2025-09-07T22:55:25,384 Created temporary directory: /tmp/pip-build-tracker-0d2uwxle 2025-09-07T22:55:25,384 Initialized build tracking at /tmp/pip-build-tracker-0d2uwxle 2025-09-07T22:55:25,385 Created build tracker: /tmp/pip-build-tracker-0d2uwxle 2025-09-07T22:55:25,385 Entered build tracker: /tmp/pip-build-tracker-0d2uwxle 2025-09-07T22:55:25,385 Created temporary directory: /tmp/pip-wheel-s5d6unbu 2025-09-07T22:55:25,388 Created temporary directory: /tmp/pip-ephem-wheel-cache-4hylb9kb 2025-09-07T22:55:25,448 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T22:55:25,450 2 location(s) to search for versions of khmer: 2025-09-07T22:55:25,450 * https://pypi.org/simple/khmer/ 2025-09-07T22:55:25,450 * https://www.piwheels.org/simple/khmer/ 2025-09-07T22:55:25,451 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2025-09-07T22:55:25,451 Getting page https://pypi.org/simple/khmer/ 2025-09-07T22:55:25,452 Found index url https://pypi.org/simple/ 2025-09-07T22:55:25,523 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2025-09-07T22:55:25,529 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/) 2025-09-07T22:55:25,529 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/) 2025-09-07T22:55:25,529 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2025-09-07T22:55:25,529 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 2025-09-07T22:55:25,529 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/) 2025-09-07T22:55:25,530 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2025-09-07T22:55:25,530 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/) 2025-09-07T22:55:25,530 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 2025-09-07T22:55:25,530 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/) 2025-09-07T22:55:25,530 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2025-09-07T22:55:25,531 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/) 2025-09-07T22:55:25,531 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2025-09-07T22:55:25,531 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/) 2025-09-07T22:55:25,531 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 2025-09-07T22:55:25,531 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2025-09-07T22:55:25,532 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/) 2025-09-07T22:55:25,532 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2025-09-07T22:55:25,532 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/) 2025-09-07T22:55:25,532 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2025-09-07T22:55:25,532 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/) 2025-09-07T22:55:25,532 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2025-09-07T22:55:25,533 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/) 2025-09-07T22:55:25,533 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/) 2025-09-07T22:55:25,533 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 2025-09-07T22:55:25,533 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/) 2025-09-07T22:55:25,533 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/) 2025-09-07T22:55:25,533 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/) 2025-09-07T22:55:25,534 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/) 2025-09-07T22:55:25,534 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2025-09-07T22:55:25,534 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2025-09-07T22:55:25,534 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/) 2025-09-07T22:55:25,534 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2025-09-07T22:55:25,535 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/) 2025-09-07T22:55:25,535 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/) 2025-09-07T22:55:25,535 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/) 2025-09-07T22:55:25,535 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/) 2025-09-07T22:55:25,535 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/) 2025-09-07T22:55:25,535 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 2025-09-07T22:55:25,536 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2025-09-07T22:55:25,536 Getting page https://www.piwheels.org/simple/khmer/ 2025-09-07T22:55:25,537 Found index url https://www.piwheels.org/simple/ 2025-09-07T22:55:25,625 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2025-09-07T22:55:25,626 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2025-09-07T22:55:25,626 Skipping link: not a file: https://pypi.org/simple/khmer/ 2025-09-07T22:55:25,654 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2025-09-07T22:55:25,655 Collecting khmer==0.6.1 2025-09-07T22:55:25,657 Created temporary directory: /tmp/pip-unpack-uyyz2uon 2025-09-07T22:55:25,804 Downloading khmer-0.6.1.tar.gz (19.2 MB) 2025-09-07T22:55:30,607 Added khmer==0.6.1 from https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz to build tracker '/tmp/pip-build-tracker-0d2uwxle' 2025-09-07T22:55:30,609 Running setup.py (path:/tmp/pip-wheel-s5d6unbu/khmer_8c11474a384a490f9834329aec5a95ca/setup.py) egg_info for package khmer 2025-09-07T22:55:30,610 Created temporary directory: /tmp/pip-pip-egg-info-xeb7ip3d 2025-09-07T22:55:30,610 Preparing metadata (setup.py): started 2025-09-07T22:55:30,611 Running command python setup.py egg_info 2025-09-07T22:55:31,142 /tmp/pip-wheel-s5d6unbu/khmer_8c11474a384a490f9834329aec5a95ca/ez_setup.py:114: 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. 2025-09-07T22:55:31,142 import pkg_resources 2025-09-07T22:55:31,656 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T22:55:31,656 !! 2025-09-07T22:55:31,657 ******************************************************************************** 2025-09-07T22:55:31,657 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T22:55:31,657 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T22:55:31,657 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T22:55:31,657 or your builds will no longer be supported. 2025-09-07T22:55:31,657 ******************************************************************************** 2025-09-07T22:55:31,657 !! 2025-09-07T22:55:31,657 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T22:55:41,047 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T22:55:41,047 !! 2025-09-07T22:55:41,047 ******************************************************************************** 2025-09-07T22:55:41,048 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T22:55:41,048 License :: OSI Approved :: BSD License 2025-09-07T22:55:41,048 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T22:55:41,048 ******************************************************************************** 2025-09-07T22:55:41,048 !! 2025-09-07T22:55:41,048 self._finalize_license_expression() 2025-09-07T22:55:41,125 running egg_info 2025-09-07T22:55:41,204 creating /tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info 2025-09-07T22:55:41,204 writing /tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info/PKG-INFO 2025-09-07T22:55:41,205 writing dependency_links to /tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info/dependency_links.txt 2025-09-07T22:55:41,205 writing requirements to /tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info/requires.txt 2025-09-07T22:55:41,206 writing top-level names to /tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info/top_level.txt 2025-09-07T22:55:41,206 writing manifest file '/tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info/SOURCES.txt' 2025-09-07T22:55:41,536 reading manifest file '/tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info/SOURCES.txt' 2025-09-07T22:55:41,537 reading manifest template 'MANIFEST.in' 2025-09-07T22:55:41,538 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T22:55:41,541 writing manifest file '/tmp/pip-pip-egg-info-xeb7ip3d/khmer.egg-info/SOURCES.txt' 2025-09-07T22:55:41,669 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T22:55:41,673 Source in /tmp/pip-wheel-s5d6unbu/khmer_8c11474a384a490f9834329aec5a95ca has version 0.6.1, which satisfies requirement khmer==0.6.1 from https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz 2025-09-07T22:55:41,674 Removed khmer==0.6.1 from https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz from build tracker '/tmp/pip-build-tracker-0d2uwxle' 2025-09-07T22:55:41,677 Created temporary directory: /tmp/pip-unpack-vd7kfsnn 2025-09-07T22:55:41,678 Created temporary directory: /tmp/pip-unpack-azipe4wf 2025-09-07T22:55:41,678 Building wheels for collected packages: khmer 2025-09-07T22:55:41,679 Created temporary directory: /tmp/pip-wheel-10zt04sa 2025-09-07T22:55:41,680 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 2025-09-07T22:55:41,681 Building wheel for khmer (setup.py): started 2025-09-07T22:55:41,681 Destination directory: /tmp/pip-wheel-10zt04sa 2025-09-07T22:55:41,681 Running command python setup.py bdist_wheel 2025-09-07T22:55:42,252 /tmp/pip-wheel-s5d6unbu/khmer_8c11474a384a490f9834329aec5a95ca/ez_setup.py:114: 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. 2025-09-07T22:55:42,252 import pkg_resources 2025-09-07T22:55:42,756 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T22:55:42,756 !! 2025-09-07T22:55:42,757 ******************************************************************************** 2025-09-07T22:55:42,757 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T22:55:42,757 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T22:55:42,757 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T22:55:42,757 or your builds will no longer be supported. 2025-09-07T22:55:42,757 ******************************************************************************** 2025-09-07T22:55:42,757 !! 2025-09-07T22:55:42,757 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T22:55:44,422 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T22:55:44,422 !! 2025-09-07T22:55:44,422 ******************************************************************************** 2025-09-07T22:55:44,422 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T22:55:44,422 License :: OSI Approved :: BSD License 2025-09-07T22:55:44,422 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T22:55:44,423 ******************************************************************************** 2025-09-07T22:55:44,423 !! 2025-09-07T22:55:44,423 self._finalize_license_expression() 2025-09-07T22:55:44,423 running bdist_wheel 2025-09-07T22:55:44,741 running build 2025-09-07T22:55:44,742 running build_py 2025-09-07T22:55:44,826 creating build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,827 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,827 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,828 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,828 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,829 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,829 copying khmer/counting_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,830 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:44,830 running egg_info 2025-09-07T22:55:44,911 writing khmer.egg-info/PKG-INFO 2025-09-07T22:55:44,912 writing dependency_links to khmer.egg-info/dependency_links.txt 2025-09-07T22:55:44,912 writing requirements to khmer.egg-info/requires.txt 2025-09-07T22:55:44,913 writing top-level names to khmer.egg-info/top_level.txt 2025-09-07T22:55:45,003 reading manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T22:55:45,046 reading manifest template 'MANIFEST.in' 2025-09-07T22:55:45,047 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T22:55:45,066 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T22:55:45,078 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T22:55:45,079 running build_ext 2025-09-07T22:55:45,141 Checking for gcc... 2025-09-07T22:55:45,225 Checking for shared library support... 2025-09-07T22:55:45,411 Building shared library libz.so.1.2.3 with gcc. 2025-09-07T22:55:45,510 Checking for unistd.h... Yes. 2025-09-07T22:55:45,635 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf() 2025-09-07T22:55:45,840 Checking for vsnprintf() in stdio.h... Yes. 2025-09-07T22:55:45,946 Checking for return value of vsnprintf()... Yes. 2025-09-07T22:55:46,037 Checking for errno.h... Yes. 2025-09-07T22:55:46,145 Checking for mmap support... Yes. 2025-09-07T22:55:46,179 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2025-09-07T22:55:46,493 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2025-09-07T22:55:46,616 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2025-09-07T22:55:47,073 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2025-09-07T22:55:48,199 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2025-09-07T22:55:48,310 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2025-09-07T22:55:49,918 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2025-09-07T22:55:51,425 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2025-09-07T22:55:51,567 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2025-09-07T22:55:53,411 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2025-09-07T22:55:54,288 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2025-09-07T22:55:54,818 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2025-09-07T22:55:55,315 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 2025-09-07T22:55:55,505 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2025-09-07T22:55:56,494 In function ‘mainSimpleSort’, 2025-09-07T22:55:56,494 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2025-09-07T22:55:56,494 inlined from ‘mainSort’ at blocksort.c:897:19: 2025-09-07T22:55:56,495 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T22:55:56,495 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T22:55:56,495 | ^~~~~~~ 2025-09-07T22:55:56,495 blocksort.c:514:18: note: called from here 2025-09-07T22:55:56,496 514 | while ( mainGtU ( 2025-09-07T22:55:56,496 | ^~~~~~~~~ 2025-09-07T22:55:56,496 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T22:55:56,496 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:55:56,496 516 | ) ) { 2025-09-07T22:55:56,496 | ~ 2025-09-07T22:55:56,496 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T22:55:56,497 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T22:55:56,497 | ^~~~~~~ 2025-09-07T22:55:56,497 blocksort.c:528:18: note: called from here 2025-09-07T22:55:56,497 528 | while ( mainGtU ( 2025-09-07T22:55:56,497 | ^~~~~~~~~ 2025-09-07T22:55:56,497 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T22:55:56,498 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:55:56,498 530 | ) ) { 2025-09-07T22:55:56,498 | ~ 2025-09-07T22:55:56,498 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T22:55:56,498 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T22:55:56,498 | ^~~~~~~ 2025-09-07T22:55:56,499 blocksort.c:542:18: note: called from here 2025-09-07T22:55:56,499 542 | while ( mainGtU ( 2025-09-07T22:55:56,499 | ^~~~~~~~~ 2025-09-07T22:55:56,499 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T22:55:56,499 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:55:56,499 544 | ) ) { 2025-09-07T22:55:56,499 | ~ 2025-09-07T22:55:57,376 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2025-09-07T22:55:57,866 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2025-09-07T22:55:57,980 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2025-09-07T22:55:58,102 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2025-09-07T22:56:02,720 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2025-09-07T22:56:05,368 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2025-09-07T22:56:07,356 #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 2025-09-07T22:56:07,359 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2025-09-07T22:56:07,361 #rm -f libbz2.so.1.0 2025-09-07T22:56:07,363 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2025-09-07T22:56:07,373 building 'khmer._khmermodule' extension 2025-09-07T22:56:07,377 creating build/temp.linux-armv7l-cpython-313/khmer 2025-09-07T22:56:07,378 creating build/temp.linux-armv7l-cpython-313/lib 2025-09-07T22:56:07,380 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.13 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-cpython-313/khmer/_khmermodule.o -O3 2025-09-07T22:56:09,903 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2025-09-07T22:56:09,903 khmer/_khmermodule.cc:81:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2025-09-07T22:56:09,904 81 | tobj.ob_size = 0; 2025-09-07T22:56:09,904 | ^~~~~~~ 2025-09-07T22:56:09,904 khmer/_khmermodule.cc:82:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T22:56:09,904 82 | tobj.ob_type = &PyType_Type; 2025-09-07T22:56:09,904 | ^~~~~~~ 2025-09-07T22:56:09,908 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:56:09,908 khmer/_khmermodule.cc:217:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:09,908 217 | }; 2025-09-07T22:56:09,909 | ^ 2025-09-07T22:56:09,909 khmer/_khmermodule.cc:198:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:09,909 198 | "Config", sizeof(khmer_ConfigObject), 2025-09-07T22:56:09,909 | ^~~~~~~~ 2025-09-07T22:56:09,909 | | 2025-09-07T22:56:09,909 | const char* 2025-09-07T22:56:09,909 khmer/_khmermodule.cc:217:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:09,909 217 | }; 2025-09-07T22:56:09,909 | ^ 2025-09-07T22:56:09,910 | | 2025-09-07T22:56:09,910 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:56:09,910 khmer/_khmermodule.cc:217:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:56:09,910 217 | }; 2025-09-07T22:56:09,910 | ^ 2025-09-07T22:56:09,910 | | 2025-09-07T22:56:09,910 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:56:09,910 In file included from /usr/include/python3.13/Python.h:72, 2025-09-07T22:56:09,910 from khmer/_khmermodule.cc:13: 2025-09-07T22:56:09,910 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:56:09,911 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:56:09,911 | ~~~ 2025-09-07T22:56:09,911 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:56:09,911 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:56:09,911 | | 2025-09-07T22:56:09,911 | int 2025-09-07T22:56:09,911 731 | 0) 2025-09-07T22:56:09,911 | ~~ 2025-09-07T22:56:09,912 khmer/_khmermodule.cc:215:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:56:09,912 215 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:56:09,912 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:09,912 khmer/_khmermodule.cc:216:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:56:09,912 216 | "config object", /* tp_doc */ 2025-09-07T22:56:09,912 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:09,912 | | 2025-09-07T22:56:09,912 | const char* 2025-09-07T22:56:09,933 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2025-09-07T22:56:09,933 khmer/_khmermodule.cc:300:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T22:56:09,933 300 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2025-09-07T22:56:09,933 | ^~~~~~~~~~~~~~~~ 2025-09-07T22:56:09,933 | PyLong_FromSize_t 2025-09-07T22:56:09,957 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2025-09-07T22:56:09,957 khmer/_khmermodule.cc:358:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T22:56:09,957 358 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2025-09-07T22:56:09,957 | ^~~~~~~~~~~~~~~~ 2025-09-07T22:56:09,957 | PyLong_FromSize_t 2025-09-07T22:56:09,980 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2025-09-07T22:56:09,980 khmer/_khmermodule.cc:386:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T22:56:09,980 386 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2025-09-07T22:56:09,980 | ^~~~~~~~~~~~~~~~ 2025-09-07T22:56:09,980 | PyLong_FromSize_t 2025-09-07T22:56:10,003 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2025-09-07T22:56:10,003 khmer/_khmermodule.cc:434:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:56:10,003 434 | return Py_FindMethod(khmer_config_methods, obj, name); 2025-09-07T22:56:10,003 | ^~~~~~~~~~~~~ 2025-09-07T22:56:10,003 | PyCMethod 2025-09-07T22:56:10,003 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:56:10,004 khmer/_khmermodule.cc:450:62: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:10,004 450 | static PyTypeObject Read_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T22:56:10,004 | ^ 2025-09-07T22:56:10,029 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2025-09-07T22:56:10,029 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:56:10,029 472 | PyString_FromString( \ 2025-09-07T22:56:10,029 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,029 khmer/_khmermodule.cc:480:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:56:10,030 480 | { return KHMER_READ_STRING_GETTER( self, name ); } 2025-09-07T22:56:10,030 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,054 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2025-09-07T22:56:10,054 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:56:10,054 472 | PyString_FromString( \ 2025-09-07T22:56:10,055 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,055 khmer/_khmermodule.cc:486:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:56:10,055 486 | { return KHMER_READ_STRING_GETTER( self, sequence ); } 2025-09-07T22:56:10,055 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,079 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2025-09-07T22:56:10,080 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:56:10,080 472 | PyString_FromString( \ 2025-09-07T22:56:10,080 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,080 khmer/_khmermodule.cc:492:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:56:10,080 492 | { return KHMER_READ_STRING_GETTER( self, accuracy ); } 2025-09-07T22:56:10,080 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,105 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2025-09-07T22:56:10,105 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:56:10,105 472 | PyString_FromString( \ 2025-09-07T22:56:10,105 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,105 khmer/_khmermodule.cc:498:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:56:10,105 498 | { return KHMER_READ_STRING_GETTER( self, annotations ); } 2025-09-07T22:56:10,106 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,106 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:56:10,107 khmer/_khmermodule.cc:550:68: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:10,107 550 | static PyTypeObject ReadParser_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T22:56:10,107 | ^ 2025-09-07T22:56:10,107 khmer/_khmermodule.cc:551:74: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:10,107 551 | static PyTypeObject ReadPairIterator_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T22:56:10,107 | ^ 2025-09-07T22:56:10,144 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2025-09-07T22:56:10,144 khmer/_khmermodule.cc:816:9: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,144 816 | PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ) 2025-09-07T22:56:10,144 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,144 | PyLong_FromLong 2025-09-07T22:56:10,171 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2025-09-07T22:56:10,171 khmer/_khmermodule.cc:959:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:56:10,171 959 | return PyString_FromString(khmer::_revhash(val, ktable->ksize()).c_str()); 2025-09-07T22:56:10,172 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,172 | PyLong_FromString 2025-09-07T22:56:10,192 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2025-09-07T22:56:10,193 khmer/_khmermodule.cc:985:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,193 985 | return PyInt_FromLong(1); 2025-09-07T22:56:10,193 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,193 | PyLong_FromLong 2025-09-07T22:56:10,214 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2025-09-07T22:56:10,214 khmer/_khmermodule.cc:1013:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,214 1013 | return PyInt_FromLong(n_consumed); 2025-09-07T22:56:10,215 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,215 | PyLong_FromLong 2025-09-07T22:56:10,232 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2025-09-07T22:56:10,232 khmer/_khmermodule.cc:1032:14: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:56:10,232 1032 | } else if (PyInt_Check(arg)) { 2025-09-07T22:56:10,232 | ^~~~~~~~~~~ 2025-09-07T22:56:10,233 | PySet_Check 2025-09-07T22:56:10,250 khmer/_khmermodule.cc:1033:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:56:10,250 1033 | long pos = PyInt_AsLong(arg); 2025-09-07T22:56:10,250 | ^~~~~~~~~~~~ 2025-09-07T22:56:10,251 | PyLong_AsLong 2025-09-07T22:56:10,272 khmer/_khmermodule.cc:1035:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:56:10,272 1035 | } else if (PyString_Check(arg)) { 2025-09-07T22:56:10,272 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,273 | PyMapping_Check 2025-09-07T22:56:10,298 khmer/_khmermodule.cc:1036:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:56:10,298 1036 | std::string s = PyString_AsString(arg); 2025-09-07T22:56:10,298 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,319 khmer/_khmermodule.cc:1040:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,319 1040 | return PyInt_FromLong(count); 2025-09-07T22:56:10,319 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,319 | PyLong_FromLong 2025-09-07T22:56:10,341 khmer/_khmermodule.cc: In function ‘PyObject* ktable__getitem__(PyObject*, Py_ssize_t)’: 2025-09-07T22:56:10,341 khmer/_khmermodule.cc:1050:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,341 1050 | return PyInt_FromLong(count); 2025-09-07T22:56:10,341 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,342 | PyLong_FromLong 2025-09-07T22:56:10,367 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2025-09-07T22:56:10,367 khmer/_khmermodule.cc:1058:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:56:10,367 1058 | char * kmer_str = PyString_AsString( val ); 2025-09-07T22:56:10,368 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,386 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2025-09-07T22:56:10,386 khmer/_khmermodule.cc:1076:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:56:10,386 1076 | if (PyInt_Check(arg)) { 2025-09-07T22:56:10,386 | ^~~~~~~~~~~ 2025-09-07T22:56:10,386 | PySet_Check 2025-09-07T22:56:10,404 khmer/_khmermodule.cc:1077:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:56:10,404 1077 | long pos = PyInt_AsLong(arg); 2025-09-07T22:56:10,404 | ^~~~~~~~~~~~ 2025-09-07T22:56:10,405 | PyLong_AsLong 2025-09-07T22:56:10,427 khmer/_khmermodule.cc:1079:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:56:10,428 1079 | } else if (PyString_Check(arg)) { 2025-09-07T22:56:10,428 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,428 | PyMapping_Check 2025-09-07T22:56:10,453 khmer/_khmermodule.cc:1080:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:56:10,453 1080 | std::string s = PyString_AsString(arg); 2025-09-07T22:56:10,453 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,475 khmer/_khmermodule.cc: In function ‘PyObject* ktable_max_hash(PyObject*, PyObject*)’: 2025-09-07T22:56:10,475 khmer/_khmermodule.cc:1097:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,475 1097 | return PyInt_FromLong(ktable->max_hash()); 2025-09-07T22:56:10,475 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,475 | PyLong_FromLong 2025-09-07T22:56:10,496 khmer/_khmermodule.cc: In function ‘PyObject* ktable_n_entries(PyObject*, PyObject*)’: 2025-09-07T22:56:10,496 khmer/_khmermodule.cc:1109:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,496 1109 | return PyInt_FromLong(ktable->n_entries()); 2025-09-07T22:56:10,496 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,496 | PyLong_FromLong 2025-09-07T22:56:10,517 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2025-09-07T22:56:10,517 khmer/_khmermodule.cc:1129:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,517 1129 | return PyInt_FromLong(ktable->ksize()); 2025-09-07T22:56:10,517 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,517 | PyLong_FromLong 2025-09-07T22:56:10,540 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2025-09-07T22:56:10,541 khmer/_khmermodule.cc:1175:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:56:10,541 1175 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2025-09-07T22:56:10,541 | ^~~~~~~~~~~~~ 2025-09-07T22:56:10,541 | PyCMethod 2025-09-07T22:56:10,541 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:56:10,541 khmer/_khmermodule.cc:1215:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:10,541 1215 | }; 2025-09-07T22:56:10,541 | ^ 2025-09-07T22:56:10,542 khmer/_khmermodule.cc:1196:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:10,542 1196 | "KTable", sizeof(khmer_KTableObject), 2025-09-07T22:56:10,542 | ^~~~~~~~ 2025-09-07T22:56:10,542 | | 2025-09-07T22:56:10,542 | const char* 2025-09-07T22:56:10,542 khmer/_khmermodule.cc:1215:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:10,542 1215 | }; 2025-09-07T22:56:10,542 | ^ 2025-09-07T22:56:10,542 | | 2025-09-07T22:56:10,542 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:56:10,543 khmer/_khmermodule.cc:1215:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:56:10,543 1215 | }; 2025-09-07T22:56:10,543 | ^ 2025-09-07T22:56:10,543 | | 2025-09-07T22:56:10,543 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:56:10,543 khmer/_khmermodule.cc:1205:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2025-09-07T22:56:10,543 1205 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2025-09-07T22:56:10,543 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,543 | | 2025-09-07T22:56:10,543 | PySequenceMethods* 2025-09-07T22:56:10,544 khmer/_khmermodule.cc:1333:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:10,545 1333 | }; 2025-09-07T22:56:10,545 | ^ 2025-09-07T22:56:10,545 khmer/_khmermodule.cc:1314:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:10,545 1314 | "KHashbits", sizeof(khmer_KHashbitsObject), 2025-09-07T22:56:10,545 | ^~~~~~~~~~~ 2025-09-07T22:56:10,545 | | 2025-09-07T22:56:10,545 | const char* 2025-09-07T22:56:10,545 khmer/_khmermodule.cc:1333:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:10,545 1333 | }; 2025-09-07T22:56:10,546 | ^ 2025-09-07T22:56:10,546 | | 2025-09-07T22:56:10,546 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:56:10,546 khmer/_khmermodule.cc:1333:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:56:10,546 1333 | }; 2025-09-07T22:56:10,546 | ^ 2025-09-07T22:56:10,546 | | 2025-09-07T22:56:10,546 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:56:10,546 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:56:10,546 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:56:10,547 | ~~~ 2025-09-07T22:56:10,547 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:56:10,547 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:56:10,547 | | 2025-09-07T22:56:10,547 | int 2025-09-07T22:56:10,547 731 | 0) 2025-09-07T22:56:10,547 | ~~ 2025-09-07T22:56:10,547 khmer/_khmermodule.cc:1331:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:56:10,547 1331 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:56:10,548 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,548 khmer/_khmermodule.cc:1332:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:56:10,548 1332 | "hashbits object", /* tp_doc */ 2025-09-07T22:56:10,548 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,548 | | 2025-09-07T22:56:10,548 | const char* 2025-09-07T22:56:10,568 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_occupied(PyObject*, PyObject*)’: 2025-09-07T22:56:10,568 khmer/_khmermodule.cc:1389:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,568 1389 | return PyInt_FromLong(n); 2025-09-07T22:56:10,568 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,568 | PyLong_FromLong 2025-09-07T22:56:10,589 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_entries(PyObject*, PyObject*)’: 2025-09-07T22:56:10,589 khmer/_khmermodule.cc:1401:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,589 1401 | return PyInt_FromLong(counting->n_entries()); 2025-09-07T22:56:10,589 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,590 | PyLong_FromLong 2025-09-07T22:56:10,610 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2025-09-07T22:56:10,611 khmer/_khmermodule.cc:1423:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,611 1423 | return PyInt_FromLong(1); 2025-09-07T22:56:10,611 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,611 | PyLong_FromLong 2025-09-07T22:56:10,632 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2025-09-07T22:56:10,632 khmer/_khmermodule.cc:1440:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,632 1440 | return PyInt_FromLong(0); 2025-09-07T22:56:10,632 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,633 | PyLong_FromLong 2025-09-07T22:56:10,656 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2025-09-07T22:56:10,656 khmer/_khmermodule.cc:1526:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,656 1526 | return PyInt_FromLong(n_consumed); 2025-09-07T22:56:10,656 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,656 | PyLong_FromLong 2025-09-07T22:56:10,678 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2025-09-07T22:56:10,678 khmer/_khmermodule.cc:1558:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,678 1558 | return PyInt_FromLong(n_consumed); 2025-09-07T22:56:10,678 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,678 | PyLong_FromLong 2025-09-07T22:56:10,700 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2025-09-07T22:56:10,700 khmer/_khmermodule.cc:1581:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,700 1581 | return PyInt_FromLong(N); 2025-09-07T22:56:10,700 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,700 | PyLong_FromLong 2025-09-07T22:56:10,721 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2025-09-07T22:56:10,722 khmer/_khmermodule.cc:1604:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,722 1604 | return PyInt_FromLong(N); 2025-09-07T22:56:10,722 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,722 | PyLong_FromLong 2025-09-07T22:56:10,742 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2025-09-07T22:56:10,743 khmer/_khmermodule.cc:1707:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:56:10,743 1707 | if (PyInt_Check(arg)) { 2025-09-07T22:56:10,743 | ^~~~~~~~~~~ 2025-09-07T22:56:10,743 | PySet_Check 2025-09-07T22:56:10,761 khmer/_khmermodule.cc:1708:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:56:10,761 1708 | long pos = PyInt_AsLong(arg); 2025-09-07T22:56:10,761 | ^~~~~~~~~~~~ 2025-09-07T22:56:10,761 | PyLong_AsLong 2025-09-07T22:56:10,783 khmer/_khmermodule.cc:1710:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:56:10,783 1710 | } else if (PyString_Check(arg)) { 2025-09-07T22:56:10,783 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,783 | PyMapping_Check 2025-09-07T22:56:10,809 khmer/_khmermodule.cc:1711:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:56:10,809 1711 | std::string s = PyString_AsString(arg); 2025-09-07T22:56:10,809 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,830 khmer/_khmermodule.cc:1715:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,830 1715 | return PyInt_FromLong(count); 2025-09-07T22:56:10,830 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,830 | PyLong_FromLong 2025-09-07T22:56:10,852 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2025-09-07T22:56:10,852 khmer/_khmermodule.cc:1731:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,852 1731 | return PyInt_FromLong(count); 2025-09-07T22:56:10,852 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,852 | PyLong_FromLong 2025-09-07T22:56:10,879 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2025-09-07T22:56:10,879 khmer/_khmermodule.cc:1755:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:56:10,880 1755 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:56:10,880 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,880 | PyBytes_FromStringAndSize 2025-09-07T22:56:10,907 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2025-09-07T22:56:10,907 khmer/_khmermodule.cc:1782:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:56:10,907 1782 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:56:10,907 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:10,907 | PyBytes_FromStringAndSize 2025-09-07T22:56:10,930 In file included from /usr/include/python3.13/Python.h:63: 2025-09-07T22:56:10,930 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution(PyObject*, PyObject*)’: 2025-09-07T22:56:10,930 khmer/_khmermodule.cc:1814:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,930 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:56:10,930 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,930 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:56:10,931 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:56:10,931 | ^~~~ 2025-09-07T22:56:10,931 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:56:10,931 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:56:10,931 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,931 khmer/_khmermodule.cc:1814:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:56:10,931 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:56:10,931 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:10,952 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution_with_reads_parser(PyObject*, PyObject*)’: 2025-09-07T22:56:10,953 khmer/_khmermodule.cc:1850:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,953 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:56:10,953 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,953 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:56:10,953 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:56:10,953 | ^~~~ 2025-09-07T22:56:10,953 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:56:10,953 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:56:10,953 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,953 khmer/_khmermodule.cc:1850:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:56:10,954 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:56:10,954 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:10,975 khmer/_khmermodule.cc: In function ‘PyObject* hash_fasta_count_kmers_by_position(PyObject*, PyObject*)’: 2025-09-07T22:56:10,975 khmer/_khmermodule.cc:1880:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:10,975 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2025-09-07T22:56:10,975 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,975 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:56:10,975 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:56:10,975 | ^~~~ 2025-09-07T22:56:10,975 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:56:10,975 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:56:10,976 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:10,976 khmer/_khmermodule.cc:1880:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:56:10,976 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2025-09-07T22:56:10,976 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:11,000 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2025-09-07T22:56:11,000 khmer/_khmermodule.cc:1987:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,000 1987 | return PyInt_FromLong(k); 2025-09-07T22:56:11,000 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,000 | PyLong_FromLong 2025-09-07T22:56:11,022 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_hashsizes(PyObject*, PyObject*)’: 2025-09-07T22:56:11,022 khmer/_khmermodule.cc:2004:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,022 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:56:11,022 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,022 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:56:11,022 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:56:11,022 | ^~~~ 2025-09-07T22:56:11,022 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:56:11,022 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:56:11,023 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,023 khmer/_khmermodule.cc:2004:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:56:11,023 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:56:11,023 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:11,046 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2025-09-07T22:56:11,046 khmer/_khmermodule.cc:2052:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:56:11,046 2052 | return Py_FindMethod(khmer_counting_methods, obj, name); 2025-09-07T22:56:11,046 | ^~~~~~~~~~~~~ 2025-09-07T22:56:11,046 | PyCMethod 2025-09-07T22:56:11,046 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:56:11,046 khmer/_khmermodule.cc:2079:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:11,046 2079 | }; 2025-09-07T22:56:11,047 | ^ 2025-09-07T22:56:11,047 khmer/_khmermodule.cc:2060:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:11,047 2060 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2025-09-07T22:56:11,047 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:11,047 | | 2025-09-07T22:56:11,047 | const char* 2025-09-07T22:56:11,047 khmer/_khmermodule.cc:2079:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:11,047 2079 | }; 2025-09-07T22:56:11,047 | ^ 2025-09-07T22:56:11,047 | | 2025-09-07T22:56:11,048 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:56:11,048 khmer/_khmermodule.cc:2079:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:56:11,048 2079 | }; 2025-09-07T22:56:11,048 | ^ 2025-09-07T22:56:11,048 | | 2025-09-07T22:56:11,048 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:56:11,048 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:56:11,048 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:56:11,048 | ~~~ 2025-09-07T22:56:11,048 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:56:11,048 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:56:11,049 | | 2025-09-07T22:56:11,049 | int 2025-09-07T22:56:11,049 731 | 0) 2025-09-07T22:56:11,049 | ~~ 2025-09-07T22:56:11,049 khmer/_khmermodule.cc:2077:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:56:11,049 2077 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:56:11,049 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,049 khmer/_khmermodule.cc:2078:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:56:11,049 2078 | "counting hash object", /* tp_doc */ 2025-09-07T22:56:11,049 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,050 | | 2025-09-07T22:56:11,050 | const char* 2025-09-07T22:56:11,070 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_unique_kmers(PyObject*, PyObject*)’: 2025-09-07T22:56:11,071 khmer/_khmermodule.cc:2147:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,071 2147 | return PyInt_FromLong(n); 2025-09-07T22:56:11,071 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,071 | PyLong_FromLong 2025-09-07T22:56:11,094 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_occupied(PyObject*, PyObject*)’: 2025-09-07T22:56:11,094 khmer/_khmermodule.cc:2209:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,094 2209 | return PyInt_FromLong(n); 2025-09-07T22:56:11,094 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,094 | PyLong_FromLong 2025-09-07T22:56:11,115 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2025-09-07T22:56:11,115 khmer/_khmermodule.cc:2221:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,116 2221 | return PyInt_FromLong(hashbits->n_tags()); 2025-09-07T22:56:11,116 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,116 | PyLong_FromLong 2025-09-07T22:56:11,137 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2025-09-07T22:56:11,137 khmer/_khmermodule.cc:2243:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,137 2243 | return PyInt_FromLong(1); 2025-09-07T22:56:11,137 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,137 | PyLong_FromLong 2025-09-07T22:56:11,159 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2025-09-07T22:56:11,159 khmer/_khmermodule.cc:2266:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,159 2266 | return PyInt_FromLong(n_consumed); 2025-09-07T22:56:11,159 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,159 | PyLong_FromLong 2025-09-07T22:56:11,191 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2025-09-07T22:56:11,191 khmer/_khmermodule.cc:2377:43: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,191 2377 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2025-09-07T22:56:11,191 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,192 | PyLong_AsVoidPtr 2025-09-07T22:56:11,212 khmer/_khmermodule.cc:2386:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,212 2386 | return PyInt_FromLong(next_largest); 2025-09-07T22:56:11,212 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,213 | PyLong_FromLong 2025-09-07T22:56:11,231 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2025-09-07T22:56:11,231 khmer/_khmermodule.cc:2423:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:56:11,231 2423 | if (PyInt_Check(arg)) { 2025-09-07T22:56:11,231 | ^~~~~~~~~~~ 2025-09-07T22:56:11,231 | PySet_Check 2025-09-07T22:56:11,249 khmer/_khmermodule.cc:2424:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:56:11,249 2424 | long pos = PyInt_AsLong(arg); 2025-09-07T22:56:11,250 | ^~~~~~~~~~~~ 2025-09-07T22:56:11,250 | PyLong_AsLong 2025-09-07T22:56:11,271 khmer/_khmermodule.cc:2426:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:56:11,272 2426 | } else if (PyString_Check(arg)) { 2025-09-07T22:56:11,272 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,272 | PyMapping_Check 2025-09-07T22:56:11,298 khmer/_khmermodule.cc:2427:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:56:11,298 2427 | std::string s = PyString_AsString(arg); 2025-09-07T22:56:11,298 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,319 khmer/_khmermodule.cc:2431:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,319 2431 | return PyInt_FromLong(count); 2025-09-07T22:56:11,319 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,319 | PyLong_FromLong 2025-09-07T22:56:11,341 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_calc_connected_graph_size(PyObject*, PyObject*)’: 2025-09-07T22:56:11,341 khmer/_khmermodule.cc:2459:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,341 2459 | return PyInt_FromLong(size); 2025-09-07T22:56:11,341 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,341 | PyLong_FromLong 2025-09-07T22:56:11,362 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2025-09-07T22:56:11,363 khmer/_khmermodule.cc:2474:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,363 2474 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2025-09-07T22:56:11,363 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,363 | PyLong_FromLong 2025-09-07T22:56:11,390 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_degree(PyObject*, PyObject*)’: 2025-09-07T22:56:11,390 khmer/_khmermodule.cc:2496:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:56:11,390 2496 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:56:11,390 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,391 | PyBytes_FromStringAndSize 2025-09-07T22:56:11,418 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_sodd(PyObject*, PyObject*)’: 2025-09-07T22:56:11,418 khmer/_khmermodule.cc:2522:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:56:11,418 2522 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:56:11,418 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,418 | PyBytes_FromStringAndSize 2025-09-07T22:56:11,446 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2025-09-07T22:56:11,446 khmer/_khmermodule.cc:2547:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:56:11,446 2547 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:56:11,446 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,446 | PyBytes_FromStringAndSize 2025-09-07T22:56:11,485 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2025-09-07T22:56:11,485 khmer/_khmermodule.cc:2625:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T22:56:11,485 2625 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T22:56:11,486 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,486 | PyLong_FromVoidPtr 2025-09-07T22:56:11,510 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2025-09-07T22:56:11,510 khmer/_khmermodule.cc:2654:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T22:56:11,510 2654 | if (!PyCObject_Check(subset_obj)) { 2025-09-07T22:56:11,510 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:11,510 | PyODict_Check 2025-09-07T22:56:11,538 khmer/_khmermodule.cc:2659:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,538 2659 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:56:11,538 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,538 | PyLong_AsVoidPtr 2025-09-07T22:56:11,578 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2025-09-07T22:56:11,578 khmer/_khmermodule.cc:2951:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T22:56:11,579 2951 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2025-09-07T22:56:11,579 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,579 | PyLong_FromVoidPtr 2025-09-07T22:56:11,603 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2025-09-07T22:56:11,603 khmer/_khmermodule.cc:2964:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T22:56:11,603 2964 | if (!PyCObject_Check(ppi_obj)) { 2025-09-07T22:56:11,604 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:11,604 | PyODict_Check 2025-09-07T22:56:11,633 khmer/_khmermodule.cc:2969:33: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,633 2969 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2025-09-07T22:56:11,633 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,633 | PyLong_AsVoidPtr 2025-09-07T22:56:11,654 khmer/_khmermodule.cc:2975:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,654 2975 | return PyInt_FromLong(p); 2025-09-07T22:56:11,654 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,654 | PyLong_FromLong 2025-09-07T22:56:11,680 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2025-09-07T22:56:11,680 khmer/_khmermodule.cc:3093:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,680 3093 | return PyInt_FromLong(n_partitions); 2025-09-07T22:56:11,681 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,681 | PyLong_FromLong 2025-09-07T22:56:11,702 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2025-09-07T22:56:11,703 khmer/_khmermodule.cc:3124:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,703 3124 | return PyInt_FromLong(n_singletons); 2025-09-07T22:56:11,703 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,703 | PyLong_FromLong 2025-09-07T22:56:11,734 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2025-09-07T22:56:11,735 khmer/_khmermodule.cc:3227:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,735 3227 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:56:11,735 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,735 | PyLong_AsVoidPtr 2025-09-07T22:56:11,763 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2025-09-07T22:56:11,764 khmer/_khmermodule.cc:3245:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,764 3245 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:56:11,764 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,764 | PyLong_AsVoidPtr 2025-09-07T22:56:11,814 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T22:56:11,815 khmer/_khmermodule.cc:3347:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,815 3347 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:56:11,815 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,815 | PyLong_AsVoidPtr 2025-09-07T22:56:11,845 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T22:56:11,845 khmer/_khmermodule.cc:3379:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T22:56:11,845 3379 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T22:56:11,845 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,845 | PyLong_FromVoidPtr 2025-09-07T22:56:11,867 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2025-09-07T22:56:11,867 khmer/_khmermodule.cc:3409:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,867 3409 | return PyInt_FromLong(d); 2025-09-07T22:56:11,867 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,868 | PyLong_FromLong 2025-09-07T22:56:11,896 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2025-09-07T22:56:11,896 khmer/_khmermodule.cc:3425:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,896 3425 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T22:56:11,896 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,897 | PyLong_AsVoidPtr 2025-09-07T22:56:11,925 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2025-09-07T22:56:11,925 khmer/_khmermodule.cc:3451:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,926 3451 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T22:56:11,926 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,926 | PyLong_AsVoidPtr 2025-09-07T22:56:11,955 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T22:56:11,955 khmer/_khmermodule.cc:3472:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:56:11,955 3472 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:56:11,955 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:11,955 | PyLong_AsVoidPtr 2025-09-07T22:56:11,977 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2025-09-07T22:56:11,978 khmer/_khmermodule.cc:3510:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:11,978 3510 | return PyInt_FromLong(p1); 2025-09-07T22:56:11,978 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:11,978 | PyLong_FromLong 2025-09-07T22:56:11,999 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2025-09-07T22:56:11,999 khmer/_khmermodule.cc:3527:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:12,000 3527 | return PyInt_FromLong(partition_id); 2025-09-07T22:56:12,000 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:12,000 | PyLong_FromLong 2025-09-07T22:56:12,031 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_density_explosion(PyObject*, PyObject*)’: 2025-09-07T22:56:12,031 khmer/_khmermodule.cc:3651:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:56:12,031 3651 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:56:12,032 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:12,032 | PyBytes_FromStringAndSize 2025-09-07T22:56:12,054 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2025-09-07T22:56:12,054 khmer/_khmermodule.cc:3696:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:12,054 3696 | return PyInt_FromLong(k); 2025-09-07T22:56:12,054 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:12,055 | PyLong_FromLong 2025-09-07T22:56:12,076 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_hashsizes(PyObject*, PyObject*)’: 2025-09-07T22:56:12,076 khmer/_khmermodule.cc:3713:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:56:12,077 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:56:12,077 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:12,077 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:56:12,077 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:56:12,077 | ^~~~ 2025-09-07T22:56:12,077 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:56:12,077 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:56:12,077 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:12,077 khmer/_khmermodule.cc:3713:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:56:12,077 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:56:12,078 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:12,111 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2025-09-07T22:56:12,112 khmer/_khmermodule.cc:3736:27: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:56:12,112 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T22:56:12,112 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:12,112 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:56:12,112 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:56:12,112 | ^~~~ 2025-09-07T22:56:12,112 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:56:12,112 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:56:12,112 | ^~~~~~~~~~~~~~ 2025-09-07T22:56:12,113 khmer/_khmermodule.cc:3736:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:56:12,113 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T22:56:12,113 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:12,139 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2025-09-07T22:56:12,139 khmer/_khmermodule.cc:3847:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:56:12,139 3847 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2025-09-07T22:56:12,139 | ^~~~~~~~~~~~~ 2025-09-07T22:56:12,139 | PyCMethod 2025-09-07T22:56:12,167 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2025-09-07T22:56:12,167 khmer/_khmermodule.cc:3922:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:56:12,167 3922 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2025-09-07T22:56:12,167 | ^~~~~~~~~~~~~ 2025-09-07T22:56:12,167 | PyCMethod 2025-09-07T22:56:12,167 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:56:12,168 khmer/_khmermodule.cc:3959:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:56:12,168 3959 | }; 2025-09-07T22:56:12,168 | ^ 2025-09-07T22:56:12,168 khmer/_khmermodule.cc:3940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:12,168 3940 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2025-09-07T22:56:12,168 | ^~~~~~~~~~~~~ 2025-09-07T22:56:12,168 | | 2025-09-07T22:56:12,168 | const char* 2025-09-07T22:56:12,168 khmer/_khmermodule.cc:3959:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:56:12,168 3959 | }; 2025-09-07T22:56:12,169 | ^ 2025-09-07T22:56:12,169 | | 2025-09-07T22:56:12,169 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:56:12,169 khmer/_khmermodule.cc:3959:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:56:12,169 3959 | }; 2025-09-07T22:56:12,169 | ^ 2025-09-07T22:56:12,169 | | 2025-09-07T22:56:12,169 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:56:12,169 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:56:12,169 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:56:12,170 | ~~~ 2025-09-07T22:56:12,170 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:56:12,170 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:56:12,170 | | 2025-09-07T22:56:12,170 | int 2025-09-07T22:56:12,170 731 | 0) 2025-09-07T22:56:12,170 | ~~ 2025-09-07T22:56:12,170 khmer/_khmermodule.cc:3957:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:56:12,170 3957 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:56:12,170 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:12,171 khmer/_khmermodule.cc:3958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:56:12,171 3958 | "ReadAligner object", /* tp_doc */ 2025-09-07T22:56:12,171 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:12,171 | | 2025-09-07T22:56:12,171 | const char* 2025-09-07T22:56:12,202 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2025-09-07T22:56:12,203 khmer/_khmermodule.cc:4139:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:56:12,203 4139 | return PyString_FromString(khmer::_revhash(val, ksize).c_str()); 2025-09-07T22:56:12,203 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:12,203 | PyLong_FromString 2025-09-07T22:56:12,204 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:56:12,204 khmer/_khmermodule.cc:4195:17: error: expected constructor, destructor, or type conversion before ‘init_khmer’ 2025-09-07T22:56:12,204 4195 | DL_EXPORT(void) init_khmer(void) 2025-09-07T22:56:12,204 | ^~~~~~~~~~ 2025-09-07T22:56:12,874 khmer/_khmermodule.cc:4162:20: warning: ‘KhmerMethods’ defined but not used [-Wunused-variable] 2025-09-07T22:56:12,874 4162 | static PyMethodDef KhmerMethods[] = { 2025-09-07T22:56:12,874 | ^~~~~~~~~~~~ 2025-09-07T22:56:12,874 khmer/_khmermodule.cc:845:1: warning: ‘void khmer::python::_init_ReadPairIterator_Type()’ defined but not used [-Wunused-function] 2025-09-07T22:56:12,875 845 | _init_ReadPairIterator_Type( ) 2025-09-07T22:56:12,875 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:12,875 khmer/_khmermodule.cc:789:1: warning: ‘void khmer::python::_init_ReadParser_Type()’ defined but not used [-Wunused-function] 2025-09-07T22:56:12,875 789 | _init_ReadParser_Type( ) 2025-09-07T22:56:12,875 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:56:12,875 khmer/_khmermodule.cc:525:1: warning: ‘void khmer::python::_init_Read_Type()’ defined but not used [-Wunused-function] 2025-09-07T22:56:12,875 525 | _init_Read_Type( ) 2025-09-07T22:56:12,875 | ^~~~~~~~~~~~~~~ 2025-09-07T22:56:12,875 khmer/_khmermodule.cc:134:18: warning: ‘KhmerError’ defined but not used [-Wunused-variable] 2025-09-07T22:56:12,876 134 | static PyObject *KhmerError; 2025-09-07T22:56:12,876 | ^~~~~~~~~~ 2025-09-07T22:56:12,892 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-07T22:56:13,019 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T22:56:13,030 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T22:56:13,030 exec(compile('"'"''"'"''"'"' 2025-09-07T22:56:13,030 # This is -- a caller that pip uses to run setup.py 2025-09-07T22:56:13,030 # 2025-09-07T22:56:13,030 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T22:56:13,030 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T22:56:13,030 # - It provides a clear error message when setuptools is not installed. 2025-09-07T22:56:13,030 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T22:56:13,030 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T22:56:13,030 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T22:56:13,030 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T22:56:13,030 import os, sys, tokenize, traceback 2025-09-07T22:56:13,030 2025-09-07T22:56:13,030 try: 2025-09-07T22:56:13,030 import setuptools 2025-09-07T22:56:13,030 except ImportError: 2025-09-07T22:56:13,030 print( 2025-09-07T22:56:13,030 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T22:56:13,030 "the build environment with exception:", 2025-09-07T22:56:13,030 file=sys.stderr, 2025-09-07T22:56:13,030 ) 2025-09-07T22:56:13,030 traceback.print_exc() 2025-09-07T22:56:13,030 sys.exit(1) 2025-09-07T22:56:13,030 2025-09-07T22:56:13,030 __file__ = %r 2025-09-07T22:56:13,030 sys.argv[0] = __file__ 2025-09-07T22:56:13,030 2025-09-07T22:56:13,030 if os.path.exists(__file__): 2025-09-07T22:56:13,030 filename = __file__ 2025-09-07T22:56:13,030 with tokenize.open(__file__) as f: 2025-09-07T22:56:13,030 setup_py_code = f.read() 2025-09-07T22:56:13,030 else: 2025-09-07T22:56:13,030 filename = "" 2025-09-07T22:56:13,030 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T22:56:13,030 2025-09-07T22:56:13,030 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T22:56:13,030 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-s5d6unbu/khmer_8c11474a384a490f9834329aec5a95ca/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-10zt04sa[/] 2025-09-07T22:56:13,030 [bold magenta]cwd[/]: /tmp/pip-wheel-s5d6unbu/khmer_8c11474a384a490f9834329aec5a95ca/ 2025-09-07T22:56:13,030 Building wheel for khmer (setup.py): finished with status 'error' 2025-09-07T22:56:13,031 ERROR: Failed building wheel for khmer 2025-09-07T22:56:13,032 Running setup.py clean for khmer 2025-09-07T22:56:13,032 Running command python setup.py clean 2025-09-07T22:56:13,594 /tmp/pip-wheel-s5d6unbu/khmer_8c11474a384a490f9834329aec5a95ca/ez_setup.py:114: 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. 2025-09-07T22:56:13,594 import pkg_resources 2025-09-07T22:56:14,096 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T22:56:14,097 !! 2025-09-07T22:56:14,097 ******************************************************************************** 2025-09-07T22:56:14,097 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T22:56:14,097 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T22:56:14,097 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T22:56:14,097 or your builds will no longer be supported. 2025-09-07T22:56:14,097 ******************************************************************************** 2025-09-07T22:56:14,098 !! 2025-09-07T22:56:14,098 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T22:56:15,753 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T22:56:15,753 !! 2025-09-07T22:56:15,754 ******************************************************************************** 2025-09-07T22:56:15,754 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T22:56:15,754 License :: OSI Approved :: BSD License 2025-09-07T22:56:15,754 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T22:56:15,754 ******************************************************************************** 2025-09-07T22:56:15,754 !! 2025-09-07T22:56:15,754 self._finalize_license_expression() 2025-09-07T22:56:15,832 running clean 2025-09-07T22:56:15,992 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T22:56:15,993 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T22:56:15,993 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T22:56:15,993 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T22:56:15,993 removing 'build' 2025-09-07T22:56:16,115 Failed to build khmer 2025-09-07T22:56:16,116 ERROR: Failed to build one or more wheels 2025-09-07T22:56:16,117 Exception information: 2025-09-07T22:56:16,117 Traceback (most recent call last): 2025-09-07T22:56:16,117 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T22:56:16,117 status = _inner_run() 2025-09-07T22:56:16,117 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T22:56:16,117 return self.run(options, args) 2025-09-07T22:56:16,117 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T22:56:16,117 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T22:56:16,117 return func(self, options, args) 2025-09-07T22:56:16,117 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T22:56:16,117 raise CommandError("Failed to build one or more wheels") 2025-09-07T22:56:16,117 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T22:56:16,121 Removed build tracker: '/tmp/pip-build-tracker-0d2uwxle'