2023-09-08T13:21:55,435 Created temporary directory: /tmp/pip-build-tracker-qc7gx5dk 2023-09-08T13:21:55,436 Initialized build tracking at /tmp/pip-build-tracker-qc7gx5dk 2023-09-08T13:21:55,437 Created build tracker: /tmp/pip-build-tracker-qc7gx5dk 2023-09-08T13:21:55,437 Entered build tracker: /tmp/pip-build-tracker-qc7gx5dk 2023-09-08T13:21:55,438 Created temporary directory: /tmp/pip-wheel-rz4xp1kp 2023-09-08T13:21:55,441 Created temporary directory: /tmp/pip-ephem-wheel-cache-9_ahtnr5 2023-09-08T13:21:55,462 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T13:21:55,466 2 location(s) to search for versions of khmer: 2023-09-08T13:21:55,466 * https://pypi.org/simple/khmer/ 2023-09-08T13:21:55,466 * https://www.piwheels.org/simple/khmer/ 2023-09-08T13:21:55,467 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2023-09-08T13:21:55,468 Getting page https://pypi.org/simple/khmer/ 2023-09-08T13:21:55,469 Found index url https://pypi.org/simple/ 2023-09-08T13:21:55,610 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2023-09-08T13:21:55,617 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/) 2023-09-08T13:21:55,618 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/) 2023-09-08T13:21:55,618 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2023-09-08T13:21:55,619 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 2023-09-08T13:21:55,620 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/) 2023-09-08T13:21:55,620 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2023-09-08T13:21:55,621 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/) 2023-09-08T13:21:55,622 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 2023-09-08T13:21:55,623 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/) 2023-09-08T13:21:55,623 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2023-09-08T13:21:55,624 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/) 2023-09-08T13:21:55,624 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2023-09-08T13:21:55,625 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/) 2023-09-08T13:21:55,626 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 2023-09-08T13:21:55,627 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2023-09-08T13:21:55,627 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/) 2023-09-08T13:21:55,628 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2023-09-08T13:21:55,628 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/) 2023-09-08T13:21:55,629 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2023-09-08T13:21:55,629 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/) 2023-09-08T13:21:55,630 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2023-09-08T13:21:55,630 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/) 2023-09-08T13:21:55,631 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/) 2023-09-08T13:21:55,632 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 2023-09-08T13:21:55,632 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/) 2023-09-08T13:21:55,633 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/) 2023-09-08T13:21:55,634 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/) 2023-09-08T13:21:55,634 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/) 2023-09-08T13:21:55,635 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2023-09-08T13:21:55,635 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2023-09-08T13:21:55,636 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/) 2023-09-08T13:21:55,637 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2023-09-08T13:21:55,637 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/) 2023-09-08T13:21:55,638 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/) 2023-09-08T13:21:55,638 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/) 2023-09-08T13:21:55,639 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/) 2023-09-08T13:21:55,639 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/) 2023-09-08T13:21:55,640 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 2023-09-08T13:21:55,640 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2023-09-08T13:21:55,641 Getting page https://www.piwheels.org/simple/khmer/ 2023-09-08T13:21:55,642 Found index url https://www.piwheels.org/simple/ 2023-09-08T13:21:55,963 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2023-09-08T13:21:55,965 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2023-09-08T13:21:55,965 Skipping link: not a file: https://pypi.org/simple/khmer/ 2023-09-08T13:21:55,995 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2023-09-08T13:21:56,021 Collecting khmer==0.6.1 2023-09-08T13:21:56,023 Created temporary directory: /tmp/pip-unpack-tvgme0qu 2023-09-08T13:21:56,500 Downloading khmer-0.6.1.tar.gz (19.2 MB) 2023-09-08T13:22:06,982 Added khmer==0.6.1 from https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz to build tracker '/tmp/pip-build-tracker-qc7gx5dk' 2023-09-08T13:22:06,984 Running setup.py (path:/tmp/pip-wheel-rz4xp1kp/khmer_0006bddfc16a4d52b2efc9a14c508ee9/setup.py) egg_info for package khmer 2023-09-08T13:22:06,985 Created temporary directory: /tmp/pip-pip-egg-info-dvo2dued 2023-09-08T13:22:06,986 Preparing metadata (setup.py): started 2023-09-08T13:22:06,987 Running command python setup.py egg_info 2023-09-08T13:22:07,756 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-08T13:22:07,756 !! 2023-09-08T13:22:07,758 ******************************************************************************** 2023-09-08T13:22:07,758 Requirements should be satisfied by a PEP 517 installer. 2023-09-08T13:22:07,759 If you are using pip, you can try `pip install --use-pep517`. 2023-09-08T13:22:07,759 ******************************************************************************** 2023-09-08T13:22:07,761 !! 2023-09-08T13:22:07,761 dist.fetch_build_eggs(dist.setup_requires) 2023-09-08T13:22:50,329 running egg_info 2023-09-08T13:22:50,331 creating /tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info 2023-09-08T13:22:50,373 writing /tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info/PKG-INFO 2023-09-08T13:22:50,376 writing dependency_links to /tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info/dependency_links.txt 2023-09-08T13:22:50,378 writing requirements to /tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info/requires.txt 2023-09-08T13:22:50,379 writing top-level names to /tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info/top_level.txt 2023-09-08T13:22:50,380 writing manifest file '/tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info/SOURCES.txt' 2023-09-08T13:22:50,583 reading manifest file '/tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info/SOURCES.txt' 2023-09-08T13:22:50,585 reading manifest template 'MANIFEST.in' 2023-09-08T13:22:50,586 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T13:22:50,589 writing manifest file '/tmp/pip-pip-egg-info-dvo2dued/khmer.egg-info/SOURCES.txt' 2023-09-08T13:22:50,709 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T13:22:50,712 Source in /tmp/pip-wheel-rz4xp1kp/khmer_0006bddfc16a4d52b2efc9a14c508ee9 has version 0.6.1, which satisfies requirement khmer==0.6.1 from https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz 2023-09-08T13:22:50,713 Removed khmer==0.6.1 from https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz from build tracker '/tmp/pip-build-tracker-qc7gx5dk' 2023-09-08T13:22:50,718 Created temporary directory: /tmp/pip-unpack-n5wnhack 2023-09-08T13:22:50,719 Created temporary directory: /tmp/pip-unpack-3xs7vqzg 2023-09-08T13:22:50,724 Building wheels for collected packages: khmer 2023-09-08T13:22:50,728 Created temporary directory: /tmp/pip-wheel-9mpnaamr 2023-09-08T13:22:50,729 Building wheel for khmer (setup.py): started 2023-09-08T13:22:50,730 Destination directory: /tmp/pip-wheel-9mpnaamr 2023-09-08T13:22:50,731 Running command python setup.py bdist_wheel 2023-09-08T13:22:51,455 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-08T13:22:51,455 !! 2023-09-08T13:22:51,457 ******************************************************************************** 2023-09-08T13:22:51,457 Requirements should be satisfied by a PEP 517 installer. 2023-09-08T13:22:51,458 If you are using pip, you can try `pip install --use-pep517`. 2023-09-08T13:22:51,458 ******************************************************************************** 2023-09-08T13:22:51,459 !! 2023-09-08T13:22:51,460 dist.fetch_build_eggs(dist.setup_requires) 2023-09-08T13:22:54,002 running bdist_wheel 2023-09-08T13:22:54,128 running build 2023-09-08T13:22:54,129 running build_py 2023-09-08T13:22:54,175 creating build 2023-09-08T13:22:54,175 creating build/lib.linux-armv7l-cpython-311 2023-09-08T13:22:54,176 creating build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,177 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,179 copying khmer/counting_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,181 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,183 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,185 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,187 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,188 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,190 running egg_info 2023-09-08T13:22:54,276 writing khmer.egg-info/PKG-INFO 2023-09-08T13:22:54,279 writing dependency_links to khmer.egg-info/dependency_links.txt 2023-09-08T13:22:54,281 writing requirements to khmer.egg-info/requires.txt 2023-09-08T13:22:54,282 writing top-level names to khmer.egg-info/top_level.txt 2023-09-08T13:22:54,337 reading manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T13:22:54,434 reading manifest template 'MANIFEST.in' 2023-09-08T13:22:54,435 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T13:22:54,455 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T13:22:54,473 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T13:22:54,478 running build_ext 2023-09-08T13:22:54,524 Checking for gcc... 2023-09-08T13:22:54,601 Checking for shared library support... 2023-09-08T13:22:54,773 Building shared library libz.so.1.2.3 with gcc. 2023-09-08T13:22:54,892 Checking for unistd.h... Yes. 2023-09-08T13:22:55,044 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf() 2023-09-08T13:22:55,237 Checking for vsnprintf() in stdio.h... Yes. 2023-09-08T13:22:55,335 Checking for return value of vsnprintf()... Yes. 2023-09-08T13:22:55,413 Checking for errno.h... Yes. 2023-09-08T13:22:55,509 Checking for mmap support... Yes. 2023-09-08T13:22:55,539 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2023-09-08T13:22:55,873 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2023-09-08T13:22:55,997 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2023-09-08T13:22:56,412 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2023-09-08T13:22:57,477 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2023-09-08T13:22:57,590 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2023-09-08T13:22:59,156 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2023-09-08T13:23:00,571 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2023-09-08T13:23:00,708 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2023-09-08T13:23:02,419 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2023-09-08T13:23:03,237 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2023-09-08T13:23:03,720 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2023-09-08T13:23:04,155 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 2023-09-08T13:23:04,359 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2023-09-08T13:23:05,250 In function ‘mainSimpleSort’, 2023-09-08T13:23:05,251 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2023-09-08T13:23:05,252 inlined from ‘mainSort’ at blocksort.c:897:19: 2023-09-08T13:23:05,252 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T13:23:05,253 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T13:23:05,253 | ^~~~~~~ 2023-09-08T13:23:05,254 blocksort.c:514:18: note: called from here 2023-09-08T13:23:05,255 514 | while ( mainGtU ( 2023-09-08T13:23:05,255 | ^~~~~~~~~ 2023-09-08T13:23:05,256 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T13:23:05,256 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:05,257 516 | ) ) { 2023-09-08T13:23:05,258 | ~ 2023-09-08T13:23:05,258 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T13:23:05,259 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T13:23:05,259 | ^~~~~~~ 2023-09-08T13:23:05,260 blocksort.c:528:18: note: called from here 2023-09-08T13:23:05,261 528 | while ( mainGtU ( 2023-09-08T13:23:05,262 | ^~~~~~~~~ 2023-09-08T13:23:05,262 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T13:23:05,263 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:05,264 530 | ) ) { 2023-09-08T13:23:05,265 | ~ 2023-09-08T13:23:05,265 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T13:23:05,266 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T13:23:05,266 | ^~~~~~~ 2023-09-08T13:23:05,267 blocksort.c:542:18: note: called from here 2023-09-08T13:23:05,267 542 | while ( mainGtU ( 2023-09-08T13:23:05,268 | ^~~~~~~~~ 2023-09-08T13:23:05,268 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T13:23:05,269 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:05,269 544 | ) ) { 2023-09-08T13:23:05,270 | ~ 2023-09-08T13:23:06,062 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2023-09-08T13:23:06,521 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2023-09-08T13:23:06,632 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2023-09-08T13:23:06,744 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2023-09-08T13:23:11,259 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2023-09-08T13:23:13,808 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2023-09-08T13:23:15,746 #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 2023-09-08T13:23:15,748 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2023-09-08T13:23:15,751 #rm -f libbz2.so.1.0 2023-09-08T13:23:15,753 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2023-09-08T13:23:15,762 building 'khmer._khmermodule' extension 2023-09-08T13:23:15,763 creating build/temp.linux-armv7l-cpython-311 2023-09-08T13:23:15,764 creating build/temp.linux-armv7l-cpython-311/khmer 2023-09-08T13:23:15,765 creating build/temp.linux-armv7l-cpython-311/lib 2023-09-08T13:23:15,767 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.11 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-cpython-311/khmer/_khmermodule.o -O3 2023-09-08T13:23:18,548 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2023-09-08T13:23:18,548 khmer/_khmermodule.cc:81:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2023-09-08T13:23:18,549 81 | tobj.ob_size = 0; 2023-09-08T13:23:18,550 | ^~~~~~~ 2023-09-08T13:23:18,551 khmer/_khmermodule.cc:82:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T13:23:18,552 82 | tobj.ob_type = &PyType_Type; 2023-09-08T13:23:18,553 | ^~~~~~~ 2023-09-08T13:23:18,557 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:23:18,558 khmer/_khmermodule.cc:198:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:18,559 198 | "Config", sizeof(khmer_ConfigObject), 2023-09-08T13:23:18,560 | ^~~~~~~~ 2023-09-08T13:23:18,561 | | 2023-09-08T13:23:18,563 | const char* 2023-09-08T13:23:18,564 khmer/_khmermodule.cc:200:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:18,565 200 | khmer_config_dealloc, /*tp_dealloc*/ 2023-09-08T13:23:18,566 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,566 | | 2023-09-08T13:23:18,567 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:23:18,569 khmer/_khmermodule.cc:202:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:23:18,570 202 | khmer_config_getattr, /*tp_getattr*/ 2023-09-08T13:23:18,571 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,571 | | 2023-09-08T13:23:18,572 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:23:18,573 In file included from /usr/include/python3.11/Python.h:44, 2023-09-08T13:23:18,574 from khmer/_khmermodule.cc:13: 2023-09-08T13:23:18,574 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:23:18,575 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:23:18,575 | ~~~ 2023-09-08T13:23:18,576 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:23:18,577 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:23:18,577 | | 2023-09-08T13:23:18,577 | int 2023-09-08T13:23:18,578 424 | 0) 2023-09-08T13:23:18,578 | ~~ 2023-09-08T13:23:18,579 khmer/_khmermodule.cc:215:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:23:18,579 215 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:23:18,580 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,580 khmer/_khmermodule.cc:216:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:23:18,581 216 | "config object", /* tp_doc */ 2023-09-08T13:23:18,582 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:18,582 | | 2023-09-08T13:23:18,583 | const char* 2023-09-08T13:23:18,589 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2023-09-08T13:23:18,590 khmer/_khmermodule.cc:300:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T13:23:18,591 300 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2023-09-08T13:23:18,592 | ^~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,593 | PyLong_FromSize_t 2023-09-08T13:23:18,614 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2023-09-08T13:23:18,615 khmer/_khmermodule.cc:358:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T13:23:18,616 358 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2023-09-08T13:23:18,617 | ^~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,617 | PyLong_FromSize_t 2023-09-08T13:23:18,638 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2023-09-08T13:23:18,639 khmer/_khmermodule.cc:386:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T13:23:18,640 386 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2023-09-08T13:23:18,640 | ^~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,641 | PyLong_FromSize_t 2023-09-08T13:23:18,662 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2023-09-08T13:23:18,663 khmer/_khmermodule.cc:434:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:23:18,664 434 | return Py_FindMethod(khmer_config_methods, obj, name); 2023-09-08T13:23:18,665 | ^~~~~~~~~~~~~ 2023-09-08T13:23:18,666 | PyCMethod 2023-09-08T13:23:18,689 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2023-09-08T13:23:18,690 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:23:18,691 472 | PyString_FromString( \ 2023-09-08T13:23:18,691 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,692 khmer/_khmermodule.cc:480:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:23:18,692 480 | { return KHMER_READ_STRING_GETTER( self, name ); } 2023-09-08T13:23:18,693 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,715 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2023-09-08T13:23:18,716 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:23:18,717 472 | PyString_FromString( \ 2023-09-08T13:23:18,717 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,718 khmer/_khmermodule.cc:486:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:23:18,719 486 | { return KHMER_READ_STRING_GETTER( self, sequence ); } 2023-09-08T13:23:18,719 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,742 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2023-09-08T13:23:18,743 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:23:18,743 472 | PyString_FromString( \ 2023-09-08T13:23:18,744 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,744 khmer/_khmermodule.cc:492:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:23:18,745 492 | { return KHMER_READ_STRING_GETTER( self, accuracy ); } 2023-09-08T13:23:18,746 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,768 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2023-09-08T13:23:18,769 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:23:18,770 472 | PyString_FromString( \ 2023-09-08T13:23:18,770 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,771 khmer/_khmermodule.cc:498:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:23:18,772 498 | { return KHMER_READ_STRING_GETTER( self, annotations ); } 2023-09-08T13:23:18,773 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,815 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2023-09-08T13:23:18,816 khmer/_khmermodule.cc:816:9: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:18,816 816 | PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ) 2023-09-08T13:23:18,817 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:18,818 | PyLong_FromLong 2023-09-08T13:23:18,844 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2023-09-08T13:23:18,845 khmer/_khmermodule.cc:959:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:23:18,846 959 | return PyString_FromString(khmer::_revhash(val, ktable->ksize()).c_str()); 2023-09-08T13:23:18,846 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,847 | PyLong_FromString 2023-09-08T13:23:18,866 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2023-09-08T13:23:18,867 khmer/_khmermodule.cc:985:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:18,868 985 | return PyInt_FromLong(1); 2023-09-08T13:23:18,869 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:18,870 | PyLong_FromLong 2023-09-08T13:23:18,890 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2023-09-08T13:23:18,890 khmer/_khmermodule.cc:1013:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:18,891 1013 | return PyInt_FromLong(n_consumed); 2023-09-08T13:23:18,892 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:18,892 | PyLong_FromLong 2023-09-08T13:23:18,908 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2023-09-08T13:23:18,909 khmer/_khmermodule.cc:1032:14: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:23:18,910 1032 | } else if (PyInt_Check(arg)) { 2023-09-08T13:23:18,910 | ^~~~~~~~~~~ 2023-09-08T13:23:18,911 | PySet_Check 2023-09-08T13:23:18,928 khmer/_khmermodule.cc:1033:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:23:18,928 1033 | long pos = PyInt_AsLong(arg); 2023-09-08T13:23:18,929 | ^~~~~~~~~~~~ 2023-09-08T13:23:18,930 | PyLong_AsLong 2023-09-08T13:23:18,950 khmer/_khmermodule.cc:1035:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:23:18,951 1035 | } else if (PyString_Check(arg)) { 2023-09-08T13:23:18,952 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:18,953 | PyMapping_Check 2023-09-08T13:23:18,977 khmer/_khmermodule.cc:1036:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:23:18,978 1036 | std::string s = PyString_AsString(arg); 2023-09-08T13:23:18,979 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:23:18,999 khmer/_khmermodule.cc:1040:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,000 1040 | return PyInt_FromLong(count); 2023-09-08T13:23:19,001 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,002 | PyLong_FromLong 2023-09-08T13:23:19,021 khmer/_khmermodule.cc: In function ‘PyObject* ktable__getitem__(PyObject*, Py_ssize_t)’: 2023-09-08T13:23:19,022 khmer/_khmermodule.cc:1050:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,023 1050 | return PyInt_FromLong(count); 2023-09-08T13:23:19,024 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,025 | PyLong_FromLong 2023-09-08T13:23:19,049 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2023-09-08T13:23:19,049 khmer/_khmermodule.cc:1058:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:23:19,050 1058 | char * kmer_str = PyString_AsString( val ); 2023-09-08T13:23:19,051 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,066 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2023-09-08T13:23:19,067 khmer/_khmermodule.cc:1076:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:23:19,068 1076 | if (PyInt_Check(arg)) { 2023-09-08T13:23:19,069 | ^~~~~~~~~~~ 2023-09-08T13:23:19,070 | PySet_Check 2023-09-08T13:23:19,086 khmer/_khmermodule.cc:1077:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:23:19,087 1077 | long pos = PyInt_AsLong(arg); 2023-09-08T13:23:19,088 | ^~~~~~~~~~~~ 2023-09-08T13:23:19,088 | PyLong_AsLong 2023-09-08T13:23:19,109 khmer/_khmermodule.cc:1079:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:23:19,110 1079 | } else if (PyString_Check(arg)) { 2023-09-08T13:23:19,111 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,112 | PyMapping_Check 2023-09-08T13:23:19,135 khmer/_khmermodule.cc:1080:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:23:19,136 1080 | std::string s = PyString_AsString(arg); 2023-09-08T13:23:19,137 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,157 khmer/_khmermodule.cc: In function ‘PyObject* ktable_max_hash(PyObject*, PyObject*)’: 2023-09-08T13:23:19,158 khmer/_khmermodule.cc:1097:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,159 1097 | return PyInt_FromLong(ktable->max_hash()); 2023-09-08T13:23:19,159 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,160 | PyLong_FromLong 2023-09-08T13:23:19,179 khmer/_khmermodule.cc: In function ‘PyObject* ktable_n_entries(PyObject*, PyObject*)’: 2023-09-08T13:23:19,180 khmer/_khmermodule.cc:1109:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,181 1109 | return PyInt_FromLong(ktable->n_entries()); 2023-09-08T13:23:19,181 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,182 | PyLong_FromLong 2023-09-08T13:23:19,202 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2023-09-08T13:23:19,203 khmer/_khmermodule.cc:1129:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,203 1129 | return PyInt_FromLong(ktable->ksize()); 2023-09-08T13:23:19,204 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,204 | PyLong_FromLong 2023-09-08T13:23:19,227 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2023-09-08T13:23:19,227 khmer/_khmermodule.cc:1175:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:23:19,228 1175 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2023-09-08T13:23:19,229 | ^~~~~~~~~~~~~ 2023-09-08T13:23:19,229 | PyCMethod 2023-09-08T13:23:19,230 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:23:19,231 khmer/_khmermodule.cc:1196:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:19,232 1196 | "KTable", sizeof(khmer_KTableObject), 2023-09-08T13:23:19,233 | ^~~~~~~~ 2023-09-08T13:23:19,233 | | 2023-09-08T13:23:19,234 | const char* 2023-09-08T13:23:19,235 khmer/_khmermodule.cc:1198:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:19,236 1198 | khmer_ktable_dealloc, /*tp_dealloc*/ 2023-09-08T13:23:19,237 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,237 | | 2023-09-08T13:23:19,238 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:23:19,239 khmer/_khmermodule.cc:1200:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:23:19,240 1200 | khmer_ktable_getattr, /*tp_getattr*/ 2023-09-08T13:23:19,240 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,241 | | 2023-09-08T13:23:19,242 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:23:19,242 khmer/_khmermodule.cc:1205:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2023-09-08T13:23:19,243 1205 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2023-09-08T13:23:19,244 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,245 | | 2023-09-08T13:23:19,245 | PySequenceMethods* 2023-09-08T13:23:19,246 khmer/_khmermodule.cc:1314:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:19,247 1314 | "KHashbits", sizeof(khmer_KHashbitsObject), 2023-09-08T13:23:19,247 | ^~~~~~~~~~~ 2023-09-08T13:23:19,247 | | 2023-09-08T13:23:19,248 | const char* 2023-09-08T13:23:19,248 khmer/_khmermodule.cc:1316:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:19,249 1316 | khmer_hashbits_dealloc, /*tp_dealloc*/ 2023-09-08T13:23:19,249 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,250 | | 2023-09-08T13:23:19,250 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:23:19,250 khmer/_khmermodule.cc:1318:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:23:19,251 1318 | khmer_hashbits_getattr, /*tp_getattr*/ 2023-09-08T13:23:19,251 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,251 | | 2023-09-08T13:23:19,252 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:23:19,252 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:23:19,253 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:23:19,253 | ~~~ 2023-09-08T13:23:19,254 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:23:19,254 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:23:19,255 | | 2023-09-08T13:23:19,256 | int 2023-09-08T13:23:19,256 424 | 0) 2023-09-08T13:23:19,257 | ~~ 2023-09-08T13:23:19,257 khmer/_khmermodule.cc:1331:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:23:19,258 1331 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:23:19,259 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,259 khmer/_khmermodule.cc:1332:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:23:19,260 1332 | "hashbits object", /* tp_doc */ 2023-09-08T13:23:19,261 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,262 | | 2023-09-08T13:23:19,263 | const char* 2023-09-08T13:23:19,263 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_occupied(PyObject*, PyObject*)’: 2023-09-08T13:23:19,264 khmer/_khmermodule.cc:1389:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,265 1389 | return PyInt_FromLong(n); 2023-09-08T13:23:19,266 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,266 | PyLong_FromLong 2023-09-08T13:23:19,282 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_entries(PyObject*, PyObject*)’: 2023-09-08T13:23:19,283 khmer/_khmermodule.cc:1401:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,283 1401 | return PyInt_FromLong(counting->n_entries()); 2023-09-08T13:23:19,284 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,285 | PyLong_FromLong 2023-09-08T13:23:19,305 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2023-09-08T13:23:19,305 khmer/_khmermodule.cc:1423:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,306 1423 | return PyInt_FromLong(1); 2023-09-08T13:23:19,307 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,308 | PyLong_FromLong 2023-09-08T13:23:19,327 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2023-09-08T13:23:19,328 khmer/_khmermodule.cc:1440:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,328 1440 | return PyInt_FromLong(0); 2023-09-08T13:23:19,329 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,330 | PyLong_FromLong 2023-09-08T13:23:19,353 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2023-09-08T13:23:19,354 khmer/_khmermodule.cc:1526:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,354 1526 | return PyInt_FromLong(n_consumed); 2023-09-08T13:23:19,355 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,355 | PyLong_FromLong 2023-09-08T13:23:19,376 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2023-09-08T13:23:19,377 khmer/_khmermodule.cc:1558:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,377 1558 | return PyInt_FromLong(n_consumed); 2023-09-08T13:23:19,378 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,379 | PyLong_FromLong 2023-09-08T13:23:19,399 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2023-09-08T13:23:19,400 khmer/_khmermodule.cc:1581:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,400 1581 | return PyInt_FromLong(N); 2023-09-08T13:23:19,401 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,402 | PyLong_FromLong 2023-09-08T13:23:19,422 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2023-09-08T13:23:19,423 khmer/_khmermodule.cc:1604:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,424 1604 | return PyInt_FromLong(N); 2023-09-08T13:23:19,425 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,425 | PyLong_FromLong 2023-09-08T13:23:19,445 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2023-09-08T13:23:19,446 khmer/_khmermodule.cc:1707:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:23:19,447 1707 | if (PyInt_Check(arg)) { 2023-09-08T13:23:19,447 | ^~~~~~~~~~~ 2023-09-08T13:23:19,448 | PySet_Check 2023-09-08T13:23:19,465 khmer/_khmermodule.cc:1708:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:23:19,466 1708 | long pos = PyInt_AsLong(arg); 2023-09-08T13:23:19,466 | ^~~~~~~~~~~~ 2023-09-08T13:23:19,467 | PyLong_AsLong 2023-09-08T13:23:19,488 khmer/_khmermodule.cc:1710:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:23:19,489 1710 | } else if (PyString_Check(arg)) { 2023-09-08T13:23:19,489 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,490 | PyMapping_Check 2023-09-08T13:23:19,515 khmer/_khmermodule.cc:1711:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:23:19,516 1711 | std::string s = PyString_AsString(arg); 2023-09-08T13:23:19,516 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,537 khmer/_khmermodule.cc:1715:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,537 1715 | return PyInt_FromLong(count); 2023-09-08T13:23:19,538 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,539 | PyLong_FromLong 2023-09-08T13:23:19,559 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2023-09-08T13:23:19,560 khmer/_khmermodule.cc:1731:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,561 1731 | return PyInt_FromLong(count); 2023-09-08T13:23:19,561 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,562 | PyLong_FromLong 2023-09-08T13:23:19,587 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2023-09-08T13:23:19,588 khmer/_khmermodule.cc:1755:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:23:19,589 1755 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:23:19,589 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,590 | PyBytes_FromStringAndSize 2023-09-08T13:23:19,616 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2023-09-08T13:23:19,616 khmer/_khmermodule.cc:1782:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:23:19,617 1782 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:23:19,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,618 | PyBytes_FromStringAndSize 2023-09-08T13:23:19,640 In file included from /usr/include/python3.11/Python.h:38: 2023-09-08T13:23:19,641 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution(PyObject*, PyObject*)’: 2023-09-08T13:23:19,641 khmer/_khmermodule.cc:1814:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,642 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:23:19,643 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,644 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:23:19,644 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:23:19,645 | ^~~~ 2023-09-08T13:23:19,646 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:23:19,647 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:23:19,648 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,648 khmer/_khmermodule.cc:1814:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:23:19,649 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:23:19,650 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:19,665 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution_with_reads_parser(PyObject*, PyObject*)’: 2023-09-08T13:23:19,666 khmer/_khmermodule.cc:1850:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,666 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:23:19,667 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,668 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:23:19,669 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:23:19,669 | ^~~~ 2023-09-08T13:23:19,670 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:23:19,671 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:23:19,672 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,672 khmer/_khmermodule.cc:1850:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:23:19,673 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:23:19,674 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:19,690 khmer/_khmermodule.cc: In function ‘PyObject* hash_fasta_count_kmers_by_position(PyObject*, PyObject*)’: 2023-09-08T13:23:19,691 khmer/_khmermodule.cc:1880:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,691 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2023-09-08T13:23:19,692 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,692 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:23:19,693 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:23:19,693 | ^~~~ 2023-09-08T13:23:19,694 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:23:19,694 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:23:19,695 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,696 khmer/_khmermodule.cc:1880:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:23:19,696 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2023-09-08T13:23:19,697 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:19,718 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2023-09-08T13:23:19,719 khmer/_khmermodule.cc:1987:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,719 1987 | return PyInt_FromLong(k); 2023-09-08T13:23:19,720 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,721 | PyLong_FromLong 2023-09-08T13:23:19,741 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_hashsizes(PyObject*, PyObject*)’: 2023-09-08T13:23:19,742 khmer/_khmermodule.cc:2004:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,742 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:23:19,743 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,743 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:23:19,744 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:23:19,745 | ^~~~ 2023-09-08T13:23:19,745 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:23:19,746 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:23:19,747 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,747 khmer/_khmermodule.cc:2004:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:23:19,748 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:23:19,749 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:19,767 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2023-09-08T13:23:19,768 khmer/_khmermodule.cc:2052:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:23:19,768 2052 | return Py_FindMethod(khmer_counting_methods, obj, name); 2023-09-08T13:23:19,769 | ^~~~~~~~~~~~~ 2023-09-08T13:23:19,770 | PyCMethod 2023-09-08T13:23:19,770 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:23:19,771 khmer/_khmermodule.cc:2060:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:19,772 2060 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2023-09-08T13:23:19,772 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:19,773 | | 2023-09-08T13:23:19,774 | const char* 2023-09-08T13:23:19,774 khmer/_khmermodule.cc:2062:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:19,775 2062 | khmer_counting_dealloc, /*tp_dealloc*/ 2023-09-08T13:23:19,776 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,777 | | 2023-09-08T13:23:19,777 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:23:19,778 khmer/_khmermodule.cc:2064:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:23:19,778 2064 | khmer_counting_getattr, /*tp_getattr*/ 2023-09-08T13:23:19,779 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,779 | | 2023-09-08T13:23:19,780 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:23:19,781 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:23:19,781 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:23:19,782 | ~~~ 2023-09-08T13:23:19,782 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:23:19,782 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:23:19,783 | | 2023-09-08T13:23:19,783 | int 2023-09-08T13:23:19,784 424 | 0) 2023-09-08T13:23:19,784 | ~~ 2023-09-08T13:23:19,785 khmer/_khmermodule.cc:2077:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:23:19,785 2077 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:23:19,786 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,786 khmer/_khmermodule.cc:2078:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:23:19,787 2078 | "counting hash object", /* tp_doc */ 2023-09-08T13:23:19,787 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,788 | | 2023-09-08T13:23:19,788 | const char* 2023-09-08T13:23:19,796 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_unique_kmers(PyObject*, PyObject*)’: 2023-09-08T13:23:19,796 khmer/_khmermodule.cc:2147:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,797 2147 | return PyInt_FromLong(n); 2023-09-08T13:23:19,798 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,798 | PyLong_FromLong 2023-09-08T13:23:19,821 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_occupied(PyObject*, PyObject*)’: 2023-09-08T13:23:19,821 khmer/_khmermodule.cc:2209:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,822 2209 | return PyInt_FromLong(n); 2023-09-08T13:23:19,823 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,824 | PyLong_FromLong 2023-09-08T13:23:19,843 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2023-09-08T13:23:19,844 khmer/_khmermodule.cc:2221:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,845 2221 | return PyInt_FromLong(hashbits->n_tags()); 2023-09-08T13:23:19,845 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,846 | PyLong_FromLong 2023-09-08T13:23:19,866 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2023-09-08T13:23:19,866 khmer/_khmermodule.cc:2243:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,867 2243 | return PyInt_FromLong(1); 2023-09-08T13:23:19,868 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,869 | PyLong_FromLong 2023-09-08T13:23:19,890 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2023-09-08T13:23:19,890 khmer/_khmermodule.cc:2266:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,891 2266 | return PyInt_FromLong(n_consumed); 2023-09-08T13:23:19,891 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,892 | PyLong_FromLong 2023-09-08T13:23:19,924 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2023-09-08T13:23:19,925 khmer/_khmermodule.cc:2377:43: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:19,925 2377 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2023-09-08T13:23:19,926 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:19,926 | PyLong_AsVoidPtr 2023-09-08T13:23:19,946 khmer/_khmermodule.cc:2386:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:19,947 2386 | return PyInt_FromLong(next_largest); 2023-09-08T13:23:19,947 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:19,948 | PyLong_FromLong 2023-09-08T13:23:19,965 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2023-09-08T13:23:19,966 khmer/_khmermodule.cc:2423:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:23:19,967 2423 | if (PyInt_Check(arg)) { 2023-09-08T13:23:19,967 | ^~~~~~~~~~~ 2023-09-08T13:23:19,968 | PySet_Check 2023-09-08T13:23:19,985 khmer/_khmermodule.cc:2424:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:23:19,986 2424 | long pos = PyInt_AsLong(arg); 2023-09-08T13:23:19,987 | ^~~~~~~~~~~~ 2023-09-08T13:23:19,987 | PyLong_AsLong 2023-09-08T13:23:20,008 khmer/_khmermodule.cc:2426:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:23:20,009 2426 | } else if (PyString_Check(arg)) { 2023-09-08T13:23:20,010 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,011 | PyMapping_Check 2023-09-08T13:23:20,035 khmer/_khmermodule.cc:2427:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:23:20,036 2427 | std::string s = PyString_AsString(arg); 2023-09-08T13:23:20,037 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,057 khmer/_khmermodule.cc:2431:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,058 2431 | return PyInt_FromLong(count); 2023-09-08T13:23:20,059 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,059 | PyLong_FromLong 2023-09-08T13:23:20,080 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_calc_connected_graph_size(PyObject*, PyObject*)’: 2023-09-08T13:23:20,081 khmer/_khmermodule.cc:2459:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,082 2459 | return PyInt_FromLong(size); 2023-09-08T13:23:20,082 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,083 | PyLong_FromLong 2023-09-08T13:23:20,103 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2023-09-08T13:23:20,104 khmer/_khmermodule.cc:2474:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,105 2474 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2023-09-08T13:23:20,105 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,107 | PyLong_FromLong 2023-09-08T13:23:20,132 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_degree(PyObject*, PyObject*)’: 2023-09-08T13:23:20,132 khmer/_khmermodule.cc:2496:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:23:20,133 2496 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:23:20,133 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,134 | PyBytes_FromStringAndSize 2023-09-08T13:23:20,160 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_sodd(PyObject*, PyObject*)’: 2023-09-08T13:23:20,161 khmer/_khmermodule.cc:2522:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:23:20,162 2522 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:23:20,162 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,163 | PyBytes_FromStringAndSize 2023-09-08T13:23:20,189 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2023-09-08T13:23:20,190 khmer/_khmermodule.cc:2547:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:23:20,191 2547 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:23:20,191 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,192 | PyBytes_FromStringAndSize 2023-09-08T13:23:20,233 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2023-09-08T13:23:20,233 khmer/_khmermodule.cc:2625:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T13:23:20,234 2625 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T13:23:20,235 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,235 | PyLong_FromVoidPtr 2023-09-08T13:23:20,259 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2023-09-08T13:23:20,260 khmer/_khmermodule.cc:2654:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T13:23:20,261 2654 | if (!PyCObject_Check(subset_obj)) { 2023-09-08T13:23:20,261 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:20,262 | PyODict_Check 2023-09-08T13:23:20,288 khmer/_khmermodule.cc:2659:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,289 2659 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:23:20,290 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,290 | PyLong_AsVoidPtr 2023-09-08T13:23:20,330 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2023-09-08T13:23:20,331 khmer/_khmermodule.cc:2951:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T13:23:20,332 2951 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T13:23:20,333 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,334 | PyLong_FromVoidPtr 2023-09-08T13:23:20,356 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2023-09-08T13:23:20,357 khmer/_khmermodule.cc:2964:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T13:23:20,358 2964 | if (!PyCObject_Check(ppi_obj)) { 2023-09-08T13:23:20,359 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:20,360 | PyODict_Check 2023-09-08T13:23:20,386 khmer/_khmermodule.cc:2969:33: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,386 2969 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2023-09-08T13:23:20,387 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,387 | PyLong_AsVoidPtr 2023-09-08T13:23:20,407 khmer/_khmermodule.cc:2975:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,408 2975 | return PyInt_FromLong(p); 2023-09-08T13:23:20,409 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,409 | PyLong_FromLong 2023-09-08T13:23:20,436 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2023-09-08T13:23:20,437 khmer/_khmermodule.cc:3093:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,437 3093 | return PyInt_FromLong(n_partitions); 2023-09-08T13:23:20,438 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,439 | PyLong_FromLong 2023-09-08T13:23:20,460 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2023-09-08T13:23:20,460 khmer/_khmermodule.cc:3124:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,461 3124 | return PyInt_FromLong(n_singletons); 2023-09-08T13:23:20,461 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,462 | PyLong_FromLong 2023-09-08T13:23:20,493 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2023-09-08T13:23:20,494 khmer/_khmermodule.cc:3227:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,495 3227 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:23:20,496 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,497 | PyLong_AsVoidPtr 2023-09-08T13:23:20,523 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2023-09-08T13:23:20,524 khmer/_khmermodule.cc:3245:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,525 3245 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:23:20,526 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,527 | PyLong_AsVoidPtr 2023-09-08T13:23:20,588 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T13:23:20,589 khmer/_khmermodule.cc:3347:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,589 3347 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:23:20,590 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,591 | PyLong_AsVoidPtr 2023-09-08T13:23:20,619 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T13:23:20,620 khmer/_khmermodule.cc:3379:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T13:23:20,621 3379 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T13:23:20,622 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,623 | PyLong_FromVoidPtr 2023-09-08T13:23:20,643 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2023-09-08T13:23:20,644 khmer/_khmermodule.cc:3409:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,645 3409 | return PyInt_FromLong(d); 2023-09-08T13:23:20,645 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,646 | PyLong_FromLong 2023-09-08T13:23:20,673 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2023-09-08T13:23:20,673 khmer/_khmermodule.cc:3425:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,674 3425 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T13:23:20,675 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,675 | PyLong_AsVoidPtr 2023-09-08T13:23:20,703 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2023-09-08T13:23:20,704 khmer/_khmermodule.cc:3451:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,704 3451 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T13:23:20,705 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,706 | PyLong_AsVoidPtr 2023-09-08T13:23:20,733 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T13:23:20,734 khmer/_khmermodule.cc:3472:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:23:20,735 3472 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:23:20,735 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,736 | PyLong_AsVoidPtr 2023-09-08T13:23:20,757 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2023-09-08T13:23:20,758 khmer/_khmermodule.cc:3510:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,759 3510 | return PyInt_FromLong(p1); 2023-09-08T13:23:20,760 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,761 | PyLong_FromLong 2023-09-08T13:23:20,780 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2023-09-08T13:23:20,781 khmer/_khmermodule.cc:3527:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,782 3527 | return PyInt_FromLong(partition_id); 2023-09-08T13:23:20,783 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,783 | PyLong_FromLong 2023-09-08T13:23:20,814 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_density_explosion(PyObject*, PyObject*)’: 2023-09-08T13:23:20,815 khmer/_khmermodule.cc:3651:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:23:20,816 3651 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:23:20,816 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,817 | PyBytes_FromStringAndSize 2023-09-08T13:23:20,838 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2023-09-08T13:23:20,839 khmer/_khmermodule.cc:3696:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,840 3696 | return PyInt_FromLong(k); 2023-09-08T13:23:20,841 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,842 | PyLong_FromLong 2023-09-08T13:23:20,862 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_hashsizes(PyObject*, PyObject*)’: 2023-09-08T13:23:20,862 khmer/_khmermodule.cc:3713:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:23:20,863 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:23:20,863 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,864 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:23:20,865 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:23:20,865 | ^~~~ 2023-09-08T13:23:20,866 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:23:20,866 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:23:20,867 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,867 khmer/_khmermodule.cc:3713:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:23:20,868 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:23:20,868 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:20,902 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2023-09-08T13:23:20,903 khmer/_khmermodule.cc:3736:27: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:23:20,903 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T13:23:20,904 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,904 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:23:20,905 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:23:20,905 | ^~~~ 2023-09-08T13:23:20,906 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:23:20,907 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:23:20,907 | ^~~~~~~~~~~~~~ 2023-09-08T13:23:20,908 khmer/_khmermodule.cc:3736:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:23:20,909 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T13:23:20,910 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:20,931 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2023-09-08T13:23:20,932 khmer/_khmermodule.cc:3847:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:23:20,933 3847 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2023-09-08T13:23:20,934 | ^~~~~~~~~~~~~ 2023-09-08T13:23:20,934 | PyCMethod 2023-09-08T13:23:20,961 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2023-09-08T13:23:20,962 khmer/_khmermodule.cc:3922:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:23:20,963 3922 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2023-09-08T13:23:20,963 | ^~~~~~~~~~~~~ 2023-09-08T13:23:20,964 | PyCMethod 2023-09-08T13:23:20,965 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:23:20,966 khmer/_khmermodule.cc:3940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:20,966 3940 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2023-09-08T13:23:20,967 | ^~~~~~~~~~~~~ 2023-09-08T13:23:20,968 | | 2023-09-08T13:23:20,969 | const char* 2023-09-08T13:23:20,969 khmer/_khmermodule.cc:3942:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:23:20,970 3942 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2023-09-08T13:23:20,971 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,972 | | 2023-09-08T13:23:20,972 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:23:20,973 khmer/_khmermodule.cc:3944:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:23:20,973 3944 | khmer_readaligner_getattr, /*tp_getattr*/ 2023-09-08T13:23:20,974 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,975 | | 2023-09-08T13:23:20,975 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:23:20,976 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:23:20,976 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:23:20,977 | ~~~ 2023-09-08T13:23:20,978 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:23:20,978 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:23:20,979 | | 2023-09-08T13:23:20,980 | int 2023-09-08T13:23:20,980 424 | 0) 2023-09-08T13:23:20,981 | ~~ 2023-09-08T13:23:20,982 khmer/_khmermodule.cc:3957:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:23:20,982 3957 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:23:20,983 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,984 khmer/_khmermodule.cc:3958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:23:20,984 3958 | "ReadAligner object", /* tp_doc */ 2023-09-08T13:23:20,985 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:20,986 | | 2023-09-08T13:23:20,987 | const char* 2023-09-08T13:23:21,005 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2023-09-08T13:23:21,005 khmer/_khmermodule.cc:4139:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:23:21,006 4139 | return PyString_FromString(khmer::_revhash(val, ksize).c_str()); 2023-09-08T13:23:21,007 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:21,008 | PyLong_FromString 2023-09-08T13:23:21,008 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:23:21,009 khmer/_khmermodule.cc:4195:17: error: expected constructor, destructor, or type conversion before ‘init_khmer’ 2023-09-08T13:23:21,010 4195 | DL_EXPORT(void) init_khmer(void) 2023-09-08T13:23:21,010 | ^~~~~~~~~~ 2023-09-08T13:23:21,846 khmer/_khmermodule.cc:4162:20: warning: ‘KhmerMethods’ defined but not used [-Wunused-variable] 2023-09-08T13:23:21,847 4162 | static PyMethodDef KhmerMethods[] = { 2023-09-08T13:23:21,847 | ^~~~~~~~~~~~ 2023-09-08T13:23:21,848 khmer/_khmermodule.cc:845:1: warning: ‘void khmer::python::_init_ReadPairIterator_Type()’ defined but not used [-Wunused-function] 2023-09-08T13:23:21,849 845 | _init_ReadPairIterator_Type( ) 2023-09-08T13:23:21,850 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:21,851 khmer/_khmermodule.cc:789:1: warning: ‘void khmer::python::_init_ReadParser_Type()’ defined but not used [-Wunused-function] 2023-09-08T13:23:21,851 789 | _init_ReadParser_Type( ) 2023-09-08T13:23:21,852 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:23:21,853 khmer/_khmermodule.cc:525:1: warning: ‘void khmer::python::_init_Read_Type()’ defined but not used [-Wunused-function] 2023-09-08T13:23:21,854 525 | _init_Read_Type( ) 2023-09-08T13:23:21,855 | ^~~~~~~~~~~~~~~ 2023-09-08T13:23:21,855 khmer/_khmermodule.cc:134:18: warning: ‘KhmerError’ defined but not used [-Wunused-variable] 2023-09-08T13:23:21,855 134 | static PyObject *KhmerError; 2023-09-08T13:23:21,856 | ^~~~~~~~~~ 2023-09-08T13:23:21,862 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T13:23:21,984 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T13:23:21,997 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T13:23:21,997 exec(compile('"'"''"'"''"'"' 2023-09-08T13:23:21,997 # This is -- a caller that pip uses to run setup.py 2023-09-08T13:23:21,997 # 2023-09-08T13:23:21,997 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T13:23:21,997 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T13:23:21,997 # - It provides a clear error message when setuptools is not installed. 2023-09-08T13:23:21,997 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T13:23:21,997 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T13:23:21,997 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T13:23:21,997 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T13:23:21,997 import os, sys, tokenize 2023-09-08T13:23:21,997 2023-09-08T13:23:21,997 try: 2023-09-08T13:23:21,997 import setuptools 2023-09-08T13:23:21,997 except ImportError as error: 2023-09-08T13:23:21,997 print( 2023-09-08T13:23:21,997 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T13:23:21,997 "the build environment.", 2023-09-08T13:23:21,997 file=sys.stderr, 2023-09-08T13:23:21,997 ) 2023-09-08T13:23:21,997 sys.exit(1) 2023-09-08T13:23:21,997 2023-09-08T13:23:21,997 __file__ = %r 2023-09-08T13:23:21,997 sys.argv[0] = __file__ 2023-09-08T13:23:21,997 2023-09-08T13:23:21,997 if os.path.exists(__file__): 2023-09-08T13:23:21,997 filename = __file__ 2023-09-08T13:23:21,997 with tokenize.open(__file__) as f: 2023-09-08T13:23:21,997 setup_py_code = f.read() 2023-09-08T13:23:21,997 else: 2023-09-08T13:23:21,997 filename = "" 2023-09-08T13:23:21,997 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T13:23:21,997 2023-09-08T13:23:21,997 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T13:23:21,997 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-rz4xp1kp/khmer_0006bddfc16a4d52b2efc9a14c508ee9/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-9mpnaamr[/] 2023-09-08T13:23:21,998 [bold magenta]cwd[/]: /tmp/pip-wheel-rz4xp1kp/khmer_0006bddfc16a4d52b2efc9a14c508ee9/ 2023-09-08T13:23:21,999 Building wheel for khmer (setup.py): finished with status 'error' 2023-09-08T13:23:22,000 ERROR: Failed building wheel for khmer 2023-09-08T13:23:22,001 Running setup.py clean for khmer 2023-09-08T13:23:22,002 Running command python setup.py clean 2023-09-08T13:23:22,751 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-08T13:23:22,751 !! 2023-09-08T13:23:22,752 ******************************************************************************** 2023-09-08T13:23:22,753 Requirements should be satisfied by a PEP 517 installer. 2023-09-08T13:23:22,753 If you are using pip, you can try `pip install --use-pep517`. 2023-09-08T13:23:22,754 ******************************************************************************** 2023-09-08T13:23:22,755 !! 2023-09-08T13:23:22,756 dist.fetch_build_eggs(dist.setup_requires) 2023-09-08T13:23:25,323 running clean 2023-09-08T13:23:25,408 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T13:23:25,411 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T13:23:25,415 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-08T13:23:25,415 'build/scripts-3.11' does not exist -- can't clean it 2023-09-08T13:23:25,416 removing 'build' 2023-09-08T13:23:25,535 Failed to build khmer 2023-09-08T13:23:25,537 ERROR: Failed to build one or more wheels 2023-09-08T13:23:25,538 Exception information: 2023-09-08T13:23:25,538 Traceback (most recent call last): 2023-09-08T13:23:25,538 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T13:23:25,538 status = run_func(*args) 2023-09-08T13:23:25,538 ^^^^^^^^^^^^^^^ 2023-09-08T13:23:25,538 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T13:23:25,538 return func(self, options, args) 2023-09-08T13:23:25,538 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T13:23:25,538 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T13:23:25,538 raise CommandError("Failed to build one or more wheels") 2023-09-08T13:23:25,538 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T13:23:25,542 Removed build tracker: '/tmp/pip-build-tracker-qc7gx5dk'