2025-09-07T22:53:50,878 Created temporary directory: /tmp/pip-build-tracker-pxedmvsj 2025-09-07T22:53:50,879 Initialized build tracking at /tmp/pip-build-tracker-pxedmvsj 2025-09-07T22:53:50,879 Created build tracker: /tmp/pip-build-tracker-pxedmvsj 2025-09-07T22:53:50,879 Entered build tracker: /tmp/pip-build-tracker-pxedmvsj 2025-09-07T22:53:50,879 Created temporary directory: /tmp/pip-wheel-nft9tw3k 2025-09-07T22:53:50,882 Created temporary directory: /tmp/pip-ephem-wheel-cache-d6lsljf4 2025-09-07T22:53:50,940 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T22:53:50,942 2 location(s) to search for versions of khmer: 2025-09-07T22:53:50,942 * https://pypi.org/simple/khmer/ 2025-09-07T22:53:50,942 * https://www.piwheels.org/simple/khmer/ 2025-09-07T22:53:50,942 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2025-09-07T22:53:50,943 Getting page https://pypi.org/simple/khmer/ 2025-09-07T22:53:50,944 Found index url https://pypi.org/simple/ 2025-09-07T22:53:51,094 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2025-09-07T22:53:51,105 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,105 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,106 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2025-09-07T22:53:51,106 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6.1 2025-09-07T22:53:51,107 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,107 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2025-09-07T22:53:51,108 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,108 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7.1 2025-09-07T22:53:51,108 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,109 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2025-09-07T22:53:51,109 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,110 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2025-09-07T22:53:51,110 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,110 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0.1 2025-09-07T22:53:51,111 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2025-09-07T22:53:51,111 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,112 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2025-09-07T22:53:51,112 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,112 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2025-09-07T22:53:51,113 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,113 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2025-09-07T22:53:51,114 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,114 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,114 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4.1 2025-09-07T22:53:51,115 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,115 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,115 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,116 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,116 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2025-09-07T22:53:51,116 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2025-09-07T22:53:51,117 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,117 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2025-09-07T22:53:51,117 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,117 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,117 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,118 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,118 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2025-09-07T22:53:51,118 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1.1 2025-09-07T22:53:51,118 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2025-09-07T22:53:51,118 Getting page https://www.piwheels.org/simple/khmer/ 2025-09-07T22:53:51,119 Found index url https://www.piwheels.org/simple/ 2025-09-07T22:53:51,215 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2025-09-07T22:53:51,216 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2025-09-07T22:53:51,216 Skipping link: not a file: https://pypi.org/simple/khmer/ 2025-09-07T22:53:51,244 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2025-09-07T22:53:51,245 Collecting khmer==0.6 2025-09-07T22:53:51,246 Created temporary directory: /tmp/pip-unpack-eyxv6nvx 2025-09-07T22:53:51,394 Downloading khmer-0.6.tar.gz (19.2 MB) 2025-09-07T22:53:55,320 Added khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz to build tracker '/tmp/pip-build-tracker-pxedmvsj' 2025-09-07T22:53:55,321 Running setup.py (path:/tmp/pip-wheel-nft9tw3k/khmer_3f31e6d00aa6435f8561af1b4361166f/setup.py) egg_info for package khmer 2025-09-07T22:53:55,321 Created temporary directory: /tmp/pip-pip-egg-info-5w04f0dq 2025-09-07T22:53:55,322 Preparing metadata (setup.py): started 2025-09-07T22:53:55,322 Running command python setup.py egg_info 2025-09-07T22:53:55,855 /tmp/pip-wheel-nft9tw3k/khmer_3f31e6d00aa6435f8561af1b4361166f/ez_setup.py:114: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T22:53:55,855 import pkg_resources 2025-09-07T22:53:56,700 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T22:53:56,701 !! 2025-09-07T22:53:56,701 ******************************************************************************** 2025-09-07T22:53:56,701 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T22:53:56,701 License :: OSI Approved :: BSD License 2025-09-07T22:53:56,701 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T22:53:56,701 ******************************************************************************** 2025-09-07T22:53:56,701 !! 2025-09-07T22:53:56,702 self._finalize_license_expression() 2025-09-07T22:53:57,148 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T22:53:57,273 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T22:53:57,278 Source in /tmp/pip-wheel-nft9tw3k/khmer_3f31e6d00aa6435f8561af1b4361166f has version 0.6, which satisfies requirement khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz 2025-09-07T22:53:57,278 Removed khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz from build tracker '/tmp/pip-build-tracker-pxedmvsj' 2025-09-07T22:53:57,282 Created temporary directory: /tmp/pip-unpack-lo9ttq6d 2025-09-07T22:53:57,282 Created temporary directory: /tmp/pip-unpack-j1bz0638 2025-09-07T22:53:57,282 Building wheels for collected packages: khmer 2025-09-07T22:53:57,284 Created temporary directory: /tmp/pip-wheel-q1lgspbs 2025-09-07T22:53:57,284 DEPRECATION: Building 'khmer' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'khmer'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-07T22:53:57,285 Building wheel for khmer (setup.py): started 2025-09-07T22:53:57,286 Destination directory: /tmp/pip-wheel-q1lgspbs 2025-09-07T22:53:57,286 Running command python setup.py bdist_wheel 2025-09-07T22:53:57,827 /tmp/pip-wheel-nft9tw3k/khmer_3f31e6d00aa6435f8561af1b4361166f/ez_setup.py:114: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T22:53:57,827 import pkg_resources 2025-09-07T22:53:58,676 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T22:53:58,676 !! 2025-09-07T22:53:58,677 ******************************************************************************** 2025-09-07T22:53:58,677 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T22:53:58,677 License :: OSI Approved :: BSD License 2025-09-07T22:53:58,677 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T22:53:58,677 ******************************************************************************** 2025-09-07T22:53:58,677 !! 2025-09-07T22:53:58,677 self._finalize_license_expression() 2025-09-07T22:53:59,246 warning: no previously-included files found matching 'data/1m-filtered.fa' 2025-09-07T22:53:59,327 Checking for gcc... 2025-09-07T22:53:59,403 Checking for shared library support... 2025-09-07T22:53:59,579 Building shared library libz.so.1.2.3 with gcc. 2025-09-07T22:53:59,674 Checking for unistd.h... Yes. 2025-09-07T22:53:59,791 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf() 2025-09-07T22:53:59,994 Checking for vsnprintf() in stdio.h... Yes. 2025-09-07T22:54:00,091 Checking for return value of vsnprintf()... Yes. 2025-09-07T22:54:00,169 Checking for errno.h... Yes. 2025-09-07T22:54:00,269 Checking for mmap support... Yes. 2025-09-07T22:54:00,299 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2025-09-07T22:54:00,614 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2025-09-07T22:54:00,739 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2025-09-07T22:54:01,201 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2025-09-07T22:54:02,323 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2025-09-07T22:54:02,441 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2025-09-07T22:54:04,049 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2025-09-07T22:54:05,563 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2025-09-07T22:54:05,699 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2025-09-07T22:54:07,542 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2025-09-07T22:54:08,416 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2025-09-07T22:54:08,948 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2025-09-07T22:54:09,437 ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 2025-09-07T22:54:09,619 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2025-09-07T22:54:10,591 In function ‘mainSimpleSort’, 2025-09-07T22:54:10,591 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2025-09-07T22:54:10,591 inlined from ‘mainSort’ at blocksort.c:897:19: 2025-09-07T22:54:10,592 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T22:54:10,592 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T22:54:10,592 | ^~~~~~~ 2025-09-07T22:54:10,593 blocksort.c:514:18: note: called from here 2025-09-07T22:54:10,593 514 | while ( mainGtU ( 2025-09-07T22:54:10,593 | ^~~~~~~~~ 2025-09-07T22:54:10,593 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T22:54:10,593 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:10,593 516 | ) ) { 2025-09-07T22:54:10,593 | ~ 2025-09-07T22:54:10,594 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T22:54:10,594 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T22:54:10,594 | ^~~~~~~ 2025-09-07T22:54:10,594 blocksort.c:528:18: note: called from here 2025-09-07T22:54:10,594 528 | while ( mainGtU ( 2025-09-07T22:54:10,594 | ^~~~~~~~~ 2025-09-07T22:54:10,595 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T22:54:10,595 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:10,595 530 | ) ) { 2025-09-07T22:54:10,595 | ~ 2025-09-07T22:54:10,595 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2025-09-07T22:54:10,595 347 | Bool mainGtU ( UInt32 i1, 2025-09-07T22:54:10,595 | ^~~~~~~ 2025-09-07T22:54:10,596 blocksort.c:542:18: note: called from here 2025-09-07T22:54:10,596 542 | while ( mainGtU ( 2025-09-07T22:54:10,596 | ^~~~~~~~~ 2025-09-07T22:54:10,596 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2025-09-07T22:54:10,596 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:10,596 544 | ) ) { 2025-09-07T22:54:10,596 | ~ 2025-09-07T22:54:11,471 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2025-09-07T22:54:11,953 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2025-09-07T22:54:12,068 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2025-09-07T22:54:12,181 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2025-09-07T22:54:16,775 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2025-09-07T22:54:19,412 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2025-09-07T22:54:21,630 #gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o 2025-09-07T22:54:21,632 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2025-09-07T22:54:21,634 #rm -f libbz2.so.1.0 2025-09-07T22:54:21,637 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2025-09-07T22:54:24,161 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2025-09-07T22:54:24,161 khmer/_khmermodule.cc:81:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2025-09-07T22:54:24,162 81 | tobj.ob_size = 0; 2025-09-07T22:54:24,162 | ^~~~~~~ 2025-09-07T22:54:24,162 khmer/_khmermodule.cc:82:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2025-09-07T22:54:24,162 82 | tobj.ob_type = &PyType_Type; 2025-09-07T22:54:24,162 | ^~~~~~~ 2025-09-07T22:54:24,166 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:54:24,166 khmer/_khmermodule.cc:217:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:24,166 217 | }; 2025-09-07T22:54:24,167 | ^ 2025-09-07T22:54:24,167 khmer/_khmermodule.cc:198:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:24,167 198 | "Config", sizeof(khmer_ConfigObject), 2025-09-07T22:54:24,167 | ^~~~~~~~ 2025-09-07T22:54:24,167 | | 2025-09-07T22:54:24,167 | const char* 2025-09-07T22:54:24,167 khmer/_khmermodule.cc:217:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:24,167 217 | }; 2025-09-07T22:54:24,167 | ^ 2025-09-07T22:54:24,168 | | 2025-09-07T22:54:24,168 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:54:24,168 khmer/_khmermodule.cc:217:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:54:24,168 217 | }; 2025-09-07T22:54:24,168 | ^ 2025-09-07T22:54:24,168 | | 2025-09-07T22:54:24,168 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:54:24,168 In file included from /usr/include/python3.13/Python.h:72, 2025-09-07T22:54:24,168 from khmer/_khmermodule.cc:13: 2025-09-07T22:54:24,169 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:54:24,169 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:54:24,169 | ~~~ 2025-09-07T22:54:24,169 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:54:24,169 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:54:24,169 | | 2025-09-07T22:54:24,169 | int 2025-09-07T22:54:24,169 731 | 0) 2025-09-07T22:54:24,170 | ~~ 2025-09-07T22:54:24,170 khmer/_khmermodule.cc:215:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:54:24,170 215 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:54:24,170 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,170 khmer/_khmermodule.cc:216:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:54:24,170 216 | "config object", /* tp_doc */ 2025-09-07T22:54:24,170 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:24,170 | | 2025-09-07T22:54:24,170 | const char* 2025-09-07T22:54:24,191 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2025-09-07T22:54:24,191 khmer/_khmermodule.cc:300:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T22:54:24,191 300 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2025-09-07T22:54:24,191 | ^~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,192 | PyLong_FromSize_t 2025-09-07T22:54:24,215 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2025-09-07T22:54:24,215 khmer/_khmermodule.cc:358:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T22:54:24,215 358 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2025-09-07T22:54:24,215 | ^~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,215 | PyLong_FromSize_t 2025-09-07T22:54:24,238 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2025-09-07T22:54:24,238 khmer/_khmermodule.cc:386:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2025-09-07T22:54:24,238 386 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2025-09-07T22:54:24,238 | ^~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,238 | PyLong_FromSize_t 2025-09-07T22:54:24,261 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2025-09-07T22:54:24,261 khmer/_khmermodule.cc:434:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:54:24,261 434 | return Py_FindMethod(khmer_config_methods, obj, name); 2025-09-07T22:54:24,261 | ^~~~~~~~~~~~~ 2025-09-07T22:54:24,261 | PyCMethod 2025-09-07T22:54:24,261 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:54:24,261 khmer/_khmermodule.cc:450:62: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:24,262 450 | static PyTypeObject Read_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T22:54:24,262 | ^ 2025-09-07T22:54:24,287 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2025-09-07T22:54:24,287 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:54:24,287 472 | PyString_FromString( \ 2025-09-07T22:54:24,287 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,287 khmer/_khmermodule.cc:480:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:54:24,288 480 | { return KHMER_READ_STRING_GETTER( self, name ); } 2025-09-07T22:54:24,288 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,312 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2025-09-07T22:54:24,312 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:54:24,312 472 | PyString_FromString( \ 2025-09-07T22:54:24,313 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,313 khmer/_khmermodule.cc:486:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:54:24,313 486 | { return KHMER_READ_STRING_GETTER( self, sequence ); } 2025-09-07T22:54:24,313 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,338 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2025-09-07T22:54:24,338 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:54:24,338 472 | PyString_FromString( \ 2025-09-07T22:54:24,338 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,338 khmer/_khmermodule.cc:492:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:54:24,338 492 | { return KHMER_READ_STRING_GETTER( self, accuracy ); } 2025-09-07T22:54:24,338 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,363 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2025-09-07T22:54:24,363 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:54:24,363 472 | PyString_FromString( \ 2025-09-07T22:54:24,363 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,363 khmer/_khmermodule.cc:498:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2025-09-07T22:54:24,363 498 | { return KHMER_READ_STRING_GETTER( self, annotations ); } 2025-09-07T22:54:24,364 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,364 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:54:24,365 khmer/_khmermodule.cc:550:68: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:24,365 550 | static PyTypeObject ReadParser_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T22:54:24,365 | ^ 2025-09-07T22:54:24,365 khmer/_khmermodule.cc:551:74: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:24,365 551 | static PyTypeObject ReadPairIterator_Type = { PyObject_HEAD_INIT( NULL ) }; 2025-09-07T22:54:24,365 | ^ 2025-09-07T22:54:24,402 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2025-09-07T22:54:24,402 khmer/_khmermodule.cc:816:9: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,402 816 | PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ) 2025-09-07T22:54:24,402 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,402 | PyLong_FromLong 2025-09-07T22:54:24,429 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2025-09-07T22:54:24,430 khmer/_khmermodule.cc:959:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:54:24,430 959 | return PyString_FromString(khmer::_revhash(val, ktable->ksize()).c_str()); 2025-09-07T22:54:24,430 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,430 | PyLong_FromString 2025-09-07T22:54:24,451 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2025-09-07T22:54:24,451 khmer/_khmermodule.cc:985:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,451 985 | return PyInt_FromLong(1); 2025-09-07T22:54:24,451 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,451 | PyLong_FromLong 2025-09-07T22:54:24,472 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2025-09-07T22:54:24,472 khmer/_khmermodule.cc:1013:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,473 1013 | return PyInt_FromLong(n_consumed); 2025-09-07T22:54:24,473 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,473 | PyLong_FromLong 2025-09-07T22:54:24,490 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2025-09-07T22:54:24,490 khmer/_khmermodule.cc:1032:14: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:54:24,490 1032 | } else if (PyInt_Check(arg)) { 2025-09-07T22:54:24,491 | ^~~~~~~~~~~ 2025-09-07T22:54:24,491 | PySet_Check 2025-09-07T22:54:24,508 khmer/_khmermodule.cc:1033:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:54:24,508 1033 | long pos = PyInt_AsLong(arg); 2025-09-07T22:54:24,509 | ^~~~~~~~~~~~ 2025-09-07T22:54:24,509 | PyLong_AsLong 2025-09-07T22:54:24,530 khmer/_khmermodule.cc:1035:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:54:24,530 1035 | } else if (PyString_Check(arg)) { 2025-09-07T22:54:24,531 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,531 | PyMapping_Check 2025-09-07T22:54:24,556 khmer/_khmermodule.cc:1036:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:54:24,556 1036 | std::string s = PyString_AsString(arg); 2025-09-07T22:54:24,556 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,577 khmer/_khmermodule.cc:1040:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,577 1040 | return PyInt_FromLong(count); 2025-09-07T22:54:24,577 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,577 | PyLong_FromLong 2025-09-07T22:54:24,598 khmer/_khmermodule.cc: In function ‘PyObject* ktable__getitem__(PyObject*, Py_ssize_t)’: 2025-09-07T22:54:24,598 khmer/_khmermodule.cc:1050:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,598 1050 | return PyInt_FromLong(count); 2025-09-07T22:54:24,598 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,599 | PyLong_FromLong 2025-09-07T22:54:24,624 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2025-09-07T22:54:24,624 khmer/_khmermodule.cc:1058:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:54:24,624 1058 | char * kmer_str = PyString_AsString( val ); 2025-09-07T22:54:24,624 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,641 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2025-09-07T22:54:24,642 khmer/_khmermodule.cc:1076:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:54:24,642 1076 | if (PyInt_Check(arg)) { 2025-09-07T22:54:24,642 | ^~~~~~~~~~~ 2025-09-07T22:54:24,642 | PySet_Check 2025-09-07T22:54:24,659 khmer/_khmermodule.cc:1077:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:54:24,660 1077 | long pos = PyInt_AsLong(arg); 2025-09-07T22:54:24,660 | ^~~~~~~~~~~~ 2025-09-07T22:54:24,660 | PyLong_AsLong 2025-09-07T22:54:24,682 khmer/_khmermodule.cc:1079:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:54:24,682 1079 | } else if (PyString_Check(arg)) { 2025-09-07T22:54:24,682 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,682 | PyMapping_Check 2025-09-07T22:54:24,707 khmer/_khmermodule.cc:1080:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:54:24,708 1080 | std::string s = PyString_AsString(arg); 2025-09-07T22:54:24,708 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,729 khmer/_khmermodule.cc: In function ‘PyObject* ktable_max_hash(PyObject*, PyObject*)’: 2025-09-07T22:54:24,729 khmer/_khmermodule.cc:1097:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,729 1097 | return PyInt_FromLong(ktable->max_hash()); 2025-09-07T22:54:24,729 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,729 | PyLong_FromLong 2025-09-07T22:54:24,750 khmer/_khmermodule.cc: In function ‘PyObject* ktable_n_entries(PyObject*, PyObject*)’: 2025-09-07T22:54:24,750 khmer/_khmermodule.cc:1109:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,750 1109 | return PyInt_FromLong(ktable->n_entries()); 2025-09-07T22:54:24,750 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,750 | PyLong_FromLong 2025-09-07T22:54:24,771 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2025-09-07T22:54:24,771 khmer/_khmermodule.cc:1129:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,771 1129 | return PyInt_FromLong(ktable->ksize()); 2025-09-07T22:54:24,771 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,772 | PyLong_FromLong 2025-09-07T22:54:24,795 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2025-09-07T22:54:24,795 khmer/_khmermodule.cc:1175:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:54:24,795 1175 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2025-09-07T22:54:24,795 | ^~~~~~~~~~~~~ 2025-09-07T22:54:24,795 | PyCMethod 2025-09-07T22:54:24,795 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:54:24,795 khmer/_khmermodule.cc:1215:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:24,795 1215 | }; 2025-09-07T22:54:24,796 | ^ 2025-09-07T22:54:24,796 khmer/_khmermodule.cc:1196:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:24,796 1196 | "KTable", sizeof(khmer_KTableObject), 2025-09-07T22:54:24,796 | ^~~~~~~~ 2025-09-07T22:54:24,796 | | 2025-09-07T22:54:24,796 | const char* 2025-09-07T22:54:24,796 khmer/_khmermodule.cc:1215:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:24,796 1215 | }; 2025-09-07T22:54:24,796 | ^ 2025-09-07T22:54:24,797 | | 2025-09-07T22:54:24,797 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:54:24,797 khmer/_khmermodule.cc:1215:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:54:24,797 1215 | }; 2025-09-07T22:54:24,797 | ^ 2025-09-07T22:54:24,797 | | 2025-09-07T22:54:24,797 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:54:24,797 khmer/_khmermodule.cc:1205:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2025-09-07T22:54:24,797 1205 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2025-09-07T22:54:24,797 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,798 | | 2025-09-07T22:54:24,798 | PySequenceMethods* 2025-09-07T22:54:24,799 khmer/_khmermodule.cc:1333:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:24,799 1333 | }; 2025-09-07T22:54:24,799 | ^ 2025-09-07T22:54:24,799 khmer/_khmermodule.cc:1314:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:24,799 1314 | "KHashbits", sizeof(khmer_KHashbitsObject), 2025-09-07T22:54:24,799 | ^~~~~~~~~~~ 2025-09-07T22:54:24,799 | | 2025-09-07T22:54:24,799 | const char* 2025-09-07T22:54:24,800 khmer/_khmermodule.cc:1333:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:24,800 1333 | }; 2025-09-07T22:54:24,800 | ^ 2025-09-07T22:54:24,800 | | 2025-09-07T22:54:24,800 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:54:24,800 khmer/_khmermodule.cc:1333:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:54:24,800 1333 | }; 2025-09-07T22:54:24,800 | ^ 2025-09-07T22:54:24,800 | | 2025-09-07T22:54:24,800 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:54:24,801 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:54:24,801 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:54:24,801 | ~~~ 2025-09-07T22:54:24,801 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:54:24,801 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:54:24,801 | | 2025-09-07T22:54:24,801 | int 2025-09-07T22:54:24,801 731 | 0) 2025-09-07T22:54:24,802 | ~~ 2025-09-07T22:54:24,802 khmer/_khmermodule.cc:1331:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:54:24,802 1331 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:54:24,802 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,802 khmer/_khmermodule.cc:1332:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:54:24,802 1332 | "hashbits object", /* tp_doc */ 2025-09-07T22:54:24,802 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:54:24,802 | | 2025-09-07T22:54:24,802 | const char* 2025-09-07T22:54:24,822 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_occupied(PyObject*, PyObject*)’: 2025-09-07T22:54:24,822 khmer/_khmermodule.cc:1389:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,822 1389 | return PyInt_FromLong(n); 2025-09-07T22:54:24,822 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,822 | PyLong_FromLong 2025-09-07T22:54:24,843 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_entries(PyObject*, PyObject*)’: 2025-09-07T22:54:24,843 khmer/_khmermodule.cc:1401:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,843 1401 | return PyInt_FromLong(counting->n_entries()); 2025-09-07T22:54:24,843 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,843 | PyLong_FromLong 2025-09-07T22:54:24,864 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2025-09-07T22:54:24,865 khmer/_khmermodule.cc:1423:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,865 1423 | return PyInt_FromLong(1); 2025-09-07T22:54:24,865 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,865 | PyLong_FromLong 2025-09-07T22:54:24,886 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2025-09-07T22:54:24,886 khmer/_khmermodule.cc:1440:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,886 1440 | return PyInt_FromLong(0); 2025-09-07T22:54:24,886 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,886 | PyLong_FromLong 2025-09-07T22:54:24,910 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2025-09-07T22:54:24,910 khmer/_khmermodule.cc:1526:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,910 1526 | return PyInt_FromLong(n_consumed); 2025-09-07T22:54:24,910 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,910 | PyLong_FromLong 2025-09-07T22:54:24,932 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2025-09-07T22:54:24,932 khmer/_khmermodule.cc:1558:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,932 1558 | return PyInt_FromLong(n_consumed); 2025-09-07T22:54:24,932 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,932 | PyLong_FromLong 2025-09-07T22:54:24,953 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2025-09-07T22:54:24,954 khmer/_khmermodule.cc:1581:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,954 1581 | return PyInt_FromLong(N); 2025-09-07T22:54:24,954 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,954 | PyLong_FromLong 2025-09-07T22:54:24,975 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2025-09-07T22:54:24,975 khmer/_khmermodule.cc:1604:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:24,976 1604 | return PyInt_FromLong(N); 2025-09-07T22:54:24,976 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:24,976 | PyLong_FromLong 2025-09-07T22:54:24,996 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2025-09-07T22:54:24,996 khmer/_khmermodule.cc:1707:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:54:24,997 1707 | if (PyInt_Check(arg)) { 2025-09-07T22:54:24,997 | ^~~~~~~~~~~ 2025-09-07T22:54:24,997 | PySet_Check 2025-09-07T22:54:25,014 khmer/_khmermodule.cc:1708:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:54:25,015 1708 | long pos = PyInt_AsLong(arg); 2025-09-07T22:54:25,015 | ^~~~~~~~~~~~ 2025-09-07T22:54:25,015 | PyLong_AsLong 2025-09-07T22:54:25,037 khmer/_khmermodule.cc:1710:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:54:25,037 1710 | } else if (PyString_Check(arg)) { 2025-09-07T22:54:25,037 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,037 | PyMapping_Check 2025-09-07T22:54:25,063 khmer/_khmermodule.cc:1711:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:54:25,063 1711 | std::string s = PyString_AsString(arg); 2025-09-07T22:54:25,063 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,084 khmer/_khmermodule.cc:1715:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,084 1715 | return PyInt_FromLong(count); 2025-09-07T22:54:25,084 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,084 | PyLong_FromLong 2025-09-07T22:54:25,105 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2025-09-07T22:54:25,106 khmer/_khmermodule.cc:1731:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,106 1731 | return PyInt_FromLong(count); 2025-09-07T22:54:25,106 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,106 | PyLong_FromLong 2025-09-07T22:54:25,133 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2025-09-07T22:54:25,133 khmer/_khmermodule.cc:1755:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:54:25,133 1755 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:54:25,133 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,133 | PyBytes_FromStringAndSize 2025-09-07T22:54:25,161 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2025-09-07T22:54:25,161 khmer/_khmermodule.cc:1782:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:54:25,161 1782 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:54:25,161 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,161 | PyBytes_FromStringAndSize 2025-09-07T22:54:25,183 In file included from /usr/include/python3.13/Python.h:63: 2025-09-07T22:54:25,184 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution(PyObject*, PyObject*)’: 2025-09-07T22:54:25,184 khmer/_khmermodule.cc:1814:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,184 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:54:25,184 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,184 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:54:25,184 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:54:25,184 | ^~~~ 2025-09-07T22:54:25,184 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:54:25,185 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:54:25,185 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,185 khmer/_khmermodule.cc:1814:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:54:25,185 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:54:25,185 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:25,206 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution_with_reads_parser(PyObject*, PyObject*)’: 2025-09-07T22:54:25,206 khmer/_khmermodule.cc:1850:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,206 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:54:25,206 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,207 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:54:25,207 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:54:25,207 | ^~~~ 2025-09-07T22:54:25,207 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:54:25,207 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:54:25,207 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,207 khmer/_khmermodule.cc:1850:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:54:25,207 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2025-09-07T22:54:25,207 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:25,228 khmer/_khmermodule.cc: In function ‘PyObject* hash_fasta_count_kmers_by_position(PyObject*, PyObject*)’: 2025-09-07T22:54:25,229 khmer/_khmermodule.cc:1880:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,229 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2025-09-07T22:54:25,229 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,229 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:54:25,229 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:54:25,229 | ^~~~ 2025-09-07T22:54:25,229 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:54:25,229 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:54:25,229 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,230 khmer/_khmermodule.cc:1880:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:54:25,230 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2025-09-07T22:54:25,230 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:25,254 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2025-09-07T22:54:25,254 khmer/_khmermodule.cc:1987:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,254 1987 | return PyInt_FromLong(k); 2025-09-07T22:54:25,254 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,254 | PyLong_FromLong 2025-09-07T22:54:25,275 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_hashsizes(PyObject*, PyObject*)’: 2025-09-07T22:54:25,276 khmer/_khmermodule.cc:2004:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,276 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:54:25,276 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,276 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:54:25,276 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:54:25,276 | ^~~~ 2025-09-07T22:54:25,276 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:54:25,276 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:54:25,276 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,276 khmer/_khmermodule.cc:2004:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:54:25,277 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:54:25,277 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:25,299 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2025-09-07T22:54:25,300 khmer/_khmermodule.cc:2052:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:54:25,300 2052 | return Py_FindMethod(khmer_counting_methods, obj, name); 2025-09-07T22:54:25,300 | ^~~~~~~~~~~~~ 2025-09-07T22:54:25,300 | PyCMethod 2025-09-07T22:54:25,300 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:54:25,300 khmer/_khmermodule.cc:2079:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:25,300 2079 | }; 2025-09-07T22:54:25,300 | ^ 2025-09-07T22:54:25,300 khmer/_khmermodule.cc:2060:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:25,301 2060 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2025-09-07T22:54:25,301 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:25,301 | | 2025-09-07T22:54:25,301 | const char* 2025-09-07T22:54:25,301 khmer/_khmermodule.cc:2079:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:25,301 2079 | }; 2025-09-07T22:54:25,301 | ^ 2025-09-07T22:54:25,301 | | 2025-09-07T22:54:25,301 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:54:25,302 khmer/_khmermodule.cc:2079:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:54:25,302 2079 | }; 2025-09-07T22:54:25,302 | ^ 2025-09-07T22:54:25,302 | | 2025-09-07T22:54:25,302 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:54:25,302 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:54:25,302 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:54:25,302 | ~~~ 2025-09-07T22:54:25,302 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:54:25,302 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:54:25,303 | | 2025-09-07T22:54:25,303 | int 2025-09-07T22:54:25,303 731 | 0) 2025-09-07T22:54:25,303 | ~~ 2025-09-07T22:54:25,303 khmer/_khmermodule.cc:2077:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:54:25,303 2077 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:54:25,303 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,303 khmer/_khmermodule.cc:2078:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:54:25,303 2078 | "counting hash object", /* tp_doc */ 2025-09-07T22:54:25,303 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,304 | | 2025-09-07T22:54:25,304 | const char* 2025-09-07T22:54:25,324 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_unique_kmers(PyObject*, PyObject*)’: 2025-09-07T22:54:25,324 khmer/_khmermodule.cc:2147:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,325 2147 | return PyInt_FromLong(n); 2025-09-07T22:54:25,325 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,325 | PyLong_FromLong 2025-09-07T22:54:25,348 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_occupied(PyObject*, PyObject*)’: 2025-09-07T22:54:25,348 khmer/_khmermodule.cc:2209:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,348 2209 | return PyInt_FromLong(n); 2025-09-07T22:54:25,348 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,348 | PyLong_FromLong 2025-09-07T22:54:25,369 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2025-09-07T22:54:25,369 khmer/_khmermodule.cc:2221:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,369 2221 | return PyInt_FromLong(hashbits->n_tags()); 2025-09-07T22:54:25,370 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,370 | PyLong_FromLong 2025-09-07T22:54:25,391 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2025-09-07T22:54:25,391 khmer/_khmermodule.cc:2243:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,391 2243 | return PyInt_FromLong(1); 2025-09-07T22:54:25,391 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,391 | PyLong_FromLong 2025-09-07T22:54:25,413 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2025-09-07T22:54:25,413 khmer/_khmermodule.cc:2266:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,413 2266 | return PyInt_FromLong(n_consumed); 2025-09-07T22:54:25,413 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,413 | PyLong_FromLong 2025-09-07T22:54:25,445 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2025-09-07T22:54:25,445 khmer/_khmermodule.cc:2377:43: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:25,445 2377 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2025-09-07T22:54:25,445 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,445 | PyLong_AsVoidPtr 2025-09-07T22:54:25,466 khmer/_khmermodule.cc:2386:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,466 2386 | return PyInt_FromLong(next_largest); 2025-09-07T22:54:25,466 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,466 | PyLong_FromLong 2025-09-07T22:54:25,484 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2025-09-07T22:54:25,485 khmer/_khmermodule.cc:2423:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2025-09-07T22:54:25,485 2423 | if (PyInt_Check(arg)) { 2025-09-07T22:54:25,485 | ^~~~~~~~~~~ 2025-09-07T22:54:25,485 | PySet_Check 2025-09-07T22:54:25,503 khmer/_khmermodule.cc:2424:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2025-09-07T22:54:25,503 2424 | long pos = PyInt_AsLong(arg); 2025-09-07T22:54:25,503 | ^~~~~~~~~~~~ 2025-09-07T22:54:25,503 | PyLong_AsLong 2025-09-07T22:54:25,525 khmer/_khmermodule.cc:2426:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2025-09-07T22:54:25,525 2426 | } else if (PyString_Check(arg)) { 2025-09-07T22:54:25,526 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,526 | PyMapping_Check 2025-09-07T22:54:25,551 khmer/_khmermodule.cc:2427:21: error: ‘PyString_AsString’ was not declared in this scope 2025-09-07T22:54:25,552 2427 | std::string s = PyString_AsString(arg); 2025-09-07T22:54:25,552 | ^~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,573 khmer/_khmermodule.cc:2431:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,573 2431 | return PyInt_FromLong(count); 2025-09-07T22:54:25,573 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,573 | PyLong_FromLong 2025-09-07T22:54:25,595 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_calc_connected_graph_size(PyObject*, PyObject*)’: 2025-09-07T22:54:25,595 khmer/_khmermodule.cc:2459:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,595 2459 | return PyInt_FromLong(size); 2025-09-07T22:54:25,595 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,595 | PyLong_FromLong 2025-09-07T22:54:25,616 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2025-09-07T22:54:25,616 khmer/_khmermodule.cc:2474:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,616 2474 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2025-09-07T22:54:25,616 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,617 | PyLong_FromLong 2025-09-07T22:54:25,644 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_degree(PyObject*, PyObject*)’: 2025-09-07T22:54:25,644 khmer/_khmermodule.cc:2496:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:54:25,644 2496 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:54:25,644 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,644 | PyBytes_FromStringAndSize 2025-09-07T22:54:25,672 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_sodd(PyObject*, PyObject*)’: 2025-09-07T22:54:25,672 khmer/_khmermodule.cc:2522:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:54:25,672 2522 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:54:25,672 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,672 | PyBytes_FromStringAndSize 2025-09-07T22:54:25,699 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2025-09-07T22:54:25,700 khmer/_khmermodule.cc:2547:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:54:25,700 2547 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:54:25,700 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,700 | PyBytes_FromStringAndSize 2025-09-07T22:54:25,739 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2025-09-07T22:54:25,739 khmer/_khmermodule.cc:2625:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T22:54:25,739 2625 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T22:54:25,739 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,739 | PyLong_FromVoidPtr 2025-09-07T22:54:25,763 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2025-09-07T22:54:25,763 khmer/_khmermodule.cc:2654:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T22:54:25,764 2654 | if (!PyCObject_Check(subset_obj)) { 2025-09-07T22:54:25,764 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:25,764 | PyODict_Check 2025-09-07T22:54:25,791 khmer/_khmermodule.cc:2659:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:25,792 2659 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:54:25,792 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,792 | PyLong_AsVoidPtr 2025-09-07T22:54:25,831 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2025-09-07T22:54:25,831 khmer/_khmermodule.cc:2951:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T22:54:25,831 2951 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2025-09-07T22:54:25,831 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,831 | PyLong_FromVoidPtr 2025-09-07T22:54:25,854 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2025-09-07T22:54:25,855 khmer/_khmermodule.cc:2964:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2025-09-07T22:54:25,855 2964 | if (!PyCObject_Check(ppi_obj)) { 2025-09-07T22:54:25,855 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:25,855 | PyODict_Check 2025-09-07T22:54:25,883 khmer/_khmermodule.cc:2969:33: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:25,883 2969 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2025-09-07T22:54:25,883 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,883 | PyLong_AsVoidPtr 2025-09-07T22:54:25,904 khmer/_khmermodule.cc:2975:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,904 2975 | return PyInt_FromLong(p); 2025-09-07T22:54:25,904 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,904 | PyLong_FromLong 2025-09-07T22:54:25,930 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2025-09-07T22:54:25,930 khmer/_khmermodule.cc:3093:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,931 3093 | return PyInt_FromLong(n_partitions); 2025-09-07T22:54:25,931 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,931 | PyLong_FromLong 2025-09-07T22:54:25,953 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2025-09-07T22:54:25,953 khmer/_khmermodule.cc:3124:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:25,953 3124 | return PyInt_FromLong(n_singletons); 2025-09-07T22:54:25,953 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:25,953 | PyLong_FromLong 2025-09-07T22:54:25,985 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2025-09-07T22:54:25,985 khmer/_khmermodule.cc:3227:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:25,985 3227 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:54:25,985 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:25,985 | PyLong_AsVoidPtr 2025-09-07T22:54:26,014 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2025-09-07T22:54:26,014 khmer/_khmermodule.cc:3245:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:26,014 3245 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:54:26,014 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,014 | PyLong_AsVoidPtr 2025-09-07T22:54:26,064 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T22:54:26,065 khmer/_khmermodule.cc:3347:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:26,065 3347 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:54:26,065 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,065 | PyLong_AsVoidPtr 2025-09-07T22:54:26,095 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T22:54:26,095 khmer/_khmermodule.cc:3379:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2025-09-07T22:54:26,095 3379 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2025-09-07T22:54:26,095 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,095 | PyLong_FromVoidPtr 2025-09-07T22:54:26,117 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2025-09-07T22:54:26,117 khmer/_khmermodule.cc:3409:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:26,117 3409 | return PyInt_FromLong(d); 2025-09-07T22:54:26,117 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:26,118 | PyLong_FromLong 2025-09-07T22:54:26,146 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2025-09-07T22:54:26,146 khmer/_khmermodule.cc:3425:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:26,146 3425 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T22:54:26,146 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,146 | PyLong_AsVoidPtr 2025-09-07T22:54:26,175 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2025-09-07T22:54:26,175 khmer/_khmermodule.cc:3451:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:26,175 3451 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2025-09-07T22:54:26,176 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,176 | PyLong_AsVoidPtr 2025-09-07T22:54:26,204 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2025-09-07T22:54:26,205 khmer/_khmermodule.cc:3472:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2025-09-07T22:54:26,205 3472 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2025-09-07T22:54:26,205 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,205 | PyLong_AsVoidPtr 2025-09-07T22:54:26,227 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2025-09-07T22:54:26,227 khmer/_khmermodule.cc:3510:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:26,227 3510 | return PyInt_FromLong(p1); 2025-09-07T22:54:26,227 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:26,228 | PyLong_FromLong 2025-09-07T22:54:26,249 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2025-09-07T22:54:26,249 khmer/_khmermodule.cc:3527:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:26,249 3527 | return PyInt_FromLong(partition_id); 2025-09-07T22:54:26,249 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:26,249 | PyLong_FromLong 2025-09-07T22:54:26,281 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_density_explosion(PyObject*, PyObject*)’: 2025-09-07T22:54:26,281 khmer/_khmermodule.cc:3651:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2025-09-07T22:54:26,281 3651 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2025-09-07T22:54:26,281 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,281 | PyBytes_FromStringAndSize 2025-09-07T22:54:26,303 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2025-09-07T22:54:26,304 khmer/_khmermodule.cc:3696:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:26,304 3696 | return PyInt_FromLong(k); 2025-09-07T22:54:26,304 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:26,304 | PyLong_FromLong 2025-09-07T22:54:26,326 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_hashsizes(PyObject*, PyObject*)’: 2025-09-07T22:54:26,326 khmer/_khmermodule.cc:3713:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2025-09-07T22:54:26,326 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:54:26,326 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:26,326 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:54:26,326 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:54:26,326 | ^~~~ 2025-09-07T22:54:26,327 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:54:26,327 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:54:26,327 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:26,327 khmer/_khmermodule.cc:3713:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:54:26,327 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2025-09-07T22:54:26,327 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:26,361 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2025-09-07T22:54:26,361 khmer/_khmermodule.cc:3736:27: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:54:26,361 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T22:54:26,361 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,361 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-07T22:54:26,361 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-07T22:54:26,362 | ^~~~ 2025-09-07T22:54:26,362 /usr/include/python3.13/cpython/listobject.h:50:50: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-07T22:54:26,362 50 | PyList_SET_ITEM(_PyObject_CAST(op), (index), _PyObject_CAST(value)) 2025-09-07T22:54:26,362 | ^~~~~~~~~~~~~~ 2025-09-07T22:54:26,362 khmer/_khmermodule.cc:3736:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2025-09-07T22:54:26,362 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2025-09-07T22:54:26,362 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:26,388 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2025-09-07T22:54:26,388 khmer/_khmermodule.cc:3847:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:54:26,389 3847 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2025-09-07T22:54:26,389 | ^~~~~~~~~~~~~ 2025-09-07T22:54:26,389 | PyCMethod 2025-09-07T22:54:26,416 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2025-09-07T22:54:26,416 khmer/_khmermodule.cc:3922:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2025-09-07T22:54:26,416 3922 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2025-09-07T22:54:26,417 | ^~~~~~~~~~~~~ 2025-09-07T22:54:26,417 | PyCMethod 2025-09-07T22:54:26,417 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:54:26,417 khmer/_khmermodule.cc:3959:1: warning: converting to non-pointer type ‘int’ from NULL [-Wconversion-null] 2025-09-07T22:54:26,417 3959 | }; 2025-09-07T22:54:26,417 | ^ 2025-09-07T22:54:26,417 khmer/_khmermodule.cc:3940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:26,417 3940 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2025-09-07T22:54:26,418 | ^~~~~~~~~~~~~ 2025-09-07T22:54:26,418 | | 2025-09-07T22:54:26,418 | const char* 2025-09-07T22:54:26,418 khmer/_khmermodule.cc:3959:1: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2025-09-07T22:54:26,418 3959 | }; 2025-09-07T22:54:26,418 | ^ 2025-09-07T22:54:26,418 | | 2025-09-07T22:54:26,418 | void (*)(PyObject*) {aka void (*)(_object*)} 2025-09-07T22:54:26,418 khmer/_khmermodule.cc:3959:1: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2025-09-07T22:54:26,418 3959 | }; 2025-09-07T22:54:26,419 | ^ 2025-09-07T22:54:26,419 | | 2025-09-07T22:54:26,419 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2025-09-07T22:54:26,419 /usr/include/python3.13/object.h:730:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2025-09-07T22:54:26,419 729 | #define Py_TPFLAGS_DEFAULT ( \ 2025-09-07T22:54:26,419 | ~~~ 2025-09-07T22:54:26,419 730 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2025-09-07T22:54:26,419 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2025-09-07T22:54:26,419 | | 2025-09-07T22:54:26,419 | int 2025-09-07T22:54:26,420 731 | 0) 2025-09-07T22:54:26,420 | ~~ 2025-09-07T22:54:26,420 khmer/_khmermodule.cc:3957:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2025-09-07T22:54:26,420 3957 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2025-09-07T22:54:26,420 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,420 khmer/_khmermodule.cc:3958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2025-09-07T22:54:26,420 3958 | "ReadAligner object", /* tp_doc */ 2025-09-07T22:54:26,420 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,420 | | 2025-09-07T22:54:26,420 | const char* 2025-09-07T22:54:26,452 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2025-09-07T22:54:26,452 khmer/_khmermodule.cc:4139:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2025-09-07T22:54:26,452 4139 | return PyString_FromString(khmer::_revhash(val, ksize).c_str()); 2025-09-07T22:54:26,453 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:26,453 | PyLong_FromString 2025-09-07T22:54:26,454 khmer/_khmermodule.cc: At global scope: 2025-09-07T22:54:26,454 khmer/_khmermodule.cc:4195:17: error: expected constructor, destructor, or type conversion before ‘init_khmer’ 2025-09-07T22:54:26,454 4195 | DL_EXPORT(void) init_khmer(void) 2025-09-07T22:54:26,454 | ^~~~~~~~~~ 2025-09-07T22:54:27,121 khmer/_khmermodule.cc:4162:20: warning: ‘KhmerMethods’ defined but not used [-Wunused-variable] 2025-09-07T22:54:27,122 4162 | static PyMethodDef KhmerMethods[] = { 2025-09-07T22:54:27,122 | ^~~~~~~~~~~~ 2025-09-07T22:54:27,122 khmer/_khmermodule.cc:845:1: warning: ‘void khmer::python::_init_ReadPairIterator_Type()’ defined but not used [-Wunused-function] 2025-09-07T22:54:27,122 845 | _init_ReadPairIterator_Type( ) 2025-09-07T22:54:27,122 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:27,122 khmer/_khmermodule.cc:789:1: warning: ‘void khmer::python::_init_ReadParser_Type()’ defined but not used [-Wunused-function] 2025-09-07T22:54:27,122 789 | _init_ReadParser_Type( ) 2025-09-07T22:54:27,122 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-07T22:54:27,123 khmer/_khmermodule.cc:525:1: warning: ‘void khmer::python::_init_Read_Type()’ defined but not used [-Wunused-function] 2025-09-07T22:54:27,123 525 | _init_Read_Type( ) 2025-09-07T22:54:27,123 | ^~~~~~~~~~~~~~~ 2025-09-07T22:54:27,123 khmer/_khmermodule.cc:134:18: warning: ‘KhmerError’ defined but not used [-Wunused-variable] 2025-09-07T22:54:27,123 134 | static PyObject *KhmerError; 2025-09-07T22:54:27,123 | ^~~~~~~~~~ 2025-09-07T22:54:27,137 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-07T22:54:27,262 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T22:54:27,274 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T22:54:27,274 exec(compile('"'"''"'"''"'"' 2025-09-07T22:54:27,274 # This is -- a caller that pip uses to run setup.py 2025-09-07T22:54:27,274 # 2025-09-07T22:54:27,274 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T22:54:27,274 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T22:54:27,274 # - It provides a clear error message when setuptools is not installed. 2025-09-07T22:54:27,274 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T22:54:27,274 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T22:54:27,274 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T22:54:27,274 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T22:54:27,274 import os, sys, tokenize, traceback 2025-09-07T22:54:27,274 2025-09-07T22:54:27,274 try: 2025-09-07T22:54:27,274 import setuptools 2025-09-07T22:54:27,274 except ImportError: 2025-09-07T22:54:27,274 print( 2025-09-07T22:54:27,274 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T22:54:27,274 "the build environment with exception:", 2025-09-07T22:54:27,274 file=sys.stderr, 2025-09-07T22:54:27,274 ) 2025-09-07T22:54:27,274 traceback.print_exc() 2025-09-07T22:54:27,274 sys.exit(1) 2025-09-07T22:54:27,274 2025-09-07T22:54:27,274 __file__ = %r 2025-09-07T22:54:27,274 sys.argv[0] = __file__ 2025-09-07T22:54:27,274 2025-09-07T22:54:27,274 if os.path.exists(__file__): 2025-09-07T22:54:27,274 filename = __file__ 2025-09-07T22:54:27,274 with tokenize.open(__file__) as f: 2025-09-07T22:54:27,274 setup_py_code = f.read() 2025-09-07T22:54:27,274 else: 2025-09-07T22:54:27,274 filename = "" 2025-09-07T22:54:27,274 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T22:54:27,274 2025-09-07T22:54:27,274 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T22:54:27,274 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-nft9tw3k/khmer_3f31e6d00aa6435f8561af1b4361166f/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-q1lgspbs[/] 2025-09-07T22:54:27,274 [bold magenta]cwd[/]: /tmp/pip-wheel-nft9tw3k/khmer_3f31e6d00aa6435f8561af1b4361166f/ 2025-09-07T22:54:27,274 Building wheel for khmer (setup.py): finished with status 'error' 2025-09-07T22:54:27,275 ERROR: Failed building wheel for khmer 2025-09-07T22:54:27,275 Running setup.py clean for khmer 2025-09-07T22:54:27,276 Running command python setup.py clean 2025-09-07T22:54:27,833 /tmp/pip-wheel-nft9tw3k/khmer_3f31e6d00aa6435f8561af1b4361166f/ez_setup.py:114: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T22:54:27,833 import pkg_resources 2025-09-07T22:54:28,687 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T22:54:28,688 !! 2025-09-07T22:54:28,688 ******************************************************************************** 2025-09-07T22:54:28,688 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T22:54:28,688 License :: OSI Approved :: BSD License 2025-09-07T22:54:28,688 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T22:54:28,688 ******************************************************************************** 2025-09-07T22:54:28,689 !! 2025-09-07T22:54:28,689 self._finalize_license_expression() 2025-09-07T22:54:28,911 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T22:54:28,911 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T22:54:29,033 Failed to build khmer 2025-09-07T22:54:29,034 ERROR: Failed to build one or more wheels 2025-09-07T22:54:29,035 Exception information: 2025-09-07T22:54:29,035 Traceback (most recent call last): 2025-09-07T22:54:29,035 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T22:54:29,035 status = _inner_run() 2025-09-07T22:54:29,035 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T22:54:29,035 return self.run(options, args) 2025-09-07T22:54:29,035 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T22:54:29,035 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T22:54:29,035 return func(self, options, args) 2025-09-07T22:54:29,035 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T22:54:29,035 raise CommandError("Failed to build one or more wheels") 2025-09-07T22:54:29,035 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T22:54:29,039 Removed build tracker: '/tmp/pip-build-tracker-pxedmvsj'