2025-09-07T23:02:34,477 Created temporary directory: /tmp/pip-build-tracker-rwa4bjq8 2025-09-07T23:02:34,478 Initialized build tracking at /tmp/pip-build-tracker-rwa4bjq8 2025-09-07T23:02:34,478 Created build tracker: /tmp/pip-build-tracker-rwa4bjq8 2025-09-07T23:02:34,478 Entered build tracker: /tmp/pip-build-tracker-rwa4bjq8 2025-09-07T23:02:34,478 Created temporary directory: /tmp/pip-wheel-6pnt1stx 2025-09-07T23:02:34,482 Created temporary directory: /tmp/pip-ephem-wheel-cache-sbpen2z3 2025-09-07T23:02:34,537 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:02:34,539 2 location(s) to search for versions of khmer: 2025-09-07T23:02:34,539 * https://pypi.org/simple/khmer/ 2025-09-07T23:02:34,539 * https://www.piwheels.org/simple/khmer/ 2025-09-07T23:02:34,539 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2025-09-07T23:02:34,540 Getting page https://pypi.org/simple/khmer/ 2025-09-07T23:02:34,541 Found index url https://pypi.org/simple/ 2025-09-07T23:02:34,611 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:02:34,616 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/) 2025-09-07T23:02:34,616 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/) 2025-09-07T23:02:34,617 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2025-09-07T23:02:34,617 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 2025-09-07T23:02:34,617 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/) 2025-09-07T23:02:34,617 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2025-09-07T23:02:34,617 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/) 2025-09-07T23:02:34,618 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 2025-09-07T23:02:34,618 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/) 2025-09-07T23:02:34,618 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2025-09-07T23:02:34,618 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/) 2025-09-07T23:02:34,618 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2025-09-07T23:02:34,618 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/) 2025-09-07T23:02:34,619 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 2025-09-07T23:02:34,619 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2025-09-07T23:02:34,619 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/) 2025-09-07T23:02:34,619 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2025-09-07T23:02:34,619 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/) 2025-09-07T23:02:34,619 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2025-09-07T23:02:34,620 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/) 2025-09-07T23:02:34,620 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2025-09-07T23:02:34,620 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/) 2025-09-07T23:02:34,620 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/) 2025-09-07T23:02:34,620 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 2025-09-07T23:02:34,620 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/) 2025-09-07T23:02:34,621 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/) 2025-09-07T23:02:34,621 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/) 2025-09-07T23:02:34,621 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/) 2025-09-07T23:02:34,621 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2025-09-07T23:02:34,621 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2025-09-07T23:02:34,621 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/) 2025-09-07T23:02:34,622 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2025-09-07T23:02:34,622 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/) 2025-09-07T23:02:34,622 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/) 2025-09-07T23:02:34,622 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/) 2025-09-07T23:02:34,622 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/) 2025-09-07T23:02:34,622 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/) 2025-09-07T23:02:34,622 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 2025-09-07T23:02:34,623 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:02:34,623 Getting page https://www.piwheels.org/simple/khmer/ 2025-09-07T23:02:34,624 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:02:34,706 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2025-09-07T23:02:34,707 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:02:34,707 Skipping link: not a file: https://pypi.org/simple/khmer/ 2025-09-07T23:02:34,733 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2025-09-07T23:02:34,734 Collecting khmer==0.7.1 2025-09-07T23:02:34,735 Created temporary directory: /tmp/pip-unpack-sirg4rsv 2025-09-07T23:02:34,883 Downloading khmer-0.7.1.tar.gz (18.9 MB) 2025-09-07T23:02:40,028 Added khmer==0.7.1 from https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz to build tracker '/tmp/pip-build-tracker-rwa4bjq8' 2025-09-07T23:02:40,029 Running setup.py (path:/tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/setup.py) egg_info for package khmer 2025-09-07T23:02:40,029 Created temporary directory: /tmp/pip-pip-egg-info-wo1_1l5s 2025-09-07T23:02:40,029 Preparing metadata (setup.py): started 2025-09-07T23:02:40,030 Running command python setup.py egg_info 2025-09-07T23:02:40,598 /tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/ez_setup.py:130: 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. 2025-09-07T23:02:40,599 import pkg_resources 2025-09-07T23:02:41,048 /tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/versioneer.py:149: SyntaxWarning: invalid escape sequence '\s' 2025-09-07T23:02:41,048 mo = re.search(r'=\s*"(.*)"', line) 2025-09-07T23:02:41,185 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T23:02:41,186 !! 2025-09-07T23:02:41,186 ******************************************************************************** 2025-09-07T23:02:41,186 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T23:02:41,186 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T23:02:41,186 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T23:02:41,186 or your builds will no longer be supported. 2025-09-07T23:02:41,186 ******************************************************************************** 2025-09-07T23:02:41,187 !! 2025-09-07T23:02:41,187 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T23:02:47,471 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:02:47,472 !! 2025-09-07T23:02:47,472 ******************************************************************************** 2025-09-07T23:02:47,472 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:02:47,472 License :: OSI Approved :: BSD License 2025-09-07T23:02:47,472 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:02:47,473 ******************************************************************************** 2025-09-07T23:02:47,473 !! 2025-09-07T23:02:47,473 self._finalize_license_expression() 2025-09-07T23:02:47,549 running egg_info 2025-09-07T23:02:47,624 creating /tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info 2025-09-07T23:02:47,624 writing /tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info/PKG-INFO 2025-09-07T23:02:47,625 writing dependency_links to /tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info/dependency_links.txt 2025-09-07T23:02:47,626 writing requirements to /tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info/requires.txt 2025-09-07T23:02:47,626 writing top-level names to /tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info/top_level.txt 2025-09-07T23:02:47,627 writing manifest file '/tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info/SOURCES.txt' 2025-09-07T23:02:47,859 reading manifest file '/tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info/SOURCES.txt' 2025-09-07T23:02:47,860 reading manifest template 'MANIFEST.in' 2025-09-07T23:02:48,084 no previously-included directories found matching 'doc/doxygen' 2025-09-07T23:02:48,085 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T23:02:48,103 writing manifest file '/tmp/pip-pip-egg-info-wo1_1l5s/khmer.egg-info/SOURCES.txt' 2025-09-07T23:02:48,230 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:02:48,234 Source in /tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb has version 0.7.1, which satisfies requirement khmer==0.7.1 from https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz 2025-09-07T23:02:48,235 Removed khmer==0.7.1 from https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz from build tracker '/tmp/pip-build-tracker-rwa4bjq8' 2025-09-07T23:02:48,239 Created temporary directory: /tmp/pip-unpack-5t09zwku 2025-09-07T23:02:48,239 Created temporary directory: /tmp/pip-unpack-thrh9ke0 2025-09-07T23:02:48,239 Building wheels for collected packages: khmer 2025-09-07T23:02:48,240 Created temporary directory: /tmp/pip-wheel-g3l00re9 2025-09-07T23:02:48,241 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 2025-09-07T23:02:48,242 Building wheel for khmer (setup.py): started 2025-09-07T23:02:48,243 Destination directory: /tmp/pip-wheel-g3l00re9 2025-09-07T23:02:48,243 Running command python setup.py bdist_wheel 2025-09-07T23:02:49,039 /tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/ez_setup.py:130: 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. 2025-09-07T23:02:49,039 import pkg_resources 2025-09-07T23:02:50,238 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T23:02:50,238 !! 2025-09-07T23:02:50,238 ******************************************************************************** 2025-09-07T23:02:50,238 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T23:02:50,238 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T23:02:50,239 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T23:02:50,239 or your builds will no longer be supported. 2025-09-07T23:02:50,239 ******************************************************************************** 2025-09-07T23:02:50,239 !! 2025-09-07T23:02:50,239 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T23:02:51,671 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:02:51,671 !! 2025-09-07T23:02:51,671 ******************************************************************************** 2025-09-07T23:02:51,671 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:02:51,671 License :: OSI Approved :: BSD License 2025-09-07T23:02:51,672 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:02:51,672 ******************************************************************************** 2025-09-07T23:02:51,672 !! 2025-09-07T23:02:51,672 self._finalize_license_expression() 2025-09-07T23:02:51,672 running bdist_wheel 2025-09-07T23:02:51,900 running build 2025-09-07T23:02:51,901 got version from file /tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/khmer/_version.py {'version': '0.7.1', 'full': '1307fa03d7f0f2657ff22a6acad474361a1120f7'} 2025-09-07T23:02:51,901 running build_py 2025-09-07T23:02:51,982 creating build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,982 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,983 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,983 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,984 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,985 copying khmer/counting_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,985 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,986 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,986 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:51,986 running egg_info 2025-09-07T23:02:52,064 creating khmer.egg-info 2025-09-07T23:02:52,064 writing khmer.egg-info/PKG-INFO 2025-09-07T23:02:52,065 writing dependency_links to khmer.egg-info/dependency_links.txt 2025-09-07T23:02:52,066 writing requirements to khmer.egg-info/requires.txt 2025-09-07T23:02:52,066 writing top-level names to khmer.egg-info/top_level.txt 2025-09-07T23:02:52,066 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:02:52,146 reading manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:02:52,147 reading manifest template 'MANIFEST.in' 2025-09-07T23:02:52,371 no previously-included directories found matching 'doc/doxygen' 2025-09-07T23:02:52,373 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T23:02:52,389 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:02:52,398 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:02:52,399 running build_ext 2025-09-07T23:02:52,409 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2025-09-07T23:02:52,728 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2025-09-07T23:02:52,852 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2025-09-07T23:02:53,312 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2025-09-07T23:02:54,437 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2025-09-07T23:02:54,558 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2025-09-07T23:02:56,178 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2025-09-07T23:02:57,689 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2025-09-07T23:02:57,823 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2025-09-07T23:02:59,659 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2025-09-07T23:03:00,548 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2025-09-07T23:03:01,074 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2025-09-07T23:03:01,567 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 2025-09-07T23:03:01,758 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2025-09-07T23:03:02,738 In function ‘mainSimpleSort’, 2025-09-07T23:03:02,739 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2025-09-07T23:03:02,739 inlined from ‘mainSort’ at blocksort.c:897:19: 2025-09-07T23:03:02,739 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T23:03:02,739 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T23:03:02,739 | ^~~~~~~ 2025-09-07T23:03:02,740 blocksort.c:514:18: note: called from here 2025-09-07T23:03:02,740 514 | while ( mainGtU ( 2025-09-07T23:03:02,740 | ^~~~~~~~~ 2025-09-07T23:03:02,740 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T23:03:02,740 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:02,740 516 | ) ) { 2025-09-07T23:03:02,740 | ~ 2025-09-07T23:03:02,741 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T23:03:02,741 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T23:03:02,741 | ^~~~~~~ 2025-09-07T23:03:02,742 blocksort.c:528:18: note: called from here 2025-09-07T23:03:02,742 528 | while ( mainGtU ( 2025-09-07T23:03:02,742 | ^~~~~~~~~ 2025-09-07T23:03:02,742 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T23:03:02,742 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:02,742 530 | ) ) { 2025-09-07T23:03:02,742 | ~ 2025-09-07T23:03:02,743 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T23:03:02,743 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T23:03:02,743 | ^~~~~~~ 2025-09-07T23:03:02,743 blocksort.c:542:18: note: called from here 2025-09-07T23:03:02,743 542 | while ( mainGtU ( 2025-09-07T23:03:02,743 | ^~~~~~~~~ 2025-09-07T23:03:02,744 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T23:03:02,744 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:02,744 544 | ) ) { 2025-09-07T23:03:02,744 | ~ 2025-09-07T23:03:03,610 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2025-09-07T23:03:04,097 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2025-09-07T23:03:04,213 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2025-09-07T23:03:04,328 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2025-09-07T23:03:08,957 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2025-09-07T23:03:11,600 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2025-09-07T23:03:13,587 #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 2025-09-07T23:03:13,590 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2025-09-07T23:03:13,592 #rm -f libbz2.so.1.0 2025-09-07T23:03:13,594 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2025-09-07T23:03:13,604 building 'khmer._khmermodule' extension 2025-09-07T23:03:13,608 creating build/temp.linux-armv7l-cpython-313/khmer 2025-09-07T23:03:13,609 creating build/temp.linux-armv7l-cpython-313/lib 2025-09-07T23:03:13,611 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -DVERSION=0.7.1 -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.13 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-cpython-313/khmer/_khmermodule.o -O3 2025-09-07T23:03:16,136 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2025-09-07T23:03:16,137 khmer/_khmermodule.cc:83:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2025-09-07T23:03:16,137 83 | tobj.ob_size = 0; 2025-09-07T23:03:16,137 | ^~~~~~~ 2025-09-07T23:03:16,137 khmer/_khmermodule.cc:84:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:03:16,137 84 | tobj.ob_type = &PyType_Type; 2025-09-07T23:03:16,137 | ^~~~~~~ 2025-09-07T23:03:16,141 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:03:16,142 khmer/_khmermodule.cc:219:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:16,142 219 | }; 2025-09-07T23:03:16,142 | ^ 2025-09-07T23:03:16,142 khmer/_khmermodule.cc:200:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:16,142 200 | "Config", sizeof(khmer_ConfigObject), 2025-09-07T23:03:16,142 | ^~~~~~~~ 2025-09-07T23:03:16,142 | | 2025-09-07T23:03:16,142 | const char* 2025-09-07T23:03:16,143 khmer/_khmermodule.cc:219:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:16,143 219 | }; 2025-09-07T23:03:16,143 | ^ 2025-09-07T23:03:16,143 | | 2025-09-07T23:03:16,143 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:03:16,143 khmer/_khmermodule.cc:219:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:03:16,143 219 | }; 2025-09-07T23:03:16,143 | ^ 2025-09-07T23:03:16,143 | | 2025-09-07T23:03:16,143 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:03:16,144 In file included from /usr/include/python3.13/Python.h:72, 2025-09-07T23:03:16,144 from khmer/_khmermodule.cc:12: 2025-09-07T23:03:16,144 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:03:16,144 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:03:16,144 | ~~~ 2025-09-07T23:03:16,144 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:03:16,144 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:03:16,145 | | 2025-09-07T23:03:16,145 | int 2025-09-07T23:03:16,145 731 | 0) 2025-09-07T23:03:16,145 | ~~ 2025-09-07T23:03:16,145 khmer/_khmermodule.cc:217:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:03:16,145 217 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:03:16,145 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,145 khmer/_khmermodule.cc:218:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:03:16,145 218 | "config object", /* tp_doc */ 2025-09-07T23:03:16,145 | ^~~~~~~~~~~~~~~ 2025-09-07T23:03:16,146 | | 2025-09-07T23:03:16,146 | const char* 2025-09-07T23:03:16,166 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2025-09-07T23:03:16,166 khmer/_khmermodule.cc:304:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:03:16,166 304 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2025-09-07T23:03:16,166 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,167 | PyLong_FromSize_t 2025-09-07T23:03:16,190 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2025-09-07T23:03:16,190 khmer/_khmermodule.cc:360:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:03:16,190 360 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2025-09-07T23:03:16,190 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,190 | PyLong_FromSize_t 2025-09-07T23:03:16,212 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2025-09-07T23:03:16,213 khmer/_khmermodule.cc:387:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:03:16,213 387 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2025-09-07T23:03:16,213 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,213 | PyLong_FromSize_t 2025-09-07T23:03:16,235 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2025-09-07T23:03:16,236 khmer/_khmermodule.cc:434:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:03:16,236 434 | return Py_FindMethod(khmer_config_methods, obj, name); 2025-09-07T23:03:16,236 | ^~~~~~~~~~~~~ 2025-09-07T23:03:16,236 | PyCMethod 2025-09-07T23:03:16,236 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:03:16,236 khmer/_khmermodule.cc:450:62: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:16,236 450 | static PyTypeObject Read_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T23:03:16,236 | ^ 2025-09-07T23:03:16,261 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2025-09-07T23:03:16,262 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:03:16,262 472 | PyString_FromString( \ 2025-09-07T23:03:16,262 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,262 khmer/_khmermodule.cc:480:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:03:16,262 480 | { return KHMER_READ_STRING_GETTER( self, name ); } 2025-09-07T23:03:16,262 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,287 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2025-09-07T23:03:16,287 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:03:16,287 472 | PyString_FromString( \ 2025-09-07T23:03:16,287 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,288 khmer/_khmermodule.cc:486:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:03:16,288 486 | { return KHMER_READ_STRING_GETTER( self, sequence ); } 2025-09-07T23:03:16,288 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,312 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2025-09-07T23:03:16,312 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:03:16,313 472 | PyString_FromString( \ 2025-09-07T23:03:16,313 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,313 khmer/_khmermodule.cc:492:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:03:16,313 492 | { return KHMER_READ_STRING_GETTER( self, accuracy ); } 2025-09-07T23:03:16,313 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,338 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2025-09-07T23:03:16,338 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:03:16,338 472 | PyString_FromString( \ 2025-09-07T23:03:16,338 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,338 khmer/_khmermodule.cc:498:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T23:03:16,338 498 | { return KHMER_READ_STRING_GETTER( self, annotations ); } 2025-09-07T23:03:16,338 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,339 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:03:16,339 khmer/_khmermodule.cc:550:68: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:16,339 550 | static PyTypeObject ReadParser_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T23:03:16,339 | ^ 2025-09-07T23:03:16,340 khmer/_khmermodule.cc:551:74: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:16,340 551 | static PyTypeObject ReadPairIterator_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T23:03:16,340 | ^ 2025-09-07T23:03:16,377 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2025-09-07T23:03:16,377 khmer/_khmermodule.cc:824:9: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,377 824 | PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ) 2025-09-07T23:03:16,377 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,377 | PyLong_FromLong 2025-09-07T23:03:16,404 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2025-09-07T23:03:16,404 khmer/_khmermodule.cc:965:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:03:16,404 965 | return PyString_FromString(khmer::_revhash(val, ktable->ksize()).c_str()); 2025-09-07T23:03:16,404 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,404 | PyLong_FromString 2025-09-07T23:03:16,425 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2025-09-07T23:03:16,425 khmer/_khmermodule.cc:991:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,425 991 | return PyInt_FromLong(1); 2025-09-07T23:03:16,426 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,426 | PyLong_FromLong 2025-09-07T23:03:16,448 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2025-09-07T23:03:16,449 khmer/_khmermodule.cc:1019:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T23:03:16,449 1019 | return PyInt_FromSize_t(n_consumed); 2025-09-07T23:03:16,449 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,449 | PyLong_FromSize_t 2025-09-07T23:03:16,466 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2025-09-07T23:03:16,466 khmer/_khmermodule.cc:1038:14: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:03:16,467 1038 | } else if (PyInt_Check(arg)) { 2025-09-07T23:03:16,467 | ^~~~~~~~~~~ 2025-09-07T23:03:16,467 | PySet_Check 2025-09-07T23:03:16,484 khmer/_khmermodule.cc:1039:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:03:16,485 1039 | long pos = PyInt_AsLong(arg); 2025-09-07T23:03:16,485 | ^~~~~~~~~~~~ 2025-09-07T23:03:16,485 | PyLong_AsLong 2025-09-07T23:03:16,506 khmer/_khmermodule.cc:1041:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:03:16,506 1041 | } else if (PyString_Check(arg)) { 2025-09-07T23:03:16,507 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,507 | PyMapping_Check 2025-09-07T23:03:16,532 khmer/_khmermodule.cc:1042:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:03:16,532 1042 | std::string s = PyString_AsString(arg); 2025-09-07T23:03:16,532 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,559 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2025-09-07T23:03:16,559 khmer/_khmermodule.cc:1064:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:03:16,559 1064 | char * kmer_str = PyString_AsString( val ); 2025-09-07T23:03:16,559 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,576 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2025-09-07T23:03:16,576 khmer/_khmermodule.cc:1082:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:03:16,577 1082 | if (PyInt_Check(arg)) { 2025-09-07T23:03:16,577 | ^~~~~~~~~~~ 2025-09-07T23:03:16,577 | PySet_Check 2025-09-07T23:03:16,594 khmer/_khmermodule.cc:1083:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:03:16,595 1083 | long pos = PyInt_AsLong(arg); 2025-09-07T23:03:16,595 | ^~~~~~~~~~~~ 2025-09-07T23:03:16,595 | PyLong_AsLong 2025-09-07T23:03:16,616 khmer/_khmermodule.cc:1085:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:03:16,617 1085 | } else if (PyString_Check(arg)) { 2025-09-07T23:03:16,617 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,617 | PyMapping_Check 2025-09-07T23:03:16,642 khmer/_khmermodule.cc:1086:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:03:16,643 1086 | std::string s = PyString_AsString(arg); 2025-09-07T23:03:16,643 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,664 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2025-09-07T23:03:16,665 khmer/_khmermodule.cc:1134:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,665 1134 | return PyInt_FromLong(ktable->ksize()); 2025-09-07T23:03:16,665 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,665 | PyLong_FromLong 2025-09-07T23:03:16,688 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2025-09-07T23:03:16,688 khmer/_khmermodule.cc:1179:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:03:16,688 1179 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2025-09-07T23:03:16,688 | ^~~~~~~~~~~~~ 2025-09-07T23:03:16,689 | PyCMethod 2025-09-07T23:03:16,689 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:03:16,689 khmer/_khmermodule.cc:1219:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:16,689 1219 | }; 2025-09-07T23:03:16,689 | ^ 2025-09-07T23:03:16,689 khmer/_khmermodule.cc:1200:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:16,689 1200 | "KTable", sizeof(khmer_KTableObject), 2025-09-07T23:03:16,689 | ^~~~~~~~ 2025-09-07T23:03:16,689 | | 2025-09-07T23:03:16,689 | const char* 2025-09-07T23:03:16,690 khmer/_khmermodule.cc:1219:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:16,690 1219 | }; 2025-09-07T23:03:16,690 | ^ 2025-09-07T23:03:16,690 | | 2025-09-07T23:03:16,690 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:03:16,690 khmer/_khmermodule.cc:1219:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:03:16,690 1219 | }; 2025-09-07T23:03:16,690 | ^ 2025-09-07T23:03:16,690 | | 2025-09-07T23:03:16,690 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:03:16,691 khmer/_khmermodule.cc:1209:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2025-09-07T23:03:16,691 1209 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2025-09-07T23:03:16,691 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,691 | | 2025-09-07T23:03:16,691 | PySequenceMethods* 2025-09-07T23:03:16,692 khmer/_khmermodule.cc:1346:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:16,693 1346 | }; 2025-09-07T23:03:16,693 | ^ 2025-09-07T23:03:16,693 khmer/_khmermodule.cc:1327:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:16,693 1327 | "KHashbits", sizeof(khmer_KHashbitsObject), 2025-09-07T23:03:16,693 | ^~~~~~~~~~~ 2025-09-07T23:03:16,693 | | 2025-09-07T23:03:16,693 | const char* 2025-09-07T23:03:16,693 khmer/_khmermodule.cc:1346:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:16,693 1346 | }; 2025-09-07T23:03:16,693 | ^ 2025-09-07T23:03:16,694 | | 2025-09-07T23:03:16,694 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:03:16,694 khmer/_khmermodule.cc:1346:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:03:16,694 1346 | }; 2025-09-07T23:03:16,694 | ^ 2025-09-07T23:03:16,694 | | 2025-09-07T23:03:16,694 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:03:16,694 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:03:16,694 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:03:16,695 | ~~~ 2025-09-07T23:03:16,695 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:03:16,695 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:03:16,695 | | 2025-09-07T23:03:16,695 | int 2025-09-07T23:03:16,695 731 | 0) 2025-09-07T23:03:16,695 | ~~ 2025-09-07T23:03:16,695 khmer/_khmermodule.cc:1344:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:03:16,695 1344 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:03:16,695 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,696 khmer/_khmermodule.cc:1345:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:03:16,696 1345 | "hashbits object", /* tp_doc */ 2025-09-07T23:03:16,696 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,696 | | 2025-09-07T23:03:16,696 | const char* 2025-09-07T23:03:16,717 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2025-09-07T23:03:16,717 khmer/_khmermodule.cc:1435:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,717 1435 | return PyInt_FromLong(1); 2025-09-07T23:03:16,717 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,717 | PyLong_FromLong 2025-09-07T23:03:16,738 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2025-09-07T23:03:16,738 khmer/_khmermodule.cc:1452:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,739 1452 | return PyInt_FromLong(0); 2025-09-07T23:03:16,739 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,739 | PyLong_FromLong 2025-09-07T23:03:16,762 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2025-09-07T23:03:16,762 khmer/_khmermodule.cc:1538:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,762 1538 | return PyInt_FromLong(n_consumed); 2025-09-07T23:03:16,762 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,762 | PyLong_FromLong 2025-09-07T23:03:16,784 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2025-09-07T23:03:16,784 khmer/_khmermodule.cc:1570:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,784 1570 | return PyInt_FromLong(n_consumed); 2025-09-07T23:03:16,784 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,784 | PyLong_FromLong 2025-09-07T23:03:16,806 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2025-09-07T23:03:16,806 khmer/_khmermodule.cc:1593:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,806 1593 | return PyInt_FromLong(N); 2025-09-07T23:03:16,806 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,806 | PyLong_FromLong 2025-09-07T23:03:16,827 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2025-09-07T23:03:16,828 khmer/_khmermodule.cc:1616:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,828 1616 | return PyInt_FromLong(N); 2025-09-07T23:03:16,828 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,828 | PyLong_FromLong 2025-09-07T23:03:16,848 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2025-09-07T23:03:16,848 khmer/_khmermodule.cc:1719:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:03:16,849 1719 | if (PyInt_Check(arg)) { 2025-09-07T23:03:16,849 | ^~~~~~~~~~~ 2025-09-07T23:03:16,849 | PySet_Check 2025-09-07T23:03:16,866 khmer/_khmermodule.cc:1720:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:03:16,867 1720 | long pos = PyInt_AsLong(arg); 2025-09-07T23:03:16,867 | ^~~~~~~~~~~~ 2025-09-07T23:03:16,867 | PyLong_AsLong 2025-09-07T23:03:16,889 khmer/_khmermodule.cc:1722:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:03:16,889 1722 | } else if (PyString_Check(arg)) { 2025-09-07T23:03:16,889 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,889 | PyMapping_Check 2025-09-07T23:03:16,915 khmer/_khmermodule.cc:1723:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:03:16,915 1723 | std::string s = PyString_AsString(arg); 2025-09-07T23:03:16,915 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,936 khmer/_khmermodule.cc:1727:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,936 1727 | return PyInt_FromLong(count); 2025-09-07T23:03:16,936 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,936 | PyLong_FromLong 2025-09-07T23:03:16,958 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2025-09-07T23:03:16,958 khmer/_khmermodule.cc:1743:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:16,958 1743 | return PyInt_FromLong(count); 2025-09-07T23:03:16,958 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:16,958 | PyLong_FromLong 2025-09-07T23:03:16,985 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2025-09-07T23:03:16,985 khmer/_khmermodule.cc:1767:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:03:16,985 1767 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:03:16,985 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:16,985 | PyBytes_FromStringAndSize 2025-09-07T23:03:17,013 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2025-09-07T23:03:17,013 khmer/_khmermodule.cc:1797:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:03:17,013 1797 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:03:17,013 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,013 | PyBytes_FromStringAndSize 2025-09-07T23:03:17,041 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2025-09-07T23:03:17,041 khmer/_khmermodule.cc:2013:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,041 2013 | return PyInt_FromLong(k); 2025-09-07T23:03:17,042 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,042 | PyLong_FromLong 2025-09-07T23:03:17,066 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2025-09-07T23:03:17,066 khmer/_khmermodule.cc:2078:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:03:17,066 2078 | return Py_FindMethod(khmer_counting_methods, obj, name); 2025-09-07T23:03:17,066 | ^~~~~~~~~~~~~ 2025-09-07T23:03:17,066 | PyCMethod 2025-09-07T23:03:17,066 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:03:17,067 khmer/_khmermodule.cc:2105:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:17,067 2105 | }; 2025-09-07T23:03:17,067 | ^ 2025-09-07T23:03:17,067 khmer/_khmermodule.cc:2086:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:17,067 2086 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2025-09-07T23:03:17,067 | ^~~~~~~~~~~~~~~ 2025-09-07T23:03:17,067 | | 2025-09-07T23:03:17,067 | const char* 2025-09-07T23:03:17,067 khmer/_khmermodule.cc:2105:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:17,067 2105 | }; 2025-09-07T23:03:17,068 | ^ 2025-09-07T23:03:17,068 | | 2025-09-07T23:03:17,068 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:03:17,068 khmer/_khmermodule.cc:2105:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:03:17,068 2105 | }; 2025-09-07T23:03:17,068 | ^ 2025-09-07T23:03:17,068 | | 2025-09-07T23:03:17,068 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:03:17,068 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:03:17,068 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:03:17,069 | ~~~ 2025-09-07T23:03:17,069 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:03:17,069 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:03:17,069 | | 2025-09-07T23:03:17,069 | int 2025-09-07T23:03:17,069 731 | 0) 2025-09-07T23:03:17,069 | ~~ 2025-09-07T23:03:17,069 khmer/_khmermodule.cc:2103:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:03:17,069 2103 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:03:17,069 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,070 khmer/_khmermodule.cc:2104:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:03:17,070 2104 | "counting hash object", /* tp_doc */ 2025-09-07T23:03:17,070 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,070 | | 2025-09-07T23:03:17,070 | const char* 2025-09-07T23:03:17,093 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2025-09-07T23:03:17,094 khmer/_khmermodule.cc:2259:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,094 2259 | return PyInt_FromLong(hashbits->n_tags()); 2025-09-07T23:03:17,094 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,094 | PyLong_FromLong 2025-09-07T23:03:17,115 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2025-09-07T23:03:17,115 khmer/_khmermodule.cc:2281:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,115 2281 | return PyInt_FromLong(1); 2025-09-07T23:03:17,116 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,116 | PyLong_FromLong 2025-09-07T23:03:17,137 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2025-09-07T23:03:17,137 khmer/_khmermodule.cc:2304:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,137 2304 | return PyInt_FromLong(n_consumed); 2025-09-07T23:03:17,137 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,137 | PyLong_FromLong 2025-09-07T23:03:17,169 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2025-09-07T23:03:17,169 khmer/_khmermodule.cc:2410:43: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,169 2410 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2025-09-07T23:03:17,169 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,169 | PyLong_AsVoidPtr 2025-09-07T23:03:17,190 khmer/_khmermodule.cc:2419:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,190 2419 | return PyInt_FromLong(next_largest); 2025-09-07T23:03:17,190 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,190 | PyLong_FromLong 2025-09-07T23:03:17,208 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2025-09-07T23:03:17,209 khmer/_khmermodule.cc:2455:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T23:03:17,209 2455 | if (PyInt_Check(arg)) { 2025-09-07T23:03:17,209 | ^~~~~~~~~~~ 2025-09-07T23:03:17,209 | PySet_Check 2025-09-07T23:03:17,227 khmer/_khmermodule.cc:2456:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T23:03:17,227 2456 | long pos = PyInt_AsLong(arg); 2025-09-07T23:03:17,227 | ^~~~~~~~~~~~ 2025-09-07T23:03:17,228 | PyLong_AsLong 2025-09-07T23:03:17,249 khmer/_khmermodule.cc:2458:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T23:03:17,250 2458 | } else if (PyString_Check(arg)) { 2025-09-07T23:03:17,250 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,250 | PyMapping_Check 2025-09-07T23:03:17,276 khmer/_khmermodule.cc:2459:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T23:03:17,276 2459 | std::string s = PyString_AsString(arg); 2025-09-07T23:03:17,276 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,297 khmer/_khmermodule.cc:2463:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,297 2463 | return PyInt_FromLong(count); 2025-09-07T23:03:17,297 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,297 | PyLong_FromLong 2025-09-07T23:03:17,320 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2025-09-07T23:03:17,320 khmer/_khmermodule.cc:2506:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,320 2506 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2025-09-07T23:03:17,320 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,320 | PyLong_FromLong 2025-09-07T23:03:17,347 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_degree(PyObject*, PyObject*)’: 2025-09-07T23:03:17,347 khmer/_khmermodule.cc:2528:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:03:17,348 2528 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:03:17,348 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,348 | PyBytes_FromStringAndSize 2025-09-07T23:03:17,375 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_sodd(PyObject*, PyObject*)’: 2025-09-07T23:03:17,375 khmer/_khmermodule.cc:2557:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:03:17,376 2557 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:03:17,376 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,376 | PyBytes_FromStringAndSize 2025-09-07T23:03:17,403 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2025-09-07T23:03:17,403 khmer/_khmermodule.cc:2585:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:03:17,403 2585 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:03:17,403 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,404 | PyBytes_FromStringAndSize 2025-09-07T23:03:17,442 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2025-09-07T23:03:17,443 khmer/_khmermodule.cc:2666:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T23:03:17,443 2666 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T23:03:17,443 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,443 | PyLong_FromVoidPtr 2025-09-07T23:03:17,467 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2025-09-07T23:03:17,467 khmer/_khmermodule.cc:2694:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T23:03:17,467 2694 | if (!PyCObject_Check(subset_obj)) { 2025-09-07T23:03:17,467 | ^~~~~~~~~~~~~~~ 2025-09-07T23:03:17,467 | PyODict_Check 2025-09-07T23:03:17,495 khmer/_khmermodule.cc:2700:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,495 2700 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:03:17,495 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,495 | PyLong_AsVoidPtr 2025-09-07T23:03:17,534 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2025-09-07T23:03:17,534 khmer/_khmermodule.cc:2989:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T23:03:17,534 2989 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2025-09-07T23:03:17,534 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,535 | PyLong_FromVoidPtr 2025-09-07T23:03:17,558 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2025-09-07T23:03:17,558 khmer/_khmermodule.cc:3002:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T23:03:17,558 3002 | if (!PyCObject_Check(ppi_obj)) { 2025-09-07T23:03:17,558 | ^~~~~~~~~~~~~~~ 2025-09-07T23:03:17,558 | PyODict_Check 2025-09-07T23:03:17,586 khmer/_khmermodule.cc:3008:33: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,586 3008 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2025-09-07T23:03:17,587 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,587 | PyLong_AsVoidPtr 2025-09-07T23:03:17,608 khmer/_khmermodule.cc:3014:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,608 3014 | return PyInt_FromLong(p); 2025-09-07T23:03:17,608 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,608 | PyLong_FromLong 2025-09-07T23:03:17,634 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2025-09-07T23:03:17,634 khmer/_khmermodule.cc:3130:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,634 3130 | return PyInt_FromLong(n_partitions); 2025-09-07T23:03:17,634 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,634 | PyLong_FromLong 2025-09-07T23:03:17,656 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2025-09-07T23:03:17,656 khmer/_khmermodule.cc:3161:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,657 3161 | return PyInt_FromLong(n_singletons); 2025-09-07T23:03:17,657 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,657 | PyLong_FromLong 2025-09-07T23:03:17,688 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2025-09-07T23:03:17,688 khmer/_khmermodule.cc:3260:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,688 3260 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:03:17,688 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,688 | PyLong_AsVoidPtr 2025-09-07T23:03:17,717 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2025-09-07T23:03:17,717 khmer/_khmermodule.cc:3278:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,717 3278 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:03:17,717 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,717 | PyLong_AsVoidPtr 2025-09-07T23:03:17,767 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T23:03:17,767 khmer/_khmermodule.cc:3389:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,767 3389 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:03:17,767 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,768 | PyLong_AsVoidPtr 2025-09-07T23:03:17,797 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T23:03:17,798 khmer/_khmermodule.cc:3420:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T23:03:17,798 3420 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T23:03:17,798 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,798 | PyLong_FromVoidPtr 2025-09-07T23:03:17,820 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2025-09-07T23:03:17,820 khmer/_khmermodule.cc:3449:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,820 3449 | return PyInt_FromLong(d); 2025-09-07T23:03:17,820 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,820 | PyLong_FromLong 2025-09-07T23:03:17,848 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2025-09-07T23:03:17,849 khmer/_khmermodule.cc:3465:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,849 3465 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T23:03:17,849 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,849 | PyLong_AsVoidPtr 2025-09-07T23:03:17,878 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2025-09-07T23:03:17,878 khmer/_khmermodule.cc:3491:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,878 3491 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T23:03:17,878 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,878 | PyLong_AsVoidPtr 2025-09-07T23:03:17,907 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T23:03:17,907 khmer/_khmermodule.cc:3512:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T23:03:17,907 3512 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T23:03:17,907 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,907 | PyLong_AsVoidPtr 2025-09-07T23:03:17,930 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2025-09-07T23:03:17,930 khmer/_khmermodule.cc:3548:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,930 3548 | return PyInt_FromLong(p1); 2025-09-07T23:03:17,930 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,930 | PyLong_FromLong 2025-09-07T23:03:17,951 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2025-09-07T23:03:17,952 khmer/_khmermodule.cc:3565:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:17,952 3565 | return PyInt_FromLong(partition_id); 2025-09-07T23:03:17,952 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:17,952 | PyLong_FromLong 2025-09-07T23:03:17,984 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_density_explosion(PyObject*, PyObject*)’: 2025-09-07T23:03:17,984 khmer/_khmermodule.cc:3689:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T23:03:17,984 3689 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T23:03:17,984 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:17,984 | PyBytes_FromStringAndSize 2025-09-07T23:03:18,006 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2025-09-07T23:03:18,007 khmer/_khmermodule.cc:3738:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T23:03:18,007 3738 | return PyInt_FromLong(k); 2025-09-07T23:03:18,007 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:18,007 | PyLong_FromLong 2025-09-07T23:03:18,043 In file included from /usr/include/python3.13/Python.h:63: 2025-09-07T23:03:18,043 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2025-09-07T23:03:18,043 khmer/_khmermodule.cc:3782:27: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:03:18,043 3782 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T23:03:18,043 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:18,044 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T23:03:18,044 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T23:03:18,044 | ^~~~ 2025-09-07T23:03:18,044 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T23:03:18,044 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T23:03:18,044 | ^~~~~~~~~~~~~~ 2025-09-07T23:03:18,044 khmer/_khmermodule.cc:3782:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T23:03:18,044 3782 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T23:03:18,044 | ^~~~~~~~~~~~~~~ 2025-09-07T23:03:18,070 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2025-09-07T23:03:18,070 khmer/_khmermodule.cc:3893:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:03:18,071 3893 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2025-09-07T23:03:18,071 | ^~~~~~~~~~~~~ 2025-09-07T23:03:18,071 | PyCMethod 2025-09-07T23:03:18,098 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2025-09-07T23:03:18,098 khmer/_khmermodule.cc:3967:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T23:03:18,098 3967 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2025-09-07T23:03:18,098 | ^~~~~~~~~~~~~ 2025-09-07T23:03:18,099 | PyCMethod 2025-09-07T23:03:18,099 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:03:18,099 khmer/_khmermodule.cc:4004:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T23:03:18,099 4004 | }; 2025-09-07T23:03:18,099 | ^ 2025-09-07T23:03:18,099 khmer/_khmermodule.cc:3985:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:18,099 3985 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2025-09-07T23:03:18,099 | ^~~~~~~~~~~~~ 2025-09-07T23:03:18,100 | | 2025-09-07T23:03:18,100 | const char* 2025-09-07T23:03:18,100 khmer/_khmermodule.cc:4004:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T23:03:18,100 4004 | }; 2025-09-07T23:03:18,100 | ^ 2025-09-07T23:03:18,100 | | 2025-09-07T23:03:18,100 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T23:03:18,100 khmer/_khmermodule.cc:4004:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T23:03:18,100 4004 | }; 2025-09-07T23:03:18,100 | ^ 2025-09-07T23:03:18,101 | | 2025-09-07T23:03:18,101 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T23:03:18,101 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T23:03:18,101 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T23:03:18,101 | ~~~ 2025-09-07T23:03:18,101 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T23:03:18,101 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T23:03:18,101 | | 2025-09-07T23:03:18,101 | int 2025-09-07T23:03:18,101 731 | 0) 2025-09-07T23:03:18,102 | ~~ 2025-09-07T23:03:18,102 khmer/_khmermodule.cc:4002:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T23:03:18,102 4002 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T23:03:18,102 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:18,102 khmer/_khmermodule.cc:4003:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T23:03:18,102 4003 | "ReadAligner object", /* tp_doc */ 2025-09-07T23:03:18,102 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:18,102 | | 2025-09-07T23:03:18,102 | const char* 2025-09-07T23:03:18,134 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2025-09-07T23:03:18,134 khmer/_khmermodule.cc:4195:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T23:03:18,134 4195 | return PyString_FromString(khmer::_revhash(val, ksize).c_str()); 2025-09-07T23:03:18,134 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:18,134 | PyLong_FromString 2025-09-07T23:03:18,135 khmer/_khmermodule.cc: At global scope: 2025-09-07T23:03:18,136 khmer/_khmermodule.cc:4251:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2025-09-07T23:03:18,136 4251 | init_khmer(void) 2025-09-07T23:03:18,136 | ^~~~~~~~~~ 2025-09-07T23:03:18,136 khmer/_khmermodule.cc:30:8: note: previous declaration ‘void init_khmer()’ 2025-09-07T23:03:18,136 30 | void init_khmer(); 2025-09-07T23:03:18,136 | ^~~~~~~~~~ 2025-09-07T23:03:18,136 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2025-09-07T23:03:18,136 khmer/_khmermodule.cc:4256:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:03:18,136 4256 | khmer_ConfigType.ob_type = &PyType_Type; 2025-09-07T23:03:18,137 | ^~~~~~~ 2025-09-07T23:03:18,137 khmer/_khmermodule.cc:4257:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:03:18,137 4257 | khmer_KTableType.ob_type = &PyType_Type; 2025-09-07T23:03:18,137 | ^~~~~~~ 2025-09-07T23:03:18,137 khmer/_khmermodule.cc:4258:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T23:03:18,137 4258 | khmer_KCountingHashType.ob_type = &PyType_Type; 2025-09-07T23:03:18,137 | ^~~~~~~ 2025-09-07T23:03:18,158 khmer/_khmermodule.cc:4261:9: error: ‘Py_InitModule’ was not declared in this scope 2025-09-07T23:03:18,159 4261 | m = Py_InitModule( "_khmer", KhmerMethods ); 2025-09-07T23:03:18,159 | ^~~~~~~~~~~~~ 2025-09-07T23:03:18,159 khmer/_khmermodule.cc:4263:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:03:18,159 4263 | return; 2025-09-07T23:03:18,159 | ^~~~~~ 2025-09-07T23:03:18,159 khmer/_khmermodule.cc:4268:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:03:18,159 4268 | return; 2025-09-07T23:03:18,159 | ^~~~~~ 2025-09-07T23:03:18,160 khmer/_khmermodule.cc:4275:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:03:18,160 4275 | return; 2025-09-07T23:03:18,160 | ^~~~~~ 2025-09-07T23:03:18,160 khmer/_khmermodule.cc:4281:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:03:18,160 4281 | return; 2025-09-07T23:03:18,160 | ^~~~~~ 2025-09-07T23:03:18,160 khmer/_khmermodule.cc:4284:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2025-09-07T23:03:18,160 4284 | return; 2025-09-07T23:03:18,160 | ^~~~~~ 2025-09-07T23:03:18,827 /usr/include/python3.13/object.h:851:34: warning: control reaches end of non-void function [-Wreturn-type] 2025-09-07T23:03:18,828 851 | # define Py_INCREF(op) Py_INCREF(_PyObject_CAST(op)) 2025-09-07T23:03:18,828 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-07T23:03:18,828 khmer/_khmermodule.cc:4286:5: note: in expansion of macro ‘Py_INCREF’ 2025-09-07T23:03:18,828 4286 | Py_INCREF(&ReadParser_Type); 2025-09-07T23:03:18,828 | ^~~~~~~~~ 2025-09-07T23:03:18,852 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-07T23:03:18,979 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:03:18,990 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:03:18,990 exec(compile('"'"''"'"''"'"' 2025-09-07T23:03:18,990 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:03:18,990 # 2025-09-07T23:03:18,990 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:03:18,990 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:03:18,990 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:03:18,990 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:03:18,990 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:03:18,990 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:03:18,990 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:03:18,990 import os, sys, tokenize, traceback 2025-09-07T23:03:18,990 2025-09-07T23:03:18,990 try: 2025-09-07T23:03:18,990 import setuptools 2025-09-07T23:03:18,990 except ImportError: 2025-09-07T23:03:18,990 print( 2025-09-07T23:03:18,990 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:03:18,990 "the build environment with exception:", 2025-09-07T23:03:18,990 file=sys.stderr, 2025-09-07T23:03:18,990 ) 2025-09-07T23:03:18,990 traceback.print_exc() 2025-09-07T23:03:18,990 sys.exit(1) 2025-09-07T23:03:18,990 2025-09-07T23:03:18,990 __file__ = %r 2025-09-07T23:03:18,990 sys.argv[0] = __file__ 2025-09-07T23:03:18,990 2025-09-07T23:03:18,990 if os.path.exists(__file__): 2025-09-07T23:03:18,990 filename = __file__ 2025-09-07T23:03:18,990 with tokenize.open(__file__) as f: 2025-09-07T23:03:18,990 setup_py_code = f.read() 2025-09-07T23:03:18,990 else: 2025-09-07T23:03:18,990 filename = "" 2025-09-07T23:03:18,990 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:03:18,990 2025-09-07T23:03:18,990 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:03:18,990 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-g3l00re9[/] 2025-09-07T23:03:18,990 [bold magenta]cwd[/]: /tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/ 2025-09-07T23:03:18,991 Building wheel for khmer (setup.py): finished with status 'error' 2025-09-07T23:03:18,991 ERROR: Failed building wheel for khmer 2025-09-07T23:03:18,992 Running setup.py clean for khmer 2025-09-07T23:03:18,993 Running command python setup.py clean 2025-09-07T23:03:19,606 /tmp/pip-wheel-6pnt1stx/khmer_f466f39a7a824e4885e058a13eb365fb/ez_setup.py:130: 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. 2025-09-07T23:03:19,606 import pkg_resources 2025-09-07T23:03:20,107 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-07T23:03:20,107 !! 2025-09-07T23:03:20,107 ******************************************************************************** 2025-09-07T23:03:20,108 Requirements should be satisfied by a PEP 517 installer. 2025-09-07T23:03:20,108 If you are using pip, you can try `pip install --use-pep517`. 2025-09-07T23:03:20,108 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-07T23:03:20,108 or your builds will no longer be supported. 2025-09-07T23:03:20,108 ******************************************************************************** 2025-09-07T23:03:20,108 !! 2025-09-07T23:03:20,108 dist.fetch_build_eggs(dist.setup_requires) 2025-09-07T23:03:21,319 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:03:21,319 !! 2025-09-07T23:03:21,319 ******************************************************************************** 2025-09-07T23:03:21,319 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:03:21,320 License :: OSI Approved :: BSD License 2025-09-07T23:03:21,320 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:03:21,320 ******************************************************************************** 2025-09-07T23:03:21,320 !! 2025-09-07T23:03:21,320 self._finalize_license_expression() 2025-09-07T23:03:21,396 running clean 2025-09-07T23:03:21,472 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:03:21,472 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:03:21,473 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:03:21,473 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:03:21,473 removing 'build' 2025-09-07T23:03:21,597 Failed to build khmer 2025-09-07T23:03:21,598 ERROR: Failed to build one or more wheels 2025-09-07T23:03:21,599 Exception information: 2025-09-07T23:03:21,599 Traceback (most recent call last): 2025-09-07T23:03:21,599 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:03:21,599 status = _inner_run() 2025-09-07T23:03:21,599 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:03:21,599 return self.run(options, args) 2025-09-07T23:03:21,599 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:03:21,599 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:03:21,599 return func(self, options, args) 2025-09-07T23:03:21,599 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:03:21,599 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:03:21,599 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:03:21,603 Removed build tracker: '/tmp/pip-build-tracker-rwa4bjq8'