2025-09-07T23:23:04,653 Created temporary directory: /tmp/pip-build-tracker-36l6k2f4 2025-09-07T23:23:04,654 Initialized build tracking at /tmp/pip-build-tracker-36l6k2f4 2025-09-07T23:23:04,654 Created build tracker: /tmp/pip-build-tracker-36l6k2f4 2025-09-07T23:23:04,654 Entered build tracker: /tmp/pip-build-tracker-36l6k2f4 2025-09-07T23:23:04,655 Created temporary directory: /tmp/pip-wheel-adl4vvsn 2025-09-07T23:23:04,658 Created temporary directory: /tmp/pip-ephem-wheel-cache-q94uf_wr 2025-09-07T23:23:04,718 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:23:04,721 2 location(s) to search for versions of khmer: 2025-09-07T23:23:04,721 * https://pypi.org/simple/khmer/ 2025-09-07T23:23:04,721 * https://www.piwheels.org/simple/khmer/ 2025-09-07T23:23:04,721 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2025-09-07T23:23:04,721 Getting page https://pypi.org/simple/khmer/ 2025-09-07T23:23:04,723 Found index url https://pypi.org/simple/ 2025-09-07T23:23:04,798 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:23:04,804 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,804 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,804 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2025-09-07T23:23:04,805 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6.1 2025-09-07T23:23:04,805 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,805 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2025-09-07T23:23:04,805 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,805 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7.1 2025-09-07T23:23:04,806 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,806 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2025-09-07T23:23:04,806 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,806 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2025-09-07T23:23:04,807 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,807 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0.1 2025-09-07T23:23:04,807 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2025-09-07T23:23:04,807 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,808 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2025-09-07T23:23:04,808 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,808 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2025-09-07T23:23:04,808 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,808 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2025-09-07T23:23:04,809 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,809 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,809 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4.1 2025-09-07T23:23:04,809 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,809 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,809 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,810 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,810 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2025-09-07T23:23:04,810 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2025-09-07T23:23:04,810 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,811 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2025-09-07T23:23:04,811 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,811 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,811 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,811 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,811 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T23:23:04,812 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1.1 2025-09-07T23:23:04,812 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:23:04,812 Getting page https://www.piwheels.org/simple/khmer/ 2025-09-07T23:23:04,813 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:23:05,009 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2025-09-07T23:23:05,010 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:23:05,010 Skipping link: not a file: https://pypi.org/simple/khmer/ 2025-09-07T23:23:05,037 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2025-09-07T23:23:05,038 Collecting khmer==0.8 2025-09-07T23:23:05,039 Created temporary directory: /tmp/pip-unpack-tcl62g08 2025-09-07T23:23:05,187 Downloading khmer-0.8.tar.gz (18.9 MB) 2025-09-07T23:23:09,243 Added khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz to build tracker '/tmp/pip-build-tracker-36l6k2f4' 2025-09-07T23:23:09,245 Running setup.py (path:/tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/setup.py) egg_info for package khmer 2025-09-07T23:23:09,245 Created temporary directory: /tmp/pip-pip-egg-info-9muwbxs8 2025-09-07T23:23:09,245 Preparing metadata (setup.py): started 2025-09-07T23:23:09,246 Running command python setup.py egg_info 2025-09-07T23:23:09,884 /tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/ez_setup.py:124: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T23:23:09,885 import pkg_resources 2025-09-07T23:23:10,389 /tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/versioneer.py:162: SyntaxWarning: invalid escape sequence '\s' 2025-09-07T23:23:10,389 mo = re.search(r'=\s*"(.*)"', line) 2025-09-07T23:23:10,566 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T23:23:10,566 !! 2025-09-07T23:23:10,567 ******************************************************************************** 2025-09-07T23:23:10,567 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T23:23:10,567 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T23:23:10,567 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T23:23:10,567 or your builds will no longer be supported. 2025-09-07T23:23:10,567 ******************************************************************************** 2025-09-07T23:23:10,567 !! 2025-09-07T23:23:10,568 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T23:23:18,235 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:23:18,235 !! 2025-09-07T23:23:18,235 ******************************************************************************** 2025-09-07T23:23:18,235 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:23:18,236 License :: OSI Approved :: BSD License 2025-09-07T23:23:18,236 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:23:18,236 ******************************************************************************** 2025-09-07T23:23:18,236 !! 2025-09-07T23:23:18,236 self._finalize_license_expression() 2025-09-07T23:23:18,335 running egg_info 2025-09-07T23:23:18,437 creating /tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info 2025-09-07T23:23:18,437 writing /tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info/PKG-INFO 2025-09-07T23:23:18,438 writing dependency_links to /tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info/dependency_links.txt 2025-09-07T23:23:18,439 writing requirements to /tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info/requires.txt 2025-09-07T23:23:18,439 writing top-level names to /tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info/top_level.txt 2025-09-07T23:23:18,440 writing manifest file '/tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info/SOURCES.txt' 2025-09-07T23:23:18,748 reading manifest file '/tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info/SOURCES.txt' 2025-09-07T23:23:18,748 reading manifest template 'MANIFEST.in' 2025-09-07T23:23:19,011 no previously-included directories found matching 'doc/doxygen' 2025-09-07T23:23:19,013 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T23:23:19,033 writing manifest file '/tmp/pip-pip-egg-info-9muwbxs8/khmer.egg-info/SOURCES.txt' 2025-09-07T23:23:19,188 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:23:19,193 Source in /tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1 has version 0.8, which satisfies requirement khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz 2025-09-07T23:23:19,193 Removed khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz from build tracker '/tmp/pip-build-tracker-36l6k2f4' 2025-09-07T23:23:19,198 Created temporary directory: /tmp/pip-unpack-qni46nk3 2025-09-07T23:23:19,198 Created temporary directory: /tmp/pip-unpack-h692j7lq 2025-09-07T23:23:19,198 Building wheels for collected packages: khmer 2025-09-07T23:23:19,200 Created temporary directory: /tmp/pip-wheel-dtpn24f6 2025-09-07T23:23:19,200 DEPRECATION: Building 'khmer' 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 'khmer'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-07T23:23:19,201 Building wheel for khmer (setup.py): started 2025-09-07T23:23:19,202 Destination directory: /tmp/pip-wheel-dtpn24f6 2025-09-07T23:23:19,202 Running command python setup.py bdist_wheel 2025-09-07T23:23:19,791 /tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/ez_setup.py:124: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T23:23:19,791 import pkg_resources 2025-09-07T23:23:20,373 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T23:23:20,374 !! 2025-09-07T23:23:20,374 ******************************************************************************** 2025-09-07T23:23:20,374 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T23:23:20,374 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T23:23:20,374 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T23:23:20,375 or your builds will no longer be supported. 2025-09-07T23:23:20,375 ******************************************************************************** 2025-09-07T23:23:20,375 !! 2025-09-07T23:23:20,375 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T23:23:21,750 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:23:21,750 !! 2025-09-07T23:23:21,750 ******************************************************************************** 2025-09-07T23:23:21,750 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:23:21,751 License :: OSI Approved :: BSD License 2025-09-07T23:23:21,751 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:23:21,751 ******************************************************************************** 2025-09-07T23:23:21,751 !! 2025-09-07T23:23:21,751 self._finalize_license_expression() 2025-09-07T23:23:21,752 running bdist_wheel 2025-09-07T23:23:22,030 running build 2025-09-07T23:23:22,030 got version from file /tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/khmer/_version.py {'version': '0.8', 'full': 'fd0d19f81d7a627bdffe3ab44658928074fb5acb'} 2025-09-07T23:23:22,030 running build_py 2025-09-07T23:23:22,127 creating build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,127 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,128 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,129 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,129 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,130 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,131 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,131 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,132 copying khmer/counting_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,133 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,133 running egg_info 2025-09-07T23:23:22,225 creating khmer.egg-info 2025-09-07T23:23:22,225 writing khmer.egg-info/PKG-INFO 2025-09-07T23:23:22,227 writing dependency_links to khmer.egg-info/dependency_links.txt 2025-09-07T23:23:22,228 writing requirements to khmer.egg-info/requires.txt 2025-09-07T23:23:22,228 writing top-level names to khmer.egg-info/top_level.txt 2025-09-07T23:23:22,228 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:23:22,324 reading manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:23:22,324 reading manifest template 'MANIFEST.in' 2025-09-07T23:23:22,563 no previously-included directories found matching 'doc/doxygen' 2025-09-07T23:23:22,565 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T23:23:22,584 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:23:22,592 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:22,594 running build_ext 2025-09-07T23:23:22,607 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2025-09-07T23:23:22,977 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2025-09-07T23:23:23,106 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2025-09-07T23:23:23,609 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2025-09-07T23:23:24,874 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2025-09-07T23:23:24,995 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2025-09-07T23:23:26,796 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2025-09-07T23:23:28,604 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2025-09-07T23:23:28,758 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2025-09-07T23:23:30,830 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2025-09-07T23:23:31,912 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2025-09-07T23:23:32,554 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2025-09-07T23:23:33,143 ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 2025-09-07T23:23:33,335 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2025-09-07T23:23:34,429 In function ‘mainSimpleSort’, 2025-09-07T23:23:34,429 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2025-09-07T23:23:34,429 inlined from ‘mainSort’ at blocksort.c:897:19: 2025-09-07T23:23:34,430 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T23:23:34,430 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T23:23:34,430 | ^~~~~~~ 2025-09-07T23:23:34,430 blocksort.c:514:18: note: called from here 2025-09-07T23:23:34,431 514 | while ( mainGtU ( 2025-09-07T23:23:34,431 | ^~~~~~~~~ 2025-09-07T23:23:34,431 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T23:23:34,431 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:34,431 516 | ) ) { 2025-09-07T23:23:34,431 | ~ 2025-09-07T23:23:34,432 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T23:23:34,432 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T23:23:34,432 | ^~~~~~~ 2025-09-07T23:23:34,432 blocksort.c:528:18: note: called from here 2025-09-07T23:23:34,433 528 | while ( mainGtU ( 2025-09-07T23:23:34,433 | ^~~~~~~~~ 2025-09-07T23:23:34,433 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T23:23:34,433 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:34,433 530 | ) ) { 2025-09-07T23:23:34,433 | ~ 2025-09-07T23:23:34,434 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T23:23:34,434 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T23:23:34,434 | ^~~~~~~ 2025-09-07T23:23:34,434 blocksort.c:542:18: note: called from here 2025-09-07T23:23:34,435 542 | while ( mainGtU ( 2025-09-07T23:23:34,435 | ^~~~~~~~~ 2025-09-07T23:23:34,435 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T23:23:34,435 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:34,435 544 | ) ) { 2025-09-07T23:23:34,435 | ~ 2025-09-07T23:23:35,414 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2025-09-07T23:23:35,955 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2025-09-07T23:23:36,074 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2025-09-07T23:23:36,193 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2025-09-07T23:23:41,307 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2025-09-07T23:23:44,297 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2025-09-07T23:23:46,520 #gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o 2025-09-07T23:23:46,523 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2025-09-07T23:23:46,525 #rm -f libbz2.so.1.0 2025-09-07T23:23:46,529 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2025-09-07T23:23:46,541 building 'khmer._khmermodule' extension 2025-09-07T23:23:46,544 creating build/temp.linux-armv7l-cpython-313/khmer 2025-09-07T23:23:46,545 creating build/temp.linux-armv7l-cpython-313/lib 2025-09-07T23:23:46,546 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DVERSION=0.8 -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.13 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-cpython-313/khmer/_khmermodule.o -O3 2025-09-07T23:23:49,595 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2025-09-07T23:23:49,595 khmer/_khmermodule.cc:85:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2025-09-07T23:23:49,596 85 | tobj.ob_size = 0; 2025-09-07T23:23:49,596 | ^~~~~~~ 2025-09-07T23:23:49,596 khmer/_khmermodule.cc:86:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:23:49,596 86 | tobj.ob_type = &PyType_Type; 2025-09-07T23:23:49,596 | ^~~~~~~ 2025-09-07T23:23:49,603 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:49,603 khmer/_khmermodule.cc:225:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:49,603 225 | }; 2025-09-07T23:23:49,603 | ^ 2025-09-07T23:23:49,603 khmer/_khmermodule.cc:206:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:49,604 206 | "Config", sizeof(khmer_ConfigObject), 2025-09-07T23:23:49,604 | ^~~~~~~~ 2025-09-07T23:23:49,604 | | 2025-09-07T23:23:49,604 | const char* 2025-09-07T23:23:49,604 khmer/_khmermodule.cc:225:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:49,604 225 | }; 2025-09-07T23:23:49,605 | ^ 2025-09-07T23:23:49,605 | | 2025-09-07T23:23:49,605 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:23:49,605 khmer/_khmermodule.cc:225:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:23:49,605 225 | }; 2025-09-07T23:23:49,605 | ^ 2025-09-07T23:23:49,606 | | 2025-09-07T23:23:49,606 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:23:49,607 In file included from /usr/include/python3.13/Python.h:72, 2025-09-07T23:23:49,607 from khmer/_khmermodule.cc:12: 2025-09-07T23:23:49,607 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:23:49,607 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:23:49,607 | ~~~ 2025-09-07T23:23:49,607 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:23:49,607 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:23:49,607 | | 2025-09-07T23:23:49,608 | int 2025-09-07T23:23:49,608 731 | 0) 2025-09-07T23:23:49,608 | ~~ 2025-09-07T23:23:49,608 khmer/_khmermodule.cc:223:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:23:49,608 223 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:23:49,608 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,608 khmer/_khmermodule.cc:224:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:23:49,609 224 | "config object", /* tp_doc */ 2025-09-07T23:23:49,609 | ^~~~~~~~~~~~~~~ 2025-09-07T23:23:49,609 | | 2025-09-07T23:23:49,609 | const char* 2025-09-07T23:23:49,634 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2025-09-07T23:23:49,635 khmer/_khmermodule.cc:312:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:23:49,635 312 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2025-09-07T23:23:49,635 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,635 | PyLong_FromSize_t 2025-09-07T23:23:49,661 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2025-09-07T23:23:49,661 khmer/_khmermodule.cc:370:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:23:49,661 370 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2025-09-07T23:23:49,661 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,662 | PyLong_FromSize_t 2025-09-07T23:23:49,687 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2025-09-07T23:23:49,687 khmer/_khmermodule.cc:399:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:23:49,687 399 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2025-09-07T23:23:49,687 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,687 | PyLong_FromSize_t 2025-09-07T23:23:49,713 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2025-09-07T23:23:49,713 khmer/_khmermodule.cc:466:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:23:49,713 466 | return Py_FindMethod(khmer_config_methods, obj, name); 2025-09-07T23:23:49,713 | ^~~~~~~~~~~~~ 2025-09-07T23:23:49,713 | PyCMethod 2025-09-07T23:23:49,714 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:49,714 khmer/_khmermodule.cc:482:62: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:49,714 482 | static PyTypeObject Read_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T23:23:49,715 | ^ 2025-09-07T23:23:49,743 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2025-09-07T23:23:49,743 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:23:49,743 504 | PyString_FromString( \ 2025-09-07T23:23:49,743 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,743 khmer/_khmermodule.cc:513:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:23:49,743 513 | return KHMER_READ_STRING_GETTER( self, name ); 2025-09-07T23:23:49,744 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,771 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2025-09-07T23:23:49,772 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:23:49,772 504 | PyString_FromString( \ 2025-09-07T23:23:49,772 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,772 khmer/_khmermodule.cc:521:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:23:49,772 521 | return KHMER_READ_STRING_GETTER( self, sequence ); 2025-09-07T23:23:49,772 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,802 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2025-09-07T23:23:49,802 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:23:49,803 504 | PyString_FromString( \ 2025-09-07T23:23:49,803 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,803 khmer/_khmermodule.cc:529:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:23:49,803 529 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2025-09-07T23:23:49,803 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,832 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2025-09-07T23:23:49,832 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:23:49,832 504 | PyString_FromString( \ 2025-09-07T23:23:49,832 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,833 khmer/_khmermodule.cc:537:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:23:49,833 537 | return KHMER_READ_STRING_GETTER( self, annotations ); 2025-09-07T23:23:49,833 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,834 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:49,834 khmer/_khmermodule.cc:599:36: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:49,834 599 | = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T23:23:49,834 | ^ 2025-09-07T23:23:49,835 khmer/_khmermodule.cc:600:74: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:49,835 600 | static PyTypeObject ReadPairIterator_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T23:23:49,835 | ^ 2025-09-07T23:23:49,880 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2025-09-07T23:23:49,880 khmer/_khmermodule.cc:874:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:49,880 874 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2025-09-07T23:23:49,880 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:49,881 | PyLong_FromLong 2025-09-07T23:23:49,913 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2025-09-07T23:23:49,913 khmer/_khmermodule.cc:1024:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:23:49,914 1024 | return PyString_FromString(_revhash(val, ktable->ksize()).c_str()); 2025-09-07T23:23:49,914 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,914 | PyLong_FromString 2025-09-07T23:23:49,938 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2025-09-07T23:23:49,939 khmer/_khmermodule.cc:1050:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:49,939 1050 | return PyInt_FromLong(1); 2025-09-07T23:23:49,939 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:49,939 | PyLong_FromLong 2025-09-07T23:23:49,966 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2025-09-07T23:23:49,966 khmer/_khmermodule.cc:1078:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:23:49,966 1078 | return PyInt_FromSize_t(n_consumed); 2025-09-07T23:23:49,966 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:23:49,966 | PyLong_FromSize_t 2025-09-07T23:23:49,987 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2025-09-07T23:23:49,988 khmer/_khmermodule.cc:1097:16: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:23:49,988 1097 | } else if (PyInt_Check(arg)) { 2025-09-07T23:23:49,988 | ^~~~~~~~~~~ 2025-09-07T23:23:49,988 | PySet_Check 2025-09-07T23:23:50,009 khmer/_khmermodule.cc:1098:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:23:50,009 1098 | long pos = PyInt_AsLong(arg); 2025-09-07T23:23:50,010 | ^~~~~~~~~~~~ 2025-09-07T23:23:50,010 | PyLong_AsLong 2025-09-07T23:23:50,035 khmer/_khmermodule.cc:1100:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:23:50,035 1100 | } else if (PyString_Check(arg)) { 2025-09-07T23:23:50,035 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,036 | PyMapping_Check 2025-09-07T23:23:50,065 khmer/_khmermodule.cc:1101:25: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:23:50,065 1101 | std::string s = PyString_AsString(arg); 2025-09-07T23:23:50,065 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,096 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2025-09-07T23:23:50,096 khmer/_khmermodule.cc:1123:23: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:23:50,096 1123 | char * kmer_str = PyString_AsString( val ); 2025-09-07T23:23:50,097 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,118 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2025-09-07T23:23:50,119 khmer/_khmermodule.cc:1143:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:23:50,119 1143 | if (PyInt_Check(arg)) { 2025-09-07T23:23:50,119 | ^~~~~~~~~~~ 2025-09-07T23:23:50,119 | PySet_Check 2025-09-07T23:23:50,142 khmer/_khmermodule.cc:1144:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:23:50,142 1144 | long pos = PyInt_AsLong(arg); 2025-09-07T23:23:50,142 | ^~~~~~~~~~~~ 2025-09-07T23:23:50,143 | PyLong_AsLong 2025-09-07T23:23:50,170 khmer/_khmermodule.cc:1146:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:23:50,170 1146 | } else if (PyString_Check(arg)) { 2025-09-07T23:23:50,171 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,171 | PyMapping_Check 2025-09-07T23:23:50,201 khmer/_khmermodule.cc:1147:25: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:23:50,201 1147 | std::string s = PyString_AsString(arg); 2025-09-07T23:23:50,201 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,230 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2025-09-07T23:23:50,230 khmer/_khmermodule.cc:1195:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,230 1195 | return PyInt_FromLong(ktable->ksize()); 2025-09-07T23:23:50,230 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,231 | PyLong_FromLong 2025-09-07T23:23:50,257 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2025-09-07T23:23:50,258 khmer/_khmermodule.cc:1242:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:23:50,258 1242 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2025-09-07T23:23:50,258 | ^~~~~~~~~~~~~ 2025-09-07T23:23:50,258 | PyCMethod 2025-09-07T23:23:50,258 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:50,258 khmer/_khmermodule.cc:1284:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:50,259 1284 | }; 2025-09-07T23:23:50,259 | ^ 2025-09-07T23:23:50,259 khmer/_khmermodule.cc:1265:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,259 1265 | "KTable", sizeof(khmer_KTableObject), 2025-09-07T23:23:50,259 | ^~~~~~~~ 2025-09-07T23:23:50,259 | | 2025-09-07T23:23:50,259 | const char* 2025-09-07T23:23:50,260 khmer/_khmermodule.cc:1284:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,260 1284 | }; 2025-09-07T23:23:50,260 | ^ 2025-09-07T23:23:50,260 | | 2025-09-07T23:23:50,260 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:23:50,260 khmer/_khmermodule.cc:1284:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:23:50,260 1284 | }; 2025-09-07T23:23:50,260 | ^ 2025-09-07T23:23:50,261 | | 2025-09-07T23:23:50,261 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:23:50,261 khmer/_khmermodule.cc:1274:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2025-09-07T23:23:50,261 1274 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2025-09-07T23:23:50,261 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,261 | | 2025-09-07T23:23:50,261 | PySequenceMethods* 2025-09-07T23:23:50,264 khmer/_khmermodule.cc:1424:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:50,264 1424 | }; 2025-09-07T23:23:50,264 | ^ 2025-09-07T23:23:50,265 khmer/_khmermodule.cc:1405:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,265 1405 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2025-09-07T23:23:50,265 | ^~~~~~~~~ 2025-09-07T23:23:50,265 | | 2025-09-07T23:23:50,265 | const char* 2025-09-07T23:23:50,265 khmer/_khmermodule.cc:1424:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,265 1424 | }; 2025-09-07T23:23:50,265 | ^ 2025-09-07T23:23:50,266 | | 2025-09-07T23:23:50,266 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:23:50,266 khmer/_khmermodule.cc:1424:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:23:50,266 1424 | }; 2025-09-07T23:23:50,266 | ^ 2025-09-07T23:23:50,266 | | 2025-09-07T23:23:50,266 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:23:50,267 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:23:50,267 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:23:50,267 | ~~~ 2025-09-07T23:23:50,267 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:23:50,267 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:23:50,267 | | 2025-09-07T23:23:50,267 | int 2025-09-07T23:23:50,267 731 | 0) 2025-09-07T23:23:50,268 | ~~ 2025-09-07T23:23:50,268 khmer/_khmermodule.cc:1422:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:23:50,268 1422 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:23:50,268 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,268 khmer/_khmermodule.cc:1423:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:23:50,268 1423 | "subset object", /* tp_doc */ 2025-09-07T23:23:50,268 | ^~~~~~~~~~~~~~~ 2025-09-07T23:23:50,268 | | 2025-09-07T23:23:50,269 | const char* 2025-09-07T23:23:50,294 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2025-09-07T23:23:50,294 khmer/_khmermodule.cc:1519:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,294 1519 | return PyInt_FromLong(1); 2025-09-07T23:23:50,294 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,294 | PyLong_FromLong 2025-09-07T23:23:50,319 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2025-09-07T23:23:50,319 khmer/_khmermodule.cc:1536:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,319 1536 | return PyInt_FromLong(0); 2025-09-07T23:23:50,320 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,320 | PyLong_FromLong 2025-09-07T23:23:50,347 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2025-09-07T23:23:50,348 khmer/_khmermodule.cc:1624:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,348 1624 | return PyInt_FromLong(n_consumed); 2025-09-07T23:23:50,348 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,348 | PyLong_FromLong 2025-09-07T23:23:50,373 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2025-09-07T23:23:50,374 khmer/_khmermodule.cc:1656:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,374 1656 | return PyInt_FromLong(n_consumed); 2025-09-07T23:23:50,374 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,374 | PyLong_FromLong 2025-09-07T23:23:50,399 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2025-09-07T23:23:50,400 khmer/_khmermodule.cc:1679:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,400 1679 | return PyInt_FromLong(N); 2025-09-07T23:23:50,400 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,400 | PyLong_FromLong 2025-09-07T23:23:50,425 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2025-09-07T23:23:50,425 khmer/_khmermodule.cc:1702:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,426 1702 | return PyInt_FromLong(N); 2025-09-07T23:23:50,426 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,426 | PyLong_FromLong 2025-09-07T23:23:50,451 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2025-09-07T23:23:50,451 khmer/_khmermodule.cc:1805:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:23:50,451 1805 | if (PyInt_Check(arg)) { 2025-09-07T23:23:50,451 | ^~~~~~~~~~~ 2025-09-07T23:23:50,452 | PySet_Check 2025-09-07T23:23:50,473 khmer/_khmermodule.cc:1806:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:23:50,473 1806 | long pos = PyInt_AsLong(arg); 2025-09-07T23:23:50,473 | ^~~~~~~~~~~~ 2025-09-07T23:23:50,473 | PyLong_AsLong 2025-09-07T23:23:50,499 khmer/_khmermodule.cc:1808:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:23:50,499 1808 | } else if (PyString_Check(arg)) { 2025-09-07T23:23:50,499 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,499 | PyMapping_Check 2025-09-07T23:23:50,529 khmer/_khmermodule.cc:1809:25: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:23:50,529 1809 | std::string s = PyString_AsString(arg); 2025-09-07T23:23:50,529 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,554 khmer/_khmermodule.cc:1813:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,554 1813 | return PyInt_FromLong(count); 2025-09-07T23:23:50,554 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,554 | PyLong_FromLong 2025-09-07T23:23:50,579 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2025-09-07T23:23:50,579 khmer/_khmermodule.cc:1829:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,580 1829 | return PyInt_FromLong(count); 2025-09-07T23:23:50,580 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,580 | PyLong_FromLong 2025-09-07T23:23:50,611 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2025-09-07T23:23:50,611 khmer/_khmermodule.cc:1853:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:23:50,611 1853 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:23:50,611 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,612 | PyBytes_FromStringAndSize 2025-09-07T23:23:50,643 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2025-09-07T23:23:50,643 khmer/_khmermodule.cc:1883:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:23:50,643 1883 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:23:50,643 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,644 | PyBytes_FromStringAndSize 2025-09-07T23:23:50,675 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2025-09-07T23:23:50,675 khmer/_khmermodule.cc:2024:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,675 2024 | return PyInt_FromLong(k); 2025-09-07T23:23:50,675 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,675 | PyLong_FromLong 2025-09-07T23:23:50,712 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2025-09-07T23:23:50,713 khmer/_khmermodule.cc:2136:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T23:23:50,713 2136 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2025-09-07T23:23:50,713 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,713 | PyLong_FromVoidPtr 2025-09-07T23:23:50,743 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2025-09-07T23:23:50,743 khmer/_khmermodule.cc:2242:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:23:50,743 2242 | return Py_FindMethod(khmer_counting_methods, obj, name); 2025-09-07T23:23:50,744 | ^~~~~~~~~~~~~ 2025-09-07T23:23:50,744 | PyCMethod 2025-09-07T23:23:50,744 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:50,744 khmer/_khmermodule.cc:2271:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:50,744 2271 | }; 2025-09-07T23:23:50,744 | ^ 2025-09-07T23:23:50,744 khmer/_khmermodule.cc:2252:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,745 2252 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2025-09-07T23:23:50,745 | ^~~~~~~~~~~~~~~ 2025-09-07T23:23:50,745 | | 2025-09-07T23:23:50,745 | const char* 2025-09-07T23:23:50,745 khmer/_khmermodule.cc:2271:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,745 2271 | }; 2025-09-07T23:23:50,745 | ^ 2025-09-07T23:23:50,745 | | 2025-09-07T23:23:50,746 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:23:50,746 khmer/_khmermodule.cc:2271:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:23:50,746 2271 | }; 2025-09-07T23:23:50,746 | ^ 2025-09-07T23:23:50,746 | | 2025-09-07T23:23:50,746 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:23:50,746 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:23:50,747 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:23:50,747 | ~~~ 2025-09-07T23:23:50,747 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:23:50,747 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:23:50,747 | | 2025-09-07T23:23:50,747 | int 2025-09-07T23:23:50,747 731 | 0) 2025-09-07T23:23:50,747 | ~~ 2025-09-07T23:23:50,748 khmer/_khmermodule.cc:2269:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:23:50,748 2269 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:23:50,748 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,748 khmer/_khmermodule.cc:2270:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:23:50,748 2270 | "counting hash object", /* tp_doc */ 2025-09-07T23:23:50,748 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,748 | | 2025-09-07T23:23:50,748 | const char* 2025-09-07T23:23:50,749 khmer/_khmermodule.cc:2385:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:50,749 2385 | }; 2025-09-07T23:23:50,749 | ^ 2025-09-07T23:23:50,750 khmer/_khmermodule.cc:2350:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,750 2350 | "Hashbits", sizeof(khmer_KHashbitsObject), 2025-09-07T23:23:50,750 | ^~~~~~~~~~ 2025-09-07T23:23:50,750 | | 2025-09-07T23:23:50,750 | const char* 2025-09-07T23:23:50,750 khmer/_khmermodule.cc:2352:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:50,750 2352 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2025-09-07T23:23:50,750 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,751 | | 2025-09-07T23:23:50,751 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:23:50,751 khmer/_khmermodule.cc:2385:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:23:50,751 2385 | }; 2025-09-07T23:23:50,751 | ^ 2025-09-07T23:23:50,751 | | 2025-09-07T23:23:50,751 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:23:50,752 khmer/_khmermodule.cc:2367:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:23:50,752 2367 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2025-09-07T23:23:50,752 khmer/_khmermodule.cc:2368:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:23:50,752 2368 | "hashbits object", /* tp_doc */ 2025-09-07T23:23:50,752 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,752 | | 2025-09-07T23:23:50,752 | const char* 2025-09-07T23:23:50,783 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2025-09-07T23:23:50,783 khmer/_khmermodule.cc:2541:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,783 2541 | return PyInt_FromLong(hashbits->n_tags()); 2025-09-07T23:23:50,783 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,783 | PyLong_FromLong 2025-09-07T23:23:50,808 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2025-09-07T23:23:50,808 khmer/_khmermodule.cc:2563:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,809 2563 | return PyInt_FromLong(1); 2025-09-07T23:23:50,809 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,809 | PyLong_FromLong 2025-09-07T23:23:50,834 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2025-09-07T23:23:50,834 khmer/_khmermodule.cc:2586:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,834 2586 | return PyInt_FromLong(n_consumed); 2025-09-07T23:23:50,834 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,834 | PyLong_FromLong 2025-09-07T23:23:50,871 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2025-09-07T23:23:50,871 khmer/_khmermodule.cc:2693:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:50,872 2693 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2025-09-07T23:23:50,872 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:50,872 | PyLong_AsVoidPtr 2025-09-07T23:23:50,896 khmer/_khmermodule.cc:2703:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:50,897 2703 | return PyInt_FromLong(next_largest); 2025-09-07T23:23:50,897 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,897 | PyLong_FromLong 2025-09-07T23:23:50,918 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2025-09-07T23:23:50,918 khmer/_khmermodule.cc:2719:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:23:50,918 2719 | if (PyInt_Check(arg)) { 2025-09-07T23:23:50,919 | ^~~~~~~~~~~ 2025-09-07T23:23:50,919 | PySet_Check 2025-09-07T23:23:50,940 khmer/_khmermodule.cc:2720:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:23:50,940 2720 | long pos = PyInt_AsLong(arg); 2025-09-07T23:23:50,941 | ^~~~~~~~~~~~ 2025-09-07T23:23:50,941 | PyLong_AsLong 2025-09-07T23:23:50,966 khmer/_khmermodule.cc:2722:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:23:50,967 2722 | } else if (PyString_Check(arg)) { 2025-09-07T23:23:50,967 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:50,967 | PyMapping_Check 2025-09-07T23:23:50,997 khmer/_khmermodule.cc:2723:25: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:23:50,997 2723 | std::string s = PyString_AsString(arg); 2025-09-07T23:23:50,997 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,022 khmer/_khmermodule.cc:2730:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,022 2730 | return PyInt_FromLong(count); 2025-09-07T23:23:51,022 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,022 | PyLong_FromLong 2025-09-07T23:23:51,049 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2025-09-07T23:23:51,049 khmer/_khmermodule.cc:2772:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,049 2772 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2025-09-07T23:23:51,049 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,049 | PyLong_FromLong 2025-09-07T23:23:51,080 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2025-09-07T23:23:51,081 khmer/_khmermodule.cc:2793:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:23:51,081 2793 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:23:51,081 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,081 | PyBytes_FromStringAndSize 2025-09-07T23:23:51,127 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2025-09-07T23:23:51,127 khmer/_khmermodule.cc:2868:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T23:23:51,127 2868 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T23:23:51,127 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,127 | PyLong_FromVoidPtr 2025-09-07T23:23:51,155 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2025-09-07T23:23:51,155 khmer/_khmermodule.cc:2896:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T23:23:51,155 2896 | if (!PyCObject_Check(subset_obj)) { 2025-09-07T23:23:51,156 | ^~~~~~~~~~~~~~~ 2025-09-07T23:23:51,156 | PyODict_Check 2025-09-07T23:23:51,188 khmer/_khmermodule.cc:2902:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,188 2902 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:23:51,188 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,188 | PyLong_AsVoidPtr 2025-09-07T23:23:51,234 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2025-09-07T23:23:51,234 khmer/_khmermodule.cc:3166:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T23:23:51,234 3166 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2025-09-07T23:23:51,234 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,235 | PyLong_FromVoidPtr 2025-09-07T23:23:51,262 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2025-09-07T23:23:51,262 khmer/_khmermodule.cc:3179:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T23:23:51,262 3179 | if (!PyCObject_Check(ppi_obj)) { 2025-09-07T23:23:51,262 | ^~~~~~~~~~~~~~~ 2025-09-07T23:23:51,263 | PyODict_Check 2025-09-07T23:23:51,295 khmer/_khmermodule.cc:3185:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,295 3185 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2025-09-07T23:23:51,295 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,295 | PyLong_AsVoidPtr 2025-09-07T23:23:51,322 khmer/_khmermodule.cc:3191:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,322 3191 | return PyInt_FromLong(p); 2025-09-07T23:23:51,322 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,322 | PyLong_FromLong 2025-09-07T23:23:51,355 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2025-09-07T23:23:51,355 khmer/_khmermodule.cc:3306:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,355 3306 | return PyInt_FromLong(n_partitions); 2025-09-07T23:23:51,355 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,356 | PyLong_FromLong 2025-09-07T23:23:51,384 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2025-09-07T23:23:51,384 khmer/_khmermodule.cc:3337:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,384 3337 | return PyInt_FromLong(n_singletons); 2025-09-07T23:23:51,384 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,385 | PyLong_FromLong 2025-09-07T23:23:51,424 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2025-09-07T23:23:51,425 khmer/_khmermodule.cc:3436:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,425 3436 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:23:51,425 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,425 | PyLong_AsVoidPtr 2025-09-07T23:23:51,458 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2025-09-07T23:23:51,458 khmer/_khmermodule.cc:3453:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,458 3453 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:23:51,458 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,458 | PyLong_AsVoidPtr 2025-09-07T23:23:51,520 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T23:23:51,521 khmer/_khmermodule.cc:3564:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,521 3564 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:23:51,521 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,521 | PyLong_AsVoidPtr 2025-09-07T23:23:51,555 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T23:23:51,555 khmer/_khmermodule.cc:3595:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T23:23:51,556 3595 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T23:23:51,556 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,556 | PyLong_FromVoidPtr 2025-09-07T23:23:51,581 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2025-09-07T23:23:51,582 khmer/_khmermodule.cc:3624:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,582 3624 | return PyInt_FromLong(d); 2025-09-07T23:23:51,582 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,582 | PyLong_FromLong 2025-09-07T23:23:51,615 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2025-09-07T23:23:51,615 khmer/_khmermodule.cc:3640:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,615 3640 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T23:23:51,615 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,615 | PyLong_AsVoidPtr 2025-09-07T23:23:51,648 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2025-09-07T23:23:51,648 khmer/_khmermodule.cc:3666:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,649 3666 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T23:23:51,649 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,649 | PyLong_AsVoidPtr 2025-09-07T23:23:51,682 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T23:23:51,682 khmer/_khmermodule.cc:3687:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:23:51,682 3687 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:23:51,682 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,683 | PyLong_AsVoidPtr 2025-09-07T23:23:51,709 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2025-09-07T23:23:51,709 khmer/_khmermodule.cc:3723:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,709 3723 | return PyInt_FromLong(p1); 2025-09-07T23:23:51,709 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,709 | PyLong_FromLong 2025-09-07T23:23:51,735 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2025-09-07T23:23:51,735 khmer/_khmermodule.cc:3740:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,735 3740 | return PyInt_FromLong(partition_id); 2025-09-07T23:23:51,735 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,735 | PyLong_FromLong 2025-09-07T23:23:51,766 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2025-09-07T23:23:51,767 khmer/_khmermodule.cc:3882:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,767 3882 | return PyInt_FromLong(k); 2025-09-07T23:23:51,767 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,767 | PyLong_FromLong 2025-09-07T23:23:51,809 In file included from /usr/include/python3.13/Python.h:63: 2025-09-07T23:23:51,810 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2025-09-07T23:23:51,810 khmer/_khmermodule.cc:3926:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:23:51,810 3926 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T23:23:51,810 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,810 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T23:23:51,810 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T23:23:51,810 | ^~~~ 2025-09-07T23:23:51,811 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T23:23:51,811 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T23:23:51,811 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,811 khmer/_khmermodule.cc:3926:9: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T23:23:51,811 3926 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T23:23:51,811 | ^~~~~~~~~~~~~~~ 2025-09-07T23:23:51,842 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2025-09-07T23:23:51,842 khmer/_khmermodule.cc:4033:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:23:51,842 4033 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2025-09-07T23:23:51,842 | ^~~~~~~~~~~~~ 2025-09-07T23:23:51,842 | PyCMethod 2025-09-07T23:23:51,906 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2025-09-07T23:23:51,906 khmer/_khmermodule.cc:4260:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:23:51,906 4260 | return Py_FindMethod(khmer_subset_methods, obj, name); 2025-09-07T23:23:51,906 | ^~~~~~~~~~~~~ 2025-09-07T23:23:51,906 | PyCMethod 2025-09-07T23:23:51,956 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2025-09-07T23:23:51,956 khmer/_khmermodule.cc:4612:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:23:51,956 4612 | return PyInt_FromLong(labelhash->n_labels()); 2025-09-07T23:23:51,956 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:51,957 | PyLong_FromLong 2025-09-07T23:23:51,957 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:51,958 khmer/_khmermodule.cc:4667:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:51,958 4667 | }; 2025-09-07T23:23:51,958 | ^ 2025-09-07T23:23:51,958 khmer/_khmermodule.cc:4631:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:51,958 4631 | "_LabelHash", /* tp_name */ 2025-09-07T23:23:51,958 | ^~~~~~~~~~~~ 2025-09-07T23:23:51,958 | | 2025-09-07T23:23:51,958 | const char* 2025-09-07T23:23:51,959 khmer/_khmermodule.cc:4634:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:51,959 4634 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2025-09-07T23:23:51,959 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,959 | | 2025-09-07T23:23:51,959 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:23:51,959 khmer/_khmermodule.cc:4649:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:23:51,959 4649 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2025-09-07T23:23:51,960 khmer/_khmermodule.cc:4657:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2025-09-07T23:23:51,960 4657 | khmer_labelhash_methods, /* tp_methods */ 2025-09-07T23:23:51,960 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,960 | | 2025-09-07T23:23:51,960 | PyMethodDef* 2025-09-07T23:23:51,991 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2025-09-07T23:23:51,992 khmer/_khmermodule.cc:4740:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:23:51,992 4740 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2025-09-07T23:23:51,992 | ^~~~~~~~~~~~~ 2025-09-07T23:23:51,992 | PyCMethod 2025-09-07T23:23:51,992 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:51,993 khmer/_khmermodule.cc:4777:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:23:51,993 4777 | }; 2025-09-07T23:23:51,993 | ^ 2025-09-07T23:23:51,993 khmer/_khmermodule.cc:4758:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:51,993 4758 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2025-09-07T23:23:51,993 | ^~~~~~~~~~~~~ 2025-09-07T23:23:51,993 | | 2025-09-07T23:23:51,993 | const char* 2025-09-07T23:23:51,994 khmer/_khmermodule.cc:4777:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:23:51,994 4777 | }; 2025-09-07T23:23:51,994 | ^ 2025-09-07T23:23:51,994 | | 2025-09-07T23:23:51,994 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:23:51,994 khmer/_khmermodule.cc:4777:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:23:51,994 4777 | }; 2025-09-07T23:23:51,994 | ^ 2025-09-07T23:23:51,995 | | 2025-09-07T23:23:51,995 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:23:51,995 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:23:51,995 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:23:51,995 | ~~~ 2025-09-07T23:23:51,995 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:23:51,995 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:23:51,995 | | 2025-09-07T23:23:51,996 | int 2025-09-07T23:23:51,996 731 | 0) 2025-09-07T23:23:51,996 | ~~ 2025-09-07T23:23:51,996 khmer/_khmermodule.cc:4775:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:23:51,996 4775 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:23:51,996 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,996 khmer/_khmermodule.cc:4776:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:23:51,997 4776 | "ReadAligner object", /* tp_doc */ 2025-09-07T23:23:51,997 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:51,997 | | 2025-09-07T23:23:51,997 | const char* 2025-09-07T23:23:52,003 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2025-09-07T23:23:52,003 khmer/_khmermodule.cc:4917:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2025-09-07T23:23:52,003 4917 | self->ob_type->tp_free((PyObject*)obj); 2025-09-07T23:23:52,003 | ^~~~~~~ 2025-09-07T23:23:52,036 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2025-09-07T23:23:52,036 khmer/_khmermodule.cc:4992:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:23:52,036 4992 | return PyString_FromString(_revhash(val, ksize).c_str()); 2025-09-07T23:23:52,036 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:52,036 | PyLong_FromString 2025-09-07T23:23:52,037 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:23:52,038 khmer/_khmermodule.cc:5072:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2025-09-07T23:23:52,038 5072 | init_khmer(void) 2025-09-07T23:23:52,038 | ^~~~~~~~~~ 2025-09-07T23:23:52,038 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2025-09-07T23:23:52,038 33 | void init_khmer(); 2025-09-07T23:23:52,038 | ^~~~~~~~~~ 2025-09-07T23:23:52,038 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2025-09-07T23:23:52,039 khmer/_khmermodule.cc:5076:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:23:52,039 5076 | khmer_ConfigType.ob_type = &PyType_Type; 2025-09-07T23:23:52,039 | ^~~~~~~ 2025-09-07T23:23:52,039 khmer/_khmermodule.cc:5077:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:23:52,039 5077 | khmer_KTableType.ob_type = &PyType_Type; 2025-09-07T23:23:52,039 | ^~~~~~~ 2025-09-07T23:23:52,039 khmer/_khmermodule.cc:5078:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:23:52,039 5078 | khmer_KCountingHashType.ob_type = &PyType_Type; 2025-09-07T23:23:52,040 | ^~~~~~~ 2025-09-07T23:23:52,040 khmer/_khmermodule.cc:5085:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:23:52,040 5085 | return; 2025-09-07T23:23:52,040 | ^~~~~~ 2025-09-07T23:23:52,040 khmer/_khmermodule.cc:5092:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:23:52,041 5092 | return; 2025-09-07T23:23:52,041 | ^~~~~~ 2025-09-07T23:23:52,067 khmer/_khmermodule.cc:5096:9: error: ‘Py_InitModule3’ was not declared in this scope 2025-09-07T23:23:52,068 5096 | m = Py_InitModule3( "_khmer", KhmerMethods, 2025-09-07T23:23:52,068 | ^~~~~~~~~~~~~~ 2025-09-07T23:23:52,068 khmer/_khmermodule.cc:5099:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:23:52,068 5099 | return; 2025-09-07T23:23:52,068 | ^~~~~~ 2025-09-07T23:23:52,068 khmer/_khmermodule.cc:5104:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:23:52,069 5104 | return; 2025-09-07T23:23:52,069 | ^~~~~~ 2025-09-07T23:23:52,069 khmer/_khmermodule.cc:5111:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:23:52,069 5111 | return; 2025-09-07T23:23:52,069 | ^~~~~~ 2025-09-07T23:23:52,069 khmer/_khmermodule.cc:5117:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:23:52,069 5117 | return; 2025-09-07T23:23:52,069 | ^~~~~~ 2025-09-07T23:23:52,070 khmer/_khmermodule.cc:5120:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:23:52,070 5120 | return; 2025-09-07T23:23:52,070 | ^~~~~~ 2025-09-07T23:23:53,081 khmer/_khmermodule.cc:5130:23: warning: control reaches end of non-void function [-Wreturn-type] 2025-09-07T23:23:53,081 5130 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2025-09-07T23:23:53,081 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:23:53,202 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-07T23:23:53,350 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:23:53,362 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:23:53,362 exec(compile('"'"''"'"''"'"' 2025-09-07T23:23:53,362 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:23:53,362 # 2025-09-07T23:23:53,362 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:23:53,362 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:23:53,362 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:23:53,362 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:23:53,362 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:23:53,362 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:23:53,362 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:23:53,362 import os, sys, tokenize, traceback 2025-09-07T23:23:53,362 2025-09-07T23:23:53,362 try: 2025-09-07T23:23:53,362 import setuptools 2025-09-07T23:23:53,362 except ImportError: 2025-09-07T23:23:53,362 print( 2025-09-07T23:23:53,362 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:23:53,362 "the build environment with exception:", 2025-09-07T23:23:53,362 file=sys.stderr, 2025-09-07T23:23:53,362 ) 2025-09-07T23:23:53,362 traceback.print_exc() 2025-09-07T23:23:53,362 sys.exit(1) 2025-09-07T23:23:53,362 2025-09-07T23:23:53,362 __file__ = %r 2025-09-07T23:23:53,362 sys.argv[0] = __file__ 2025-09-07T23:23:53,362 2025-09-07T23:23:53,362 if os.path.exists(__file__): 2025-09-07T23:23:53,362 filename = __file__ 2025-09-07T23:23:53,362 with tokenize.open(__file__) as f: 2025-09-07T23:23:53,362 setup_py_code = f.read() 2025-09-07T23:23:53,362 else: 2025-09-07T23:23:53,362 filename = "" 2025-09-07T23:23:53,362 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:23:53,362 2025-09-07T23:23:53,362 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:23:53,362 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-dtpn24f6[/] 2025-09-07T23:23:53,363 [bold magenta]cwd[/]: /tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/ 2025-09-07T23:23:53,363 Building wheel for khmer (setup.py): finished with status 'error' 2025-09-07T23:23:53,364 ERROR: Failed building wheel for khmer 2025-09-07T23:23:53,365 Running setup.py clean for khmer 2025-09-07T23:23:53,366 Running command python setup.py clean 2025-09-07T23:23:53,990 /tmp/pip-wheel-adl4vvsn/khmer_0e4a327f68174b93b35722e990b66bc1/ez_setup.py:124: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T23:23:53,991 import pkg_resources 2025-09-07T23:23:54,596 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T23:23:54,596 !! 2025-09-07T23:23:54,597 ******************************************************************************** 2025-09-07T23:23:54,597 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T23:23:54,597 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T23:23:54,597 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T23:23:54,597 or your builds will no longer be supported. 2025-09-07T23:23:54,597 ******************************************************************************** 2025-09-07T23:23:54,598 !! 2025-09-07T23:23:54,598 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T23:23:56,085 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:23:56,086 !! 2025-09-07T23:23:56,086 ******************************************************************************** 2025-09-07T23:23:56,086 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:23:56,086 License :: OSI Approved :: BSD License 2025-09-07T23:23:56,086 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:23:56,086 ******************************************************************************** 2025-09-07T23:23:56,087 !! 2025-09-07T23:23:56,087 self._finalize_license_expression() 2025-09-07T23:23:56,206 running clean 2025-09-07T23:23:56,313 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:23:56,313 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:23:56,314 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:23:56,314 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:23:56,314 removing 'build' 2025-09-07T23:23:56,474 Failed to build khmer 2025-09-07T23:23:56,475 ERROR: Failed to build one or more wheels 2025-09-07T23:23:56,476 Exception information: 2025-09-07T23:23:56,476 Traceback (most recent call last): 2025-09-07T23:23:56,476 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:23:56,476 status = _inner_run() 2025-09-07T23:23:56,476 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:23:56,476 return self.run(options, args) 2025-09-07T23:23:56,476 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:23:56,476 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:23:56,476 return func(self, options, args) 2025-09-07T23:23:56,476 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:23:56,476 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:23:56,476 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:23:56,480 Removed build tracker: '/tmp/pip-build-tracker-36l6k2f4'