2023-09-08T15:08:09,483 Created temporary directory: /tmp/pip-build-tracker-5liw0iku 2023-09-08T15:08:09,484 Initialized build tracking at /tmp/pip-build-tracker-5liw0iku 2023-09-08T15:08:09,484 Created build tracker: /tmp/pip-build-tracker-5liw0iku 2023-09-08T15:08:09,485 Entered build tracker: /tmp/pip-build-tracker-5liw0iku 2023-09-08T15:08:09,486 Created temporary directory: /tmp/pip-wheel-uioyt_xl 2023-09-08T15:08:09,489 Created temporary directory: /tmp/pip-ephem-wheel-cache-09mzlhxw 2023-09-08T15:08:09,513 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T15:08:09,516 2 location(s) to search for versions of khmer: 2023-09-08T15:08:09,516 * https://pypi.org/simple/khmer/ 2023-09-08T15:08:09,516 * https://www.piwheels.org/simple/khmer/ 2023-09-08T15:08:09,517 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2023-09-08T15:08:09,518 Getting page https://pypi.org/simple/khmer/ 2023-09-08T15:08:09,519 Found index url https://pypi.org/simple/ 2023-09-08T15:08:09,672 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2023-09-08T15:08:09,680 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/) 2023-09-08T15:08:09,681 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/) 2023-09-08T15:08:09,681 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2023-09-08T15:08:09,682 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 2023-09-08T15:08:09,683 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/) 2023-09-08T15:08:09,683 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2023-09-08T15:08:09,684 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/) 2023-09-08T15:08:09,685 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 2023-09-08T15:08:09,686 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/) 2023-09-08T15:08:09,686 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2023-09-08T15:08:09,687 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/) 2023-09-08T15:08:09,687 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2023-09-08T15:08:09,688 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/) 2023-09-08T15:08:09,689 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 2023-09-08T15:08:09,690 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2023-09-08T15:08:09,690 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/) 2023-09-08T15:08:09,691 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2023-09-08T15:08:09,692 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/) 2023-09-08T15:08:09,692 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2023-09-08T15:08:09,693 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/) 2023-09-08T15:08:09,693 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2023-09-08T15:08:09,694 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/) 2023-09-08T15:08:09,695 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/) 2023-09-08T15:08:09,695 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 2023-09-08T15:08:09,696 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/) 2023-09-08T15:08:09,697 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/) 2023-09-08T15:08:09,697 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/) 2023-09-08T15:08:09,698 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/) 2023-09-08T15:08:09,699 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2023-09-08T15:08:09,700 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2023-09-08T15:08:09,701 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/) 2023-09-08T15:08:09,702 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2023-09-08T15:08:09,703 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/) 2023-09-08T15:08:09,704 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/) 2023-09-08T15:08:09,705 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/) 2023-09-08T15:08:09,705 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/) 2023-09-08T15:08:09,706 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/) 2023-09-08T15:08:09,707 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 2023-09-08T15:08:09,708 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2023-09-08T15:08:09,708 Getting page https://www.piwheels.org/simple/khmer/ 2023-09-08T15:08:09,710 Found index url https://www.piwheels.org/simple/ 2023-09-08T15:08:09,962 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2023-09-08T15:08:09,964 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2023-09-08T15:08:09,964 Skipping link: not a file: https://pypi.org/simple/khmer/ 2023-09-08T15:08:09,984 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2023-09-08T15:08:10,003 Collecting khmer==0.8 2023-09-08T15:08:10,005 Created temporary directory: /tmp/pip-unpack-l92o1y8j 2023-09-08T15:08:10,804 Downloading khmer-0.8.tar.gz (18.9 MB) 2023-09-08T15:08:23,751 Added khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz to build tracker '/tmp/pip-build-tracker-5liw0iku' 2023-09-08T15:08:23,753 Running setup.py (path:/tmp/pip-wheel-uioyt_xl/khmer_1d91fc8e2196472c81e63365fb0abd1d/setup.py) egg_info for package khmer 2023-09-08T15:08:23,753 Created temporary directory: /tmp/pip-pip-egg-info-u57ao_ol 2023-09-08T15:08:23,754 Preparing metadata (setup.py): started 2023-09-08T15:08:23,755 Running command python setup.py egg_info 2023-09-08T15:08:24,485 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-08T15:08:24,485 !! 2023-09-08T15:08:24,486 ******************************************************************************** 2023-09-08T15:08:24,487 Requirements should be satisfied by a PEP 517 installer. 2023-09-08T15:08:24,487 If you are using pip, you can try `pip install --use-pep517`. 2023-09-08T15:08:24,488 ******************************************************************************** 2023-09-08T15:08:24,489 !! 2023-09-08T15:08:24,489 dist.fetch_build_eggs(dist.setup_requires) 2023-09-08T15:09:04,780 running egg_info 2023-09-08T15:09:04,781 creating /tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info 2023-09-08T15:09:04,822 writing /tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info/PKG-INFO 2023-09-08T15:09:04,825 writing dependency_links to /tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info/dependency_links.txt 2023-09-08T15:09:04,827 writing requirements to /tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info/requires.txt 2023-09-08T15:09:04,828 writing top-level names to /tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info/top_level.txt 2023-09-08T15:09:04,829 writing manifest file '/tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info/SOURCES.txt' 2023-09-08T15:09:04,966 reading manifest file '/tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info/SOURCES.txt' 2023-09-08T15:09:04,968 reading manifest template 'MANIFEST.in' 2023-09-08T15:09:06,449 no previously-included directories found matching 'doc/doxygen' 2023-09-08T15:09:06,452 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T15:09:06,471 writing manifest file '/tmp/pip-pip-egg-info-u57ao_ol/khmer.egg-info/SOURCES.txt' 2023-09-08T15:09:06,592 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T15:09:06,596 Source in /tmp/pip-wheel-uioyt_xl/khmer_1d91fc8e2196472c81e63365fb0abd1d has version 0.8, which satisfies requirement khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz 2023-09-08T15:09:06,597 Removed khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz from build tracker '/tmp/pip-build-tracker-5liw0iku' 2023-09-08T15:09:06,602 Created temporary directory: /tmp/pip-unpack-5lm9qvre 2023-09-08T15:09:06,603 Created temporary directory: /tmp/pip-unpack-ipu3pfko 2023-09-08T15:09:06,608 Building wheels for collected packages: khmer 2023-09-08T15:09:06,612 Created temporary directory: /tmp/pip-wheel-czqk_pgx 2023-09-08T15:09:06,613 Building wheel for khmer (setup.py): started 2023-09-08T15:09:06,614 Destination directory: /tmp/pip-wheel-czqk_pgx 2023-09-08T15:09:06,615 Running command python setup.py bdist_wheel 2023-09-08T15:09:07,373 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-08T15:09:07,374 !! 2023-09-08T15:09:07,375 ******************************************************************************** 2023-09-08T15:09:07,375 Requirements should be satisfied by a PEP 517 installer. 2023-09-08T15:09:07,376 If you are using pip, you can try `pip install --use-pep517`. 2023-09-08T15:09:07,376 ******************************************************************************** 2023-09-08T15:09:07,377 !! 2023-09-08T15:09:07,378 dist.fetch_build_eggs(dist.setup_requires) 2023-09-08T15:09:09,744 running bdist_wheel 2023-09-08T15:09:09,826 running build 2023-09-08T15:09:09,827 got version from file /tmp/pip-wheel-uioyt_xl/khmer_1d91fc8e2196472c81e63365fb0abd1d/khmer/_version.py {'version': '0.8', 'full': 'fd0d19f81d7a627bdffe3ab44658928074fb5acb'} 2023-09-08T15:09:09,827 running build_py 2023-09-08T15:09:09,871 creating build 2023-09-08T15:09:09,871 creating build/lib.linux-armv7l-cpython-311 2023-09-08T15:09:09,872 creating build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,873 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,875 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,877 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,879 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,880 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,882 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,884 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,885 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,887 copying khmer/counting_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:09,889 running egg_info 2023-09-08T15:09:09,930 creating khmer.egg-info 2023-09-08T15:09:09,971 writing khmer.egg-info/PKG-INFO 2023-09-08T15:09:09,974 writing dependency_links to khmer.egg-info/dependency_links.txt 2023-09-08T15:09:09,975 writing requirements to khmer.egg-info/requires.txt 2023-09-08T15:09:09,976 writing top-level names to khmer.egg-info/top_level.txt 2023-09-08T15:09:09,978 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:09:10,022 reading manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:09:10,023 reading manifest template 'MANIFEST.in' 2023-09-08T15:09:11,401 no previously-included directories found matching 'doc/doxygen' 2023-09-08T15:09:11,403 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T15:09:11,438 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:09:11,450 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:11,456 running build_ext 2023-09-08T15:09:11,467 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2023-09-08T15:09:11,797 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2023-09-08T15:09:11,925 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2023-09-08T15:09:12,337 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2023-09-08T15:09:13,398 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2023-09-08T15:09:13,510 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2023-09-08T15:09:15,076 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2023-09-08T15:09:16,498 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2023-09-08T15:09:16,635 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2023-09-08T15:09:18,332 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2023-09-08T15:09:19,149 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2023-09-08T15:09:19,630 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2023-09-08T15:09:20,069 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 2023-09-08T15:09:20,275 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2023-09-08T15:09:21,168 In function ‘mainSimpleSort’, 2023-09-08T15:09:21,168 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2023-09-08T15:09:21,169 inlined from ‘mainSort’ at blocksort.c:897:19: 2023-09-08T15:09:21,170 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:09:21,170 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:09:21,171 | ^~~~~~~ 2023-09-08T15:09:21,171 blocksort.c:514:18: note: called from here 2023-09-08T15:09:21,172 514 | while ( mainGtU ( 2023-09-08T15:09:21,172 | ^~~~~~~~~ 2023-09-08T15:09:21,173 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:09:21,174 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:21,174 516 | ) ) { 2023-09-08T15:09:21,175 | ~ 2023-09-08T15:09:21,176 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:09:21,176 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:09:21,177 | ^~~~~~~ 2023-09-08T15:09:21,178 blocksort.c:528:18: note: called from here 2023-09-08T15:09:21,178 528 | while ( mainGtU ( 2023-09-08T15:09:21,179 | ^~~~~~~~~ 2023-09-08T15:09:21,180 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:09:21,181 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:21,181 530 | ) ) { 2023-09-08T15:09:21,182 | ~ 2023-09-08T15:09:21,182 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:09:21,182 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:09:21,183 | ^~~~~~~ 2023-09-08T15:09:21,183 blocksort.c:542:18: note: called from here 2023-09-08T15:09:21,184 542 | while ( mainGtU ( 2023-09-08T15:09:21,184 | ^~~~~~~~~ 2023-09-08T15:09:21,185 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:09:21,185 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:21,186 544 | ) ) { 2023-09-08T15:09:21,186 | ~ 2023-09-08T15:09:21,989 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2023-09-08T15:09:22,452 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2023-09-08T15:09:22,564 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2023-09-08T15:09:22,679 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2023-09-08T15:09:27,188 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2023-09-08T15:09:29,754 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2023-09-08T15:09:31,692 #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 2023-09-08T15:09:31,694 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2023-09-08T15:09:31,697 #rm -f libbz2.so.1.0 2023-09-08T15:09:31,699 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2023-09-08T15:09:31,708 building 'khmer._khmermodule' extension 2023-09-08T15:09:31,709 creating build/temp.linux-armv7l-cpython-311 2023-09-08T15:09:31,710 creating build/temp.linux-armv7l-cpython-311/khmer 2023-09-08T15:09:31,711 creating build/temp.linux-armv7l-cpython-311/lib 2023-09-08T15:09:31,712 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION=0.8 -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.11 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-cpython-311/khmer/_khmermodule.o -O3 2023-09-08T15:09:34,802 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2023-09-08T15:09:34,802 khmer/_khmermodule.cc:85:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2023-09-08T15:09:34,803 85 | tobj.ob_size = 0; 2023-09-08T15:09:34,804 | ^~~~~~~ 2023-09-08T15:09:34,804 khmer/_khmermodule.cc:86:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:09:34,805 86 | tobj.ob_type = &PyType_Type; 2023-09-08T15:09:34,806 | ^~~~~~~ 2023-09-08T15:09:34,812 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:09:34,812 khmer/_khmermodule.cc:206:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:34,813 206 | "Config", sizeof(khmer_ConfigObject), 2023-09-08T15:09:34,813 | ^~~~~~~~ 2023-09-08T15:09:34,814 | | 2023-09-08T15:09:34,815 | const char* 2023-09-08T15:09:34,815 khmer/_khmermodule.cc:208:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:34,816 208 | khmer_config_dealloc, /*tp_dealloc*/ 2023-09-08T15:09:34,817 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,818 | | 2023-09-08T15:09:34,818 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:09:34,819 khmer/_khmermodule.cc:210:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:09:34,819 210 | khmer_config_getattr, /*tp_getattr*/ 2023-09-08T15:09:34,820 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,820 | | 2023-09-08T15:09:34,821 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:09:34,821 In file included from /usr/include/python3.11/Python.h:44, 2023-09-08T15:09:34,821 from khmer/_khmermodule.cc:12: 2023-09-08T15:09:34,822 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:09:34,822 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:09:34,823 | ~~~ 2023-09-08T15:09:34,823 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:09:34,824 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:09:34,825 | | 2023-09-08T15:09:34,825 | int 2023-09-08T15:09:34,826 424 | 0) 2023-09-08T15:09:34,827 | ~~ 2023-09-08T15:09:34,827 khmer/_khmermodule.cc:223:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:09:34,828 223 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:09:34,828 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,829 khmer/_khmermodule.cc:224:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:09:34,830 224 | "config object", /* tp_doc */ 2023-09-08T15:09:34,831 | ^~~~~~~~~~~~~~~ 2023-09-08T15:09:34,831 | | 2023-09-08T15:09:34,832 | const char* 2023-09-08T15:09:34,848 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2023-09-08T15:09:34,849 khmer/_khmermodule.cc:312:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:09:34,849 312 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2023-09-08T15:09:34,850 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,851 | PyLong_FromSize_t 2023-09-08T15:09:34,873 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2023-09-08T15:09:34,873 khmer/_khmermodule.cc:370:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:09:34,874 370 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2023-09-08T15:09:34,875 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,876 | PyLong_FromSize_t 2023-09-08T15:09:34,897 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2023-09-08T15:09:34,898 khmer/_khmermodule.cc:399:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:09:34,898 399 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2023-09-08T15:09:34,899 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,900 | PyLong_FromSize_t 2023-09-08T15:09:34,921 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2023-09-08T15:09:34,922 khmer/_khmermodule.cc:466:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:09:34,923 466 | return Py_FindMethod(khmer_config_methods, obj, name); 2023-09-08T15:09:34,924 | ^~~~~~~~~~~~~ 2023-09-08T15:09:34,924 | PyCMethod 2023-09-08T15:09:34,948 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2023-09-08T15:09:34,949 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:09:34,949 504 | PyString_FromString( \ 2023-09-08T15:09:34,950 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,950 khmer/_khmermodule.cc:513:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:09:34,951 513 | return KHMER_READ_STRING_GETTER( self, name ); 2023-09-08T15:09:34,952 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,974 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2023-09-08T15:09:34,975 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:09:34,976 504 | PyString_FromString( \ 2023-09-08T15:09:34,976 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:34,977 khmer/_khmermodule.cc:521:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:09:34,977 521 | return KHMER_READ_STRING_GETTER( self, sequence ); 2023-09-08T15:09:34,978 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,000 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2023-09-08T15:09:35,001 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:09:35,002 504 | PyString_FromString( \ 2023-09-08T15:09:35,002 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,003 khmer/_khmermodule.cc:529:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:09:35,004 529 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2023-09-08T15:09:35,005 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,027 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2023-09-08T15:09:35,028 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:09:35,028 504 | PyString_FromString( \ 2023-09-08T15:09:35,029 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,030 khmer/_khmermodule.cc:537:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:09:35,031 537 | return KHMER_READ_STRING_GETTER( self, annotations ); 2023-09-08T15:09:35,032 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,074 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2023-09-08T15:09:35,074 khmer/_khmermodule.cc:874:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,075 874 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2023-09-08T15:09:35,076 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,076 | PyLong_FromLong 2023-09-08T15:09:35,103 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2023-09-08T15:09:35,104 khmer/_khmermodule.cc:1024:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:09:35,105 1024 | return PyString_FromString(_revhash(val, ktable->ksize()).c_str()); 2023-09-08T15:09:35,106 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,107 | PyLong_FromString 2023-09-08T15:09:35,126 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2023-09-08T15:09:35,126 khmer/_khmermodule.cc:1050:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,127 1050 | return PyInt_FromLong(1); 2023-09-08T15:09:35,128 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,129 | PyLong_FromLong 2023-09-08T15:09:35,150 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2023-09-08T15:09:35,150 khmer/_khmermodule.cc:1078:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:09:35,151 1078 | return PyInt_FromSize_t(n_consumed); 2023-09-08T15:09:35,152 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,152 | PyLong_FromSize_t 2023-09-08T15:09:35,168 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2023-09-08T15:09:35,169 khmer/_khmermodule.cc:1097:16: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:09:35,169 1097 | } else if (PyInt_Check(arg)) { 2023-09-08T15:09:35,170 | ^~~~~~~~~~~ 2023-09-08T15:09:35,170 | PySet_Check 2023-09-08T15:09:35,187 khmer/_khmermodule.cc:1098:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:09:35,188 1098 | long pos = PyInt_AsLong(arg); 2023-09-08T15:09:35,189 | ^~~~~~~~~~~~ 2023-09-08T15:09:35,189 | PyLong_AsLong 2023-09-08T15:09:35,210 khmer/_khmermodule.cc:1100:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:09:35,210 1100 | } else if (PyString_Check(arg)) { 2023-09-08T15:09:35,211 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,212 | PyMapping_Check 2023-09-08T15:09:35,236 khmer/_khmermodule.cc:1101:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:09:35,237 1101 | std::string s = PyString_AsString(arg); 2023-09-08T15:09:35,238 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,264 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2023-09-08T15:09:35,265 khmer/_khmermodule.cc:1123:23: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:09:35,265 1123 | char * kmer_str = PyString_AsString( val ); 2023-09-08T15:09:35,266 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,282 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2023-09-08T15:09:35,283 khmer/_khmermodule.cc:1143:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:09:35,283 1143 | if (PyInt_Check(arg)) { 2023-09-08T15:09:35,284 | ^~~~~~~~~~~ 2023-09-08T15:09:35,285 | PySet_Check 2023-09-08T15:09:35,301 khmer/_khmermodule.cc:1144:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:09:35,302 1144 | long pos = PyInt_AsLong(arg); 2023-09-08T15:09:35,303 | ^~~~~~~~~~~~ 2023-09-08T15:09:35,303 | PyLong_AsLong 2023-09-08T15:09:35,324 khmer/_khmermodule.cc:1146:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:09:35,325 1146 | } else if (PyString_Check(arg)) { 2023-09-08T15:09:35,325 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,326 | PyMapping_Check 2023-09-08T15:09:35,350 khmer/_khmermodule.cc:1147:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:09:35,351 1147 | std::string s = PyString_AsString(arg); 2023-09-08T15:09:35,352 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,374 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2023-09-08T15:09:35,375 khmer/_khmermodule.cc:1195:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,376 1195 | return PyInt_FromLong(ktable->ksize()); 2023-09-08T15:09:35,376 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,377 | PyLong_FromLong 2023-09-08T15:09:35,398 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2023-09-08T15:09:35,399 khmer/_khmermodule.cc:1242:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:09:35,399 1242 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2023-09-08T15:09:35,400 | ^~~~~~~~~~~~~ 2023-09-08T15:09:35,400 | PyCMethod 2023-09-08T15:09:35,401 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:09:35,402 khmer/_khmermodule.cc:1265:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,402 1265 | "KTable", sizeof(khmer_KTableObject), 2023-09-08T15:09:35,403 | ^~~~~~~~ 2023-09-08T15:09:35,404 | | 2023-09-08T15:09:35,404 | const char* 2023-09-08T15:09:35,405 khmer/_khmermodule.cc:1267:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,405 1267 | khmer_ktable_dealloc, /*tp_dealloc*/ 2023-09-08T15:09:35,406 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,406 | | 2023-09-08T15:09:35,407 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:09:35,408 khmer/_khmermodule.cc:1269:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:09:35,408 1269 | khmer_ktable_getattr, /*tp_getattr*/ 2023-09-08T15:09:35,409 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,410 | | 2023-09-08T15:09:35,411 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:09:35,412 khmer/_khmermodule.cc:1274:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2023-09-08T15:09:35,412 1274 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2023-09-08T15:09:35,413 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,414 | | 2023-09-08T15:09:35,415 | PySequenceMethods* 2023-09-08T15:09:35,416 khmer/_khmermodule.cc:1405:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,416 1405 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2023-09-08T15:09:35,417 | ^~~~~~~~~ 2023-09-08T15:09:35,418 | | 2023-09-08T15:09:35,419 | const char* 2023-09-08T15:09:35,419 khmer/_khmermodule.cc:1407:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,420 1407 | khmer_subset_dealloc, /*tp_dealloc*/ 2023-09-08T15:09:35,420 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,421 | | 2023-09-08T15:09:35,421 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:09:35,422 khmer/_khmermodule.cc:1409:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:09:35,422 1409 | khmer_subset_getattr, /*tp_getattr*/ 2023-09-08T15:09:35,423 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,424 | | 2023-09-08T15:09:35,424 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:09:35,425 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:09:35,426 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:09:35,426 | ~~~ 2023-09-08T15:09:35,427 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:09:35,427 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:09:35,427 | | 2023-09-08T15:09:35,428 | int 2023-09-08T15:09:35,428 424 | 0) 2023-09-08T15:09:35,429 | ~~ 2023-09-08T15:09:35,429 khmer/_khmermodule.cc:1422:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:09:35,430 1422 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:09:35,430 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,431 khmer/_khmermodule.cc:1423:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:09:35,431 1423 | "subset object", /* tp_doc */ 2023-09-08T15:09:35,431 | ^~~~~~~~~~~~~~~ 2023-09-08T15:09:35,432 | | 2023-09-08T15:09:35,432 | const char* 2023-09-08T15:09:35,433 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2023-09-08T15:09:35,434 khmer/_khmermodule.cc:1519:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,434 1519 | return PyInt_FromLong(1); 2023-09-08T15:09:35,435 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,436 | PyLong_FromLong 2023-09-08T15:09:35,456 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2023-09-08T15:09:35,457 khmer/_khmermodule.cc:1536:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,457 1536 | return PyInt_FromLong(0); 2023-09-08T15:09:35,458 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,459 | PyLong_FromLong 2023-09-08T15:09:35,481 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2023-09-08T15:09:35,482 khmer/_khmermodule.cc:1624:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,483 1624 | return PyInt_FromLong(n_consumed); 2023-09-08T15:09:35,483 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,484 | PyLong_FromLong 2023-09-08T15:09:35,504 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2023-09-08T15:09:35,505 khmer/_khmermodule.cc:1656:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,506 1656 | return PyInt_FromLong(n_consumed); 2023-09-08T15:09:35,506 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,507 | PyLong_FromLong 2023-09-08T15:09:35,527 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2023-09-08T15:09:35,528 khmer/_khmermodule.cc:1679:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,529 1679 | return PyInt_FromLong(N); 2023-09-08T15:09:35,530 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,530 | PyLong_FromLong 2023-09-08T15:09:35,550 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2023-09-08T15:09:35,551 khmer/_khmermodule.cc:1702:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,552 1702 | return PyInt_FromLong(N); 2023-09-08T15:09:35,553 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,553 | PyLong_FromLong 2023-09-08T15:09:35,573 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2023-09-08T15:09:35,574 khmer/_khmermodule.cc:1805:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:09:35,574 1805 | if (PyInt_Check(arg)) { 2023-09-08T15:09:35,575 | ^~~~~~~~~~~ 2023-09-08T15:09:35,575 | PySet_Check 2023-09-08T15:09:35,593 khmer/_khmermodule.cc:1806:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:09:35,594 1806 | long pos = PyInt_AsLong(arg); 2023-09-08T15:09:35,595 | ^~~~~~~~~~~~ 2023-09-08T15:09:35,595 | PyLong_AsLong 2023-09-08T15:09:35,618 khmer/_khmermodule.cc:1808:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:09:35,618 1808 | } else if (PyString_Check(arg)) { 2023-09-08T15:09:35,619 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,620 | PyMapping_Check 2023-09-08T15:09:35,646 khmer/_khmermodule.cc:1809:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:09:35,647 1809 | std::string s = PyString_AsString(arg); 2023-09-08T15:09:35,647 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,668 khmer/_khmermodule.cc:1813:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,669 1813 | return PyInt_FromLong(count); 2023-09-08T15:09:35,669 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,670 | PyLong_FromLong 2023-09-08T15:09:35,692 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2023-09-08T15:09:35,693 khmer/_khmermodule.cc:1829:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,694 1829 | return PyInt_FromLong(count); 2023-09-08T15:09:35,695 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,695 | PyLong_FromLong 2023-09-08T15:09:35,721 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2023-09-08T15:09:35,721 khmer/_khmermodule.cc:1853:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:09:35,722 1853 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:09:35,723 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,724 | PyBytes_FromStringAndSize 2023-09-08T15:09:35,749 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2023-09-08T15:09:35,750 khmer/_khmermodule.cc:1883:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:09:35,751 1883 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:09:35,751 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,752 | PyBytes_FromStringAndSize 2023-09-08T15:09:35,778 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2023-09-08T15:09:35,778 khmer/_khmermodule.cc:2024:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,779 2024 | return PyInt_FromLong(k); 2023-09-08T15:09:35,780 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,781 | PyLong_FromLong 2023-09-08T15:09:35,812 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2023-09-08T15:09:35,813 khmer/_khmermodule.cc:2136:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:09:35,814 2136 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T15:09:35,815 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,815 | PyLong_FromVoidPtr 2023-09-08T15:09:35,839 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2023-09-08T15:09:35,840 khmer/_khmermodule.cc:2242:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:09:35,841 2242 | return Py_FindMethod(khmer_counting_methods, obj, name); 2023-09-08T15:09:35,841 | ^~~~~~~~~~~~~ 2023-09-08T15:09:35,842 | PyCMethod 2023-09-08T15:09:35,842 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:09:35,843 khmer/_khmermodule.cc:2252:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,844 2252 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2023-09-08T15:09:35,844 | ^~~~~~~~~~~~~~~ 2023-09-08T15:09:35,845 | | 2023-09-08T15:09:35,845 | const char* 2023-09-08T15:09:35,846 khmer/_khmermodule.cc:2254:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,846 2254 | khmer_counting_dealloc, /*tp_dealloc*/ 2023-09-08T15:09:35,847 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,848 | | 2023-09-08T15:09:35,848 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:09:35,849 khmer/_khmermodule.cc:2256:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:09:35,849 2256 | khmer_counting_getattr, /*tp_getattr*/ 2023-09-08T15:09:35,850 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,851 | | 2023-09-08T15:09:35,851 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:09:35,852 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:09:35,853 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:09:35,854 | ~~~ 2023-09-08T15:09:35,855 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:09:35,855 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:09:35,856 | | 2023-09-08T15:09:35,857 | int 2023-09-08T15:09:35,858 424 | 0) 2023-09-08T15:09:35,859 | ~~ 2023-09-08T15:09:35,859 khmer/_khmermodule.cc:2269:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:09:35,860 2269 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:09:35,861 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,861 khmer/_khmermodule.cc:2270:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:09:35,862 2270 | "counting hash object", /* tp_doc */ 2023-09-08T15:09:35,863 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,863 | | 2023-09-08T15:09:35,864 | const char* 2023-09-08T15:09:35,865 khmer/_khmermodule.cc:2350:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,865 2350 | "Hashbits", sizeof(khmer_KHashbitsObject), 2023-09-08T15:09:35,866 | ^~~~~~~~~~ 2023-09-08T15:09:35,866 | | 2023-09-08T15:09:35,867 | const char* 2023-09-08T15:09:35,868 khmer/_khmermodule.cc:2352:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:35,869 2352 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2023-09-08T15:09:35,869 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,870 | | 2023-09-08T15:09:35,870 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:09:35,871 khmer/_khmermodule.cc:2354:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:09:35,871 2354 | khmer_hashbits_getattr, /*tp_getattr*/ 2023-09-08T15:09:35,871 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,872 | | 2023-09-08T15:09:35,872 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:09:35,872 khmer/_khmermodule.cc:2367:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:09:35,873 2367 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2023-09-08T15:09:35,873 khmer/_khmermodule.cc:2368:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:09:35,874 2368 | "hashbits object", /* tp_doc */ 2023-09-08T15:09:35,874 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,875 | | 2023-09-08T15:09:35,875 | const char* 2023-09-08T15:09:35,878 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2023-09-08T15:09:35,879 khmer/_khmermodule.cc:2541:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,880 2541 | return PyInt_FromLong(hashbits->n_tags()); 2023-09-08T15:09:35,880 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,881 | PyLong_FromLong 2023-09-08T15:09:35,901 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2023-09-08T15:09:35,902 khmer/_khmermodule.cc:2563:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,903 2563 | return PyInt_FromLong(1); 2023-09-08T15:09:35,904 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,904 | PyLong_FromLong 2023-09-08T15:09:35,924 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2023-09-08T15:09:35,925 khmer/_khmermodule.cc:2586:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,926 2586 | return PyInt_FromLong(n_consumed); 2023-09-08T15:09:35,926 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,927 | PyLong_FromLong 2023-09-08T15:09:35,958 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2023-09-08T15:09:35,959 khmer/_khmermodule.cc:2693:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:35,960 2693 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2023-09-08T15:09:35,960 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:35,961 | PyLong_AsVoidPtr 2023-09-08T15:09:35,980 khmer/_khmermodule.cc:2703:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:35,981 2703 | return PyInt_FromLong(next_largest); 2023-09-08T15:09:35,982 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:35,983 | PyLong_FromLong 2023-09-08T15:09:35,998 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2023-09-08T15:09:35,999 khmer/_khmermodule.cc:2719:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:09:36,000 2719 | if (PyInt_Check(arg)) { 2023-09-08T15:09:36,000 | ^~~~~~~~~~~ 2023-09-08T15:09:36,001 | PySet_Check 2023-09-08T15:09:36,018 khmer/_khmermodule.cc:2720:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:09:36,019 2720 | long pos = PyInt_AsLong(arg); 2023-09-08T15:09:36,019 | ^~~~~~~~~~~~ 2023-09-08T15:09:36,020 | PyLong_AsLong 2023-09-08T15:09:36,042 khmer/_khmermodule.cc:2722:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:09:36,042 2722 | } else if (PyString_Check(arg)) { 2023-09-08T15:09:36,043 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,044 | PyMapping_Check 2023-09-08T15:09:36,069 khmer/_khmermodule.cc:2723:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:09:36,069 2723 | std::string s = PyString_AsString(arg); 2023-09-08T15:09:36,070 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,091 khmer/_khmermodule.cc:2730:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,091 2730 | return PyInt_FromLong(count); 2023-09-08T15:09:36,092 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,092 | PyLong_FromLong 2023-09-08T15:09:36,114 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2023-09-08T15:09:36,115 khmer/_khmermodule.cc:2772:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,115 2772 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2023-09-08T15:09:36,116 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,117 | PyLong_FromLong 2023-09-08T15:09:36,143 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2023-09-08T15:09:36,144 khmer/_khmermodule.cc:2793:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:09:36,144 2793 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:09:36,145 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,146 | PyBytes_FromStringAndSize 2023-09-08T15:09:36,186 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2023-09-08T15:09:36,187 khmer/_khmermodule.cc:2868:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:09:36,187 2868 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T15:09:36,188 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,189 | PyLong_FromVoidPtr 2023-09-08T15:09:36,212 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2023-09-08T15:09:36,213 khmer/_khmermodule.cc:2896:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T15:09:36,214 2896 | if (!PyCObject_Check(subset_obj)) { 2023-09-08T15:09:36,214 | ^~~~~~~~~~~~~~~ 2023-09-08T15:09:36,215 | PyODict_Check 2023-09-08T15:09:36,241 khmer/_khmermodule.cc:2902:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,242 2902 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:09:36,243 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,244 | PyLong_AsVoidPtr 2023-09-08T15:09:36,283 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2023-09-08T15:09:36,284 khmer/_khmermodule.cc:3166:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:09:36,285 3166 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T15:09:36,286 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,286 | PyLong_FromVoidPtr 2023-09-08T15:09:36,309 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2023-09-08T15:09:36,310 khmer/_khmermodule.cc:3179:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T15:09:36,310 3179 | if (!PyCObject_Check(ppi_obj)) { 2023-09-08T15:09:36,311 | ^~~~~~~~~~~~~~~ 2023-09-08T15:09:36,311 | PyODict_Check 2023-09-08T15:09:36,338 khmer/_khmermodule.cc:3185:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,339 3185 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2023-09-08T15:09:36,339 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,340 | PyLong_AsVoidPtr 2023-09-08T15:09:36,360 khmer/_khmermodule.cc:3191:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,360 3191 | return PyInt_FromLong(p); 2023-09-08T15:09:36,361 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,362 | PyLong_FromLong 2023-09-08T15:09:36,389 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2023-09-08T15:09:36,389 khmer/_khmermodule.cc:3306:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,390 3306 | return PyInt_FromLong(n_partitions); 2023-09-08T15:09:36,391 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,392 | PyLong_FromLong 2023-09-08T15:09:36,412 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2023-09-08T15:09:36,413 khmer/_khmermodule.cc:3337:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,414 3337 | return PyInt_FromLong(n_singletons); 2023-09-08T15:09:36,414 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,415 | PyLong_FromLong 2023-09-08T15:09:36,446 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2023-09-08T15:09:36,447 khmer/_khmermodule.cc:3436:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,448 3436 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:09:36,448 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,449 | PyLong_AsVoidPtr 2023-09-08T15:09:36,476 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2023-09-08T15:09:36,476 khmer/_khmermodule.cc:3453:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,477 3453 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:09:36,478 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,478 | PyLong_AsVoidPtr 2023-09-08T15:09:36,534 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:09:36,535 khmer/_khmermodule.cc:3564:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,535 3564 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:09:36,536 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,537 | PyLong_AsVoidPtr 2023-09-08T15:09:36,565 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:09:36,566 khmer/_khmermodule.cc:3595:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:09:36,566 3595 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T15:09:36,567 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,568 | PyLong_FromVoidPtr 2023-09-08T15:09:36,588 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2023-09-08T15:09:36,589 khmer/_khmermodule.cc:3624:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,590 3624 | return PyInt_FromLong(d); 2023-09-08T15:09:36,590 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,591 | PyLong_FromLong 2023-09-08T15:09:36,618 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2023-09-08T15:09:36,619 khmer/_khmermodule.cc:3640:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,619 3640 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T15:09:36,620 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,621 | PyLong_AsVoidPtr 2023-09-08T15:09:36,648 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2023-09-08T15:09:36,649 khmer/_khmermodule.cc:3666:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,649 3666 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T15:09:36,650 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,651 | PyLong_AsVoidPtr 2023-09-08T15:09:36,678 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:09:36,679 khmer/_khmermodule.cc:3687:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:09:36,680 3687 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:09:36,681 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,681 | PyLong_AsVoidPtr 2023-09-08T15:09:36,702 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2023-09-08T15:09:36,703 khmer/_khmermodule.cc:3723:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,704 3723 | return PyInt_FromLong(p1); 2023-09-08T15:09:36,704 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,705 | PyLong_FromLong 2023-09-08T15:09:36,725 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2023-09-08T15:09:36,726 khmer/_khmermodule.cc:3740:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,726 3740 | return PyInt_FromLong(partition_id); 2023-09-08T15:09:36,727 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,728 | PyLong_FromLong 2023-09-08T15:09:36,753 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2023-09-08T15:09:36,754 khmer/_khmermodule.cc:3882:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,755 3882 | return PyInt_FromLong(k); 2023-09-08T15:09:36,756 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,756 | PyLong_FromLong 2023-09-08T15:09:36,794 In file included from /usr/include/python3.11/Python.h:38: 2023-09-08T15:09:36,795 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2023-09-08T15:09:36,796 khmer/_khmermodule.cc:3926:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:09:36,796 3926 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T15:09:36,797 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,797 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T15:09:36,798 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T15:09:36,798 | ^~~~ 2023-09-08T15:09:36,799 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T15:09:36,799 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T15:09:36,800 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,800 khmer/_khmermodule.cc:3926:9: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T15:09:36,801 3926 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T15:09:36,801 | ^~~~~~~~~~~~~~~ 2023-09-08T15:09:36,825 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2023-09-08T15:09:36,826 khmer/_khmermodule.cc:4033:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:09:36,827 4033 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2023-09-08T15:09:36,827 | ^~~~~~~~~~~~~ 2023-09-08T15:09:36,828 | PyCMethod 2023-09-08T15:09:36,890 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2023-09-08T15:09:36,891 khmer/_khmermodule.cc:4260:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:09:36,892 4260 | return Py_FindMethod(khmer_subset_methods, obj, name); 2023-09-08T15:09:36,893 | ^~~~~~~~~~~~~ 2023-09-08T15:09:36,893 | PyCMethod 2023-09-08T15:09:36,937 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2023-09-08T15:09:36,938 khmer/_khmermodule.cc:4612:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:09:36,939 4612 | return PyInt_FromLong(labelhash->n_labels()); 2023-09-08T15:09:36,940 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:36,940 | PyLong_FromLong 2023-09-08T15:09:36,941 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:09:36,942 khmer/_khmermodule.cc:4631:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:36,942 4631 | "_LabelHash", /* tp_name */ 2023-09-08T15:09:36,943 | ^~~~~~~~~~~~ 2023-09-08T15:09:36,944 | | 2023-09-08T15:09:36,945 | const char* 2023-09-08T15:09:36,945 khmer/_khmermodule.cc:4634:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:36,946 4634 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2023-09-08T15:09:36,947 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,948 | | 2023-09-08T15:09:36,949 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:09:36,949 khmer/_khmermodule.cc:4649:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:09:36,950 4649 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2023-09-08T15:09:36,951 khmer/_khmermodule.cc:4657:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2023-09-08T15:09:36,952 4657 | khmer_labelhash_methods, /* tp_methods */ 2023-09-08T15:09:36,952 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,953 | | 2023-09-08T15:09:36,953 | PyMethodDef* 2023-09-08T15:09:36,972 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2023-09-08T15:09:36,972 khmer/_khmermodule.cc:4740:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:09:36,973 4740 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2023-09-08T15:09:36,973 | ^~~~~~~~~~~~~ 2023-09-08T15:09:36,974 | PyCMethod 2023-09-08T15:09:36,975 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:09:36,975 khmer/_khmermodule.cc:4758:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:36,976 4758 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2023-09-08T15:09:36,976 | ^~~~~~~~~~~~~ 2023-09-08T15:09:36,977 | | 2023-09-08T15:09:36,977 | const char* 2023-09-08T15:09:36,978 khmer/_khmermodule.cc:4760:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:09:36,979 4760 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2023-09-08T15:09:36,979 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,980 | | 2023-09-08T15:09:36,981 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:09:36,981 khmer/_khmermodule.cc:4762:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:09:36,982 4762 | khmer_readaligner_getattr, /*tp_getattr*/ 2023-09-08T15:09:36,983 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,984 | | 2023-09-08T15:09:36,984 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:09:36,985 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:09:36,986 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:09:36,987 | ~~~ 2023-09-08T15:09:36,988 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:09:36,988 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:09:36,989 | | 2023-09-08T15:09:36,990 | int 2023-09-08T15:09:36,990 424 | 0) 2023-09-08T15:09:36,991 | ~~ 2023-09-08T15:09:36,992 khmer/_khmermodule.cc:4775:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:09:36,992 4775 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:09:36,993 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,994 khmer/_khmermodule.cc:4776:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:09:36,995 4776 | "ReadAligner object", /* tp_doc */ 2023-09-08T15:09:36,995 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:36,996 | | 2023-09-08T15:09:36,997 | const char* 2023-09-08T15:09:36,997 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2023-09-08T15:09:36,998 khmer/_khmermodule.cc:4917:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2023-09-08T15:09:36,999 4917 | self->ob_type->tp_free((PyObject*)obj); 2023-09-08T15:09:36,999 | ^~~~~~~ 2023-09-08T15:09:37,016 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2023-09-08T15:09:37,016 khmer/_khmermodule.cc:4992:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:09:37,017 4992 | return PyString_FromString(_revhash(val, ksize).c_str()); 2023-09-08T15:09:37,017 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:37,018 | PyLong_FromString 2023-09-08T15:09:37,018 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:09:37,019 khmer/_khmermodule.cc:5072:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2023-09-08T15:09:37,020 5072 | init_khmer(void) 2023-09-08T15:09:37,020 | ^~~~~~~~~~ 2023-09-08T15:09:37,021 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2023-09-08T15:09:37,021 33 | void init_khmer(); 2023-09-08T15:09:37,022 | ^~~~~~~~~~ 2023-09-08T15:09:37,023 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2023-09-08T15:09:37,023 khmer/_khmermodule.cc:5076:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:09:37,024 5076 | khmer_ConfigType.ob_type = &PyType_Type; 2023-09-08T15:09:37,025 | ^~~~~~~ 2023-09-08T15:09:37,025 khmer/_khmermodule.cc:5077:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:09:37,026 5077 | khmer_KTableType.ob_type = &PyType_Type; 2023-09-08T15:09:37,027 | ^~~~~~~ 2023-09-08T15:09:37,027 khmer/_khmermodule.cc:5078:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:09:37,028 5078 | khmer_KCountingHashType.ob_type = &PyType_Type; 2023-09-08T15:09:37,029 | ^~~~~~~ 2023-09-08T15:09:37,029 khmer/_khmermodule.cc:5085:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:09:37,030 5085 | return; 2023-09-08T15:09:37,031 | ^~~~~~ 2023-09-08T15:09:37,031 khmer/_khmermodule.cc:5092:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:09:37,032 5092 | return; 2023-09-08T15:09:37,032 | ^~~~~~ 2023-09-08T15:09:37,046 khmer/_khmermodule.cc:5096:9: error: ‘Py_InitModule3’ was not declared in this scope 2023-09-08T15:09:37,047 5096 | m = Py_InitModule3( "_khmer", KhmerMethods, 2023-09-08T15:09:37,047 | ^~~~~~~~~~~~~~ 2023-09-08T15:09:37,048 khmer/_khmermodule.cc:5099:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:09:37,049 5099 | return; 2023-09-08T15:09:37,050 | ^~~~~~ 2023-09-08T15:09:37,050 khmer/_khmermodule.cc:5104:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:09:37,051 5104 | return; 2023-09-08T15:09:37,052 | ^~~~~~ 2023-09-08T15:09:37,052 khmer/_khmermodule.cc:5111:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:09:37,053 5111 | return; 2023-09-08T15:09:37,054 | ^~~~~~ 2023-09-08T15:09:37,054 khmer/_khmermodule.cc:5117:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:09:37,055 5117 | return; 2023-09-08T15:09:37,056 | ^~~~~~ 2023-09-08T15:09:37,057 khmer/_khmermodule.cc:5120:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:09:37,058 5120 | return; 2023-09-08T15:09:37,058 | ^~~~~~ 2023-09-08T15:09:38,029 khmer/_khmermodule.cc:5130:23: warning: control reaches end of non-void function [-Wreturn-type] 2023-09-08T15:09:38,029 5130 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2023-09-08T15:09:38,030 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:09:38,136 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T15:09:38,257 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T15:09:38,270 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T15:09:38,270 exec(compile('"'"''"'"''"'"' 2023-09-08T15:09:38,270 # This is -- a caller that pip uses to run setup.py 2023-09-08T15:09:38,270 # 2023-09-08T15:09:38,270 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T15:09:38,270 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T15:09:38,270 # - It provides a clear error message when setuptools is not installed. 2023-09-08T15:09:38,270 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T15:09:38,270 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T15:09:38,270 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T15:09:38,270 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T15:09:38,270 import os, sys, tokenize 2023-09-08T15:09:38,270 2023-09-08T15:09:38,270 try: 2023-09-08T15:09:38,270 import setuptools 2023-09-08T15:09:38,270 except ImportError as error: 2023-09-08T15:09:38,270 print( 2023-09-08T15:09:38,270 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T15:09:38,270 "the build environment.", 2023-09-08T15:09:38,270 file=sys.stderr, 2023-09-08T15:09:38,270 ) 2023-09-08T15:09:38,270 sys.exit(1) 2023-09-08T15:09:38,270 2023-09-08T15:09:38,270 __file__ = %r 2023-09-08T15:09:38,270 sys.argv[0] = __file__ 2023-09-08T15:09:38,270 2023-09-08T15:09:38,270 if os.path.exists(__file__): 2023-09-08T15:09:38,270 filename = __file__ 2023-09-08T15:09:38,270 with tokenize.open(__file__) as f: 2023-09-08T15:09:38,270 setup_py_code = f.read() 2023-09-08T15:09:38,270 else: 2023-09-08T15:09:38,270 filename = "" 2023-09-08T15:09:38,270 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T15:09:38,270 2023-09-08T15:09:38,270 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T15:09:38,270 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-uioyt_xl/khmer_1d91fc8e2196472c81e63365fb0abd1d/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-czqk_pgx[/] 2023-09-08T15:09:38,271 [bold magenta]cwd[/]: /tmp/pip-wheel-uioyt_xl/khmer_1d91fc8e2196472c81e63365fb0abd1d/ 2023-09-08T15:09:38,271 Building wheel for khmer (setup.py): finished with status 'error' 2023-09-08T15:09:38,273 ERROR: Failed building wheel for khmer 2023-09-08T15:09:38,274 Running setup.py clean for khmer 2023-09-08T15:09:38,275 Running command python setup.py clean 2023-09-08T15:09:39,020 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-08T15:09:39,020 !! 2023-09-08T15:09:39,021 ******************************************************************************** 2023-09-08T15:09:39,022 Requirements should be satisfied by a PEP 517 installer. 2023-09-08T15:09:39,022 If you are using pip, you can try `pip install --use-pep517`. 2023-09-08T15:09:39,023 ******************************************************************************** 2023-09-08T15:09:39,024 !! 2023-09-08T15:09:39,024 dist.fetch_build_eggs(dist.setup_requires) 2023-09-08T15:09:41,652 running clean 2023-09-08T15:09:41,693 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T15:09:41,696 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T15:09:41,700 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-08T15:09:41,701 'build/scripts-3.11' does not exist -- can't clean it 2023-09-08T15:09:41,701 removing 'build' 2023-09-08T15:09:41,821 Failed to build khmer 2023-09-08T15:09:41,822 ERROR: Failed to build one or more wheels 2023-09-08T15:09:41,823 Exception information: 2023-09-08T15:09:41,823 Traceback (most recent call last): 2023-09-08T15:09:41,823 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T15:09:41,823 status = run_func(*args) 2023-09-08T15:09:41,823 ^^^^^^^^^^^^^^^ 2023-09-08T15:09:41,823 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T15:09:41,823 return func(self, options, args) 2023-09-08T15:09:41,823 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T15:09:41,823 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T15:09:41,823 raise CommandError("Failed to build one or more wheels") 2023-09-08T15:09:41,823 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T15:09:41,827 Removed build tracker: '/tmp/pip-build-tracker-5liw0iku'