:08,563 coral/analysis/_sequencing/calign.c:8629:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T03:41:08,563 8629 | *tb = tstate->curexc_traceback; 2025-09-08T03:41:08,563 | ^~ 2025-09-08T03:41:08,572 coral/analysis/_sequencing/calign.c:8630:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T03:41:08,572 8630 | tstate->curexc_type = 0; 2025-09-08T03:41:08,573 | ^~ 2025-09-08T03:41:08,582 coral/analysis/_sequencing/calign.c:8631:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T03:41:08,582 8631 | tstate->curexc_value = 0; 2025-09-08T03:41:08,582 | ^~ 2025-09-08T03:41:08,591 coral/analysis/_sequencing/calign.c:8632:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T03:41:08,591 8632 | tstate->curexc_traceback = 0; 2025-09-08T03:41:08,591 | ^~ 2025-09-08T03:41:08,612 coral/analysis/_sequencing/calign.c: In function ‘__Pyx_Raise’: 2025-09-08T03:41:08,621 coral/analysis/_sequencing/calign.c:8784:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T03:41:08,621 8784 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T03:41:08,621 | ^~ 2025-09-08T03:41:08,631 coral/analysis/_sequencing/calign.c:8787:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T03:41:08,631 8787 | tstate->curexc_traceback = tb; 2025-09-08T03:41:08,631 | ^~ 2025-09-08T03:41:08,667 coral/analysis/_sequencing/calign.c: In function ‘__Pyx_PyUnicode_Equals’: 2025-09-08T03:41:08,678 coral/analysis/_sequencing/calign.c:87:51: error: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Wimplicit-function-declaration] 2025-09-08T03:41:08,678 87 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-08T03:41:08,678 | ^~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,678 coral/analysis/_sequencing/calign.c:442:43: note: in definition of macro ‘unlikely’ 2025-09-08T03:41:08,678 442 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T03:41:08,678 | ^ 2025-09-08T03:41:08,678 coral/analysis/_sequencing/calign.c:8965:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-08T03:41:08,678 8965 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-08T03:41:08,679 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T03:41:08,691 coral/analysis/_sequencing/calign.c: At top level: 2025-09-08T03:41:08,700 coral/analysis/_sequencing/calign.c:9073:12: fatal error: longintrepr.h: No such file or directory 2025-09-08T03:41:08,701 9073 | #include "longintrepr.h" 2025-09-08T03:41:08,701 | ^~~~~~~~~~~~~~~ 2025-09-08T03:41:08,701 compilation terminated. 2025-09-08T03:41:08,705 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T03:41:08,875 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T03:41:08,887 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T03:41:08,887 exec(compile('"'"''"'"''"'"' 2025-09-08T03:41:08,887 # This is -- a caller that pip uses to run setup.py 2025-09-08T03:41:08,887 # 2025-09-08T03:41:08,887 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T03:41:08,887 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T03:41:08,887 # - It provides a clear error message when setuptools is not installed. 2025-09-08T03:41:08,887 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T03:41:08,887 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T03:41:08,887 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T03:41:08,887 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T03:41:08,887 import os, sys, tokenize, traceback 2025-09-08T03:41:08,887 2025-09-08T03:41:08,887 try: 2025-09-08T03:41:08,887 import setuptools 2025-09-08T03:41:08,887 except ImportError: 2025-09-08T03:41:08,887 print( 2025-09-08T03:41:08,887 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T03:41:08,887 "the build environment with exception:", 2025-09-08T03:41:08,887 file=sys.stderr, 2025-09-08T03:41:08,887 ) 2025-09-08T03:41:08,887 traceback.print_exc() 2025-09-08T03:41:08,887 sys.exit(1) 2025-09-08T03:41:08,887 2025-09-08T03:41:08,887 __file__ = %r 2025-09-08T03:41:08,887 sys.argv[0] = __file__ 2025-09-08T03:41:08,887 2025-09-08T03:41:08,887 if os.path.exists(__file__): 2025-09-08T03:41:08,887 filename = __file__ 2025-09-08T03:41:08,887 with tokenize.open(__file__) as f: 2025-09-08T03:41:08,887 setup_py_code = f.read() 2025-09-08T03:41:08,887 else: 2025-09-08T03:41:08,887 filename = "" 2025-09-08T03:41:08,887 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T03:41:08,887 2025-09-08T03:41:08,887 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T03:41:08,887 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-a1ddv1y_/coral_01eea8da4eee443fbaaa4fa1d9b1cdb9/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-wvxbgegy[/] 2025-09-08T03:41:08,887 [bold magenta]cwd[/]: /tmp/pip-wheel-a1ddv1y_/coral_01eea8da4eee443fbaaa4fa1d9b1cdb9/ 2025-09-08T03:41:08,887 Building wheel for coral (setup.py): finished with status 'error' 2025-09-08T03:41:08,888 ERROR: Failed building wheel for coral 2025-09-08T03:41:08,889 Running setup.py clean for coral 2025-09-08T03:41:08,889 Running command python setup.py clean 2025-09-08T03:41:09,779 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T03:41:09,779 warnings.warn(msg) 2025-09-08T03:41:10,249 running clean 2025-09-08T03:41:10,396 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T03:41:10,396 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T03:41:10,399 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T03:41:10,399 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T03:41:10,399 removing 'build' 2025-09-08T03:41:10,535 Failed to build coral 2025-09-08T03:41:10,536 ERROR: Failed to build one or more wheels 2025-09-08T03:41:10,537 Exception information: 2025-09-08T03:41:10,537 Traceback (most recent call last): 2025-09-08T03:41:10,537 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T03:41:10,537 status = _inner_run() 2025-09-08T03:41:10,537 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T03:41:10,537 return self.run(options, args) 2025-09-08T03:41:10,537 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T03:41:10,537 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T03:41:10,537 return func(self, options, args) 2025-09-08T03:41:10,537 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T03:41:10,537 raise CommandError("Failed to build one or more wheels") 2025-09-08T03:41:10,537 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T03:41:10,541 Removed build tracker: '/tmp/pip-build-tracker-6qk7hls2'