2023-09-08T15:30:07,487 Created temporary directory: /tmp/pip-build-tracker-rlvxxff1 2023-09-08T15:30:07,488 Initialized build tracking at /tmp/pip-build-tracker-rlvxxff1 2023-09-08T15:30:07,489 Created build tracker: /tmp/pip-build-tracker-rlvxxff1 2023-09-08T15:30:07,489 Entered build tracker: /tmp/pip-build-tracker-rlvxxff1 2023-09-08T15:30:07,490 Created temporary directory: /tmp/pip-wheel-krd2gyzo 2023-09-08T15:30:07,493 Created temporary directory: /tmp/pip-ephem-wheel-cache-dgli5v36 2023-09-08T15:30:07,515 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T15:30:07,519 2 location(s) to search for versions of khmer: 2023-09-08T15:30:07,519 * https://pypi.org/simple/khmer/ 2023-09-08T15:30:07,519 * https://www.piwheels.org/simple/khmer/ 2023-09-08T15:30:07,520 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2023-09-08T15:30:07,520 Getting page https://pypi.org/simple/khmer/ 2023-09-08T15:30:07,522 Found index url https://pypi.org/simple/ 2023-09-08T15:30:07,668 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2023-09-08T15:30:07,676 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,676 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,677 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2023-09-08T15:30:07,677 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6.1 2023-09-08T15:30:07,678 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,679 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2023-09-08T15:30:07,680 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,680 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7.1 2023-09-08T15:30:07,681 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,682 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2023-09-08T15:30:07,682 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,683 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2023-09-08T15:30:07,683 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,684 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0.1 2023-09-08T15:30:07,685 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2023-09-08T15:30:07,686 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,686 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2023-09-08T15:30:07,687 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,687 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2023-09-08T15:30:07,688 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,688 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2023-09-08T15:30:07,689 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,690 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,690 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4.1 2023-09-08T15:30:07,691 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,692 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,692 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,693 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,693 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2023-09-08T15:30:07,694 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2023-09-08T15:30:07,695 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,695 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2023-09-08T15:30:07,696 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,696 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,697 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,697 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,698 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:30:07,698 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1.1 2023-09-08T15:30:07,699 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2023-09-08T15:30:07,700 Getting page https://www.piwheels.org/simple/khmer/ 2023-09-08T15:30:07,701 Found index url https://www.piwheels.org/simple/ 2023-09-08T15:30:07,997 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2023-09-08T15:30:07,999 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2023-09-08T15:30:07,999 Skipping link: not a file: https://pypi.org/simple/khmer/ 2023-09-08T15:30:08,019 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2023-09-08T15:30:08,037 Collecting khmer==1.0.1 2023-09-08T15:30:08,039 Created temporary directory: /tmp/pip-unpack-nna0j_xz 2023-09-08T15:30:08,906 Downloading khmer-1.0.1.tar.gz (19.0 MB) 2023-09-08T15:30:18,065 Added khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-rlvxxff1' 2023-09-08T15:30:18,067 Running setup.py (path:/tmp/pip-wheel-krd2gyzo/khmer_583a5c043eb54b749d7bc8a3285014ac/setup.py) egg_info for package khmer 2023-09-08T15:30:18,068 Created temporary directory: /tmp/pip-pip-egg-info-falmgw_x 2023-09-08T15:30:18,069 Preparing metadata (setup.py): started 2023-09-08T15:30:18,070 Running command python setup.py egg_info 2023-09-08T15:30:18,966 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T15:30:18,967 !! 2023-09-08T15:30:18,968 ******************************************************************************** 2023-09-08T15:30:18,969 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T15:30:18,969 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T15:30:18,970 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T15:30:18,971 or your builds will no longer be supported. 2023-09-08T15:30:18,972 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T15:30:18,973 ******************************************************************************** 2023-09-08T15:30:18,973 !! 2023-09-08T15:30:18,974 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T15:30:19,161 running egg_info 2023-09-08T15:30:19,162 creating /tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info 2023-09-08T15:30:19,188 writing /tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info/PKG-INFO 2023-09-08T15:30:19,192 writing dependency_links to /tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info/dependency_links.txt 2023-09-08T15:30:19,195 writing requirements to /tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info/requires.txt 2023-09-08T15:30:19,196 writing top-level names to /tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info/top_level.txt 2023-09-08T15:30:19,197 writing manifest file '/tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info/SOURCES.txt' 2023-09-08T15:30:19,229 dependency lib/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,229 dependency lib/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,230 dependency lib/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,230 dependency lib/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,231 dependency lib/zlib/gzclose.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,231 dependency lib/zlib/gzlib.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,232 dependency lib/zlib/gzread.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,233 dependency lib/zlib/gzwrite.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,233 dependency lib/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,234 dependency lib/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,234 dependency lib/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,235 dependency lib/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,235 dependency lib/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,236 dependency lib/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,236 dependency lib/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,237 dependency lib/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,238 dependency lib/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,238 dependency lib/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,239 dependency lib/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,239 dependency lib/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,240 dependency lib/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,241 dependency lib/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:19,288 reading manifest file '/tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info/SOURCES.txt' 2023-09-08T15:30:19,290 reading manifest template 'MANIFEST.in' 2023-09-08T15:30:20,886 warning: no previously-included files found matching 'lib/zlib/Makefile' 2023-09-08T15:30:20,887 warning: no previously-included files found matching 'lib/zlib/zconf.h' 2023-09-08T15:30:20,904 no previously-included directories found matching 'doc/doxygen' 2023-09-08T15:30:20,912 warning: no previously-included files matching '*.orig' found anywhere in distribution 2023-09-08T15:30:20,913 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-09-08T15:30:20,913 adding license file 'LICENSE' 2023-09-08T15:30:20,926 writing manifest file '/tmp/pip-pip-egg-info-falmgw_x/khmer.egg-info/SOURCES.txt' 2023-09-08T15:30:21,040 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T15:30:21,044 Source in /tmp/pip-wheel-krd2gyzo/khmer_583a5c043eb54b749d7bc8a3285014ac has version 1.0.1, which satisfies requirement khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz 2023-09-08T15:30:21,045 Removed khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-rlvxxff1' 2023-09-08T15:30:21,049 Created temporary directory: /tmp/pip-unpack-ygg_06jk 2023-09-08T15:30:21,050 Created temporary directory: /tmp/pip-unpack-y50g67ls 2023-09-08T15:30:21,065 Building wheels for collected packages: khmer 2023-09-08T15:30:21,069 Created temporary directory: /tmp/pip-wheel-tksvqms5 2023-09-08T15:30:21,070 Building wheel for khmer (setup.py): started 2023-09-08T15:30:21,071 Destination directory: /tmp/pip-wheel-tksvqms5 2023-09-08T15:30:21,072 Running command python setup.py bdist_wheel 2023-09-08T15:30:21,961 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T15:30:21,961 !! 2023-09-08T15:30:21,962 ******************************************************************************** 2023-09-08T15:30:21,963 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T15:30:21,963 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T15:30:21,965 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T15:30:21,965 or your builds will no longer be supported. 2023-09-08T15:30:21,966 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T15:30:21,967 ******************************************************************************** 2023-09-08T15:30:21,968 !! 2023-09-08T15:30:21,969 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T15:30:22,144 running bdist_wheel 2023-09-08T15:30:22,191 running build 2023-09-08T15:30:22,192 got version from file /tmp/pip-wheel-krd2gyzo/khmer_583a5c043eb54b749d7bc8a3285014ac/khmer/_version.py {'version': '1.0.1', 'full': '53a97858f0b445a323419829a0c5baef5f242e4e'} 2023-09-08T15:30:22,193 running build_py 2023-09-08T15:30:22,219 creating build 2023-09-08T15:30:22,220 creating build/lib.linux-armv7l-cpython-311 2023-09-08T15:30:22,221 creating build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,222 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,224 copying khmer/file.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,226 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,228 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,230 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,232 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,234 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,236 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:22,238 running egg_info 2023-09-08T15:30:22,272 creating khmer.egg-info 2023-09-08T15:30:22,296 writing khmer.egg-info/PKG-INFO 2023-09-08T15:30:22,301 writing dependency_links to khmer.egg-info/dependency_links.txt 2023-09-08T15:30:22,303 writing requirements to khmer.egg-info/requires.txt 2023-09-08T15:30:22,304 writing top-level names to khmer.egg-info/top_level.txt 2023-09-08T15:30:22,305 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:30:22,311 dependency lib/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,311 dependency lib/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,312 dependency lib/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,312 dependency lib/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,313 dependency lib/zlib/gzclose.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,313 dependency lib/zlib/gzlib.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,314 dependency lib/zlib/gzread.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,314 dependency lib/zlib/gzwrite.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,315 dependency lib/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,315 dependency lib/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,316 dependency lib/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,317 dependency lib/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,317 dependency lib/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,318 dependency lib/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,319 dependency lib/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,319 dependency lib/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,320 dependency lib/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,321 dependency lib/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,321 dependency lib/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,322 dependency lib/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,322 dependency lib/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,323 dependency lib/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:30:22,347 reading manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:30:22,348 reading manifest template 'MANIFEST.in' 2023-09-08T15:30:24,163 warning: no previously-included files found matching 'lib/zlib/Makefile' 2023-09-08T15:30:24,163 warning: no previously-included files found matching 'lib/zlib/zconf.h' 2023-09-08T15:30:24,180 no previously-included directories found matching 'doc/doxygen' 2023-09-08T15:30:24,187 warning: no previously-included files matching '*.orig' found anywhere in distribution 2023-09-08T15:30:24,188 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-09-08T15:30:24,189 adding license file 'LICENSE' 2023-09-08T15:30:24,201 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:30:24,212 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:24,218 running build_ext 2023-09-08T15:30:24,218 bash -c "cd lib/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC" 2023-09-08T15:30:24,325 Checking for gcc... 2023-09-08T15:30:24,559 Building static library libz.a version 1.2.8 with gcc. 2023-09-08T15:30:24,651 Checking for off64_t... Yes. 2023-09-08T15:30:24,658 Checking for fseeko... Yes. 2023-09-08T15:30:24,893 Checking for strerror... Yes. 2023-09-08T15:30:25,312 Checking for unistd.h... Yes. 2023-09-08T15:30:25,419 Checking for stdarg.h... Yes. 2023-09-08T15:30:25,552 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). 2023-09-08T15:30:25,772 Checking for vsnprintf() in stdio.h... Yes. 2023-09-08T15:30:25,886 Checking for return value of vsnprintf()... Yes. 2023-09-08T15:30:25,974 Checking for attribute(visibility) support... Yes. 2023-09-08T15:30:26,074 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c 2023-09-08T15:30:26,484 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c 2023-09-08T15:30:26,931 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c 2023-09-08T15:30:28,953 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c 2023-09-08T15:30:29,808 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c 2023-09-08T15:30:30,261 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c 2023-09-08T15:30:32,157 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c 2023-09-08T15:30:32,676 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c 2023-09-08T15:30:34,095 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c 2023-09-08T15:30:34,267 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c 2023-09-08T15:30:34,408 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c 2023-09-08T15:30:34,542 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c 2023-09-08T15:30:34,702 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c 2023-09-08T15:30:35,212 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c 2023-09-08T15:30:35,817 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c 2023-09-08T15:30:36,403 bash -c "cd lib/bzip2 && make -f Makefile-libbz2_so all" 2023-09-08T15:30:36,418 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2023-09-08T15:30:37,309 In function ‘mainSimpleSort’, 2023-09-08T15:30:37,309 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2023-09-08T15:30:37,310 inlined from ‘mainSort’ at blocksort.c:897:19: 2023-09-08T15:30:37,311 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:30:37,311 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:30:37,312 | ^~~~~~~ 2023-09-08T15:30:37,313 blocksort.c:514:18: note: called from here 2023-09-08T15:30:37,313 514 | while ( mainGtU ( 2023-09-08T15:30:37,314 | ^~~~~~~~~ 2023-09-08T15:30:37,314 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:30:37,315 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:37,316 516 | ) ) { 2023-09-08T15:30:37,317 | ~ 2023-09-08T15:30:37,317 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:30:37,318 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:30:37,319 | ^~~~~~~ 2023-09-08T15:30:37,319 blocksort.c:528:18: note: called from here 2023-09-08T15:30:37,320 528 | while ( mainGtU ( 2023-09-08T15:30:37,320 | ^~~~~~~~~ 2023-09-08T15:30:37,321 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:30:37,321 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:37,322 530 | ) ) { 2023-09-08T15:30:37,322 | ~ 2023-09-08T15:30:37,323 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:30:37,323 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:30:37,324 | ^~~~~~~ 2023-09-08T15:30:37,324 blocksort.c:542:18: note: called from here 2023-09-08T15:30:37,325 542 | while ( mainGtU ( 2023-09-08T15:30:37,325 | ^~~~~~~~~ 2023-09-08T15:30:37,326 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:30:37,326 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:37,327 544 | ) ) { 2023-09-08T15:30:37,327 | ~ 2023-09-08T15:30:38,160 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2023-09-08T15:30:38,624 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2023-09-08T15:30:38,736 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2023-09-08T15:30:38,849 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2023-09-08T15:30:43,329 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2023-09-08T15:30:45,878 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2023-09-08T15:30:47,829 #gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o 2023-09-08T15:30:47,831 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2023-09-08T15:30:47,834 #rm -f libbz2.so.1.0 2023-09-08T15:30:47,836 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2023-09-08T15:30:48,357 building 'khmer._khmermodule' extension 2023-09-08T15:30:48,358 creating build/temp.linux-armv7l-cpython-311 2023-09-08T15:30:48,358 creating build/temp.linux-armv7l-cpython-311/khmer 2023-09-08T15:30:48,359 creating build/temp.linux-armv7l-cpython-311/lib 2023-09-08T15:30:48,360 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION=1.0.1 -UNO_UNIQUE_RC -Ilib -Ilib/zlib -Ilib/bzip2 -I/usr/include/python3.11 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-cpython-311/khmer/_khmermodule.o -O3 2023-09-08T15:30:51,245 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2023-09-08T15:30:51,246 khmer/_khmermodule.cc:85:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2023-09-08T15:30:51,246 85 | tobj.ob_size = 0; 2023-09-08T15:30:51,247 | ^~~~~~~ 2023-09-08T15:30:51,248 khmer/_khmermodule.cc:86:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:30:51,248 86 | tobj.ob_type = &PyType_Type; 2023-09-08T15:30:51,249 | ^~~~~~~ 2023-09-08T15:30:51,252 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:30:51,253 khmer/_khmermodule.cc:206:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,253 206 | "Config", sizeof(khmer_ConfigObject), 2023-09-08T15:30:51,254 | ^~~~~~~~ 2023-09-08T15:30:51,255 | | 2023-09-08T15:30:51,256 | const char* 2023-09-08T15:30:51,256 khmer/_khmermodule.cc:208:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,257 208 | khmer_config_dealloc, /*tp_dealloc*/ 2023-09-08T15:30:51,258 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,258 | | 2023-09-08T15:30:51,259 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:30:51,259 khmer/_khmermodule.cc:210:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:30:51,260 210 | khmer_config_getattr, /*tp_getattr*/ 2023-09-08T15:30:51,260 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,261 | | 2023-09-08T15:30:51,261 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:30:51,262 In file included from /usr/include/python3.11/Python.h:44, 2023-09-08T15:30:51,263 from khmer/_khmermodule.cc:13: 2023-09-08T15:30:51,263 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:30:51,264 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:30:51,264 | ~~~ 2023-09-08T15:30:51,265 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:30:51,265 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:30:51,266 | | 2023-09-08T15:30:51,267 | int 2023-09-08T15:30:51,267 424 | 0) 2023-09-08T15:30:51,268 | ~~ 2023-09-08T15:30:51,269 khmer/_khmermodule.cc:223:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:30:51,269 223 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:30:51,270 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,271 khmer/_khmermodule.cc:224:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:30:51,272 224 | "config object", /* tp_doc */ 2023-09-08T15:30:51,272 | ^~~~~~~~~~~~~~~ 2023-09-08T15:30:51,273 | | 2023-09-08T15:30:51,273 | const char* 2023-09-08T15:30:51,280 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2023-09-08T15:30:51,281 khmer/_khmermodule.cc:312:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:30:51,281 312 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2023-09-08T15:30:51,282 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,283 | PyLong_FromSize_t 2023-09-08T15:30:51,305 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2023-09-08T15:30:51,305 khmer/_khmermodule.cc:370:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:30:51,306 370 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2023-09-08T15:30:51,307 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,308 | PyLong_FromSize_t 2023-09-08T15:30:51,329 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2023-09-08T15:30:51,330 khmer/_khmermodule.cc:399:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:30:51,330 399 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2023-09-08T15:30:51,331 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,332 | PyLong_FromSize_t 2023-09-08T15:30:51,353 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2023-09-08T15:30:51,354 khmer/_khmermodule.cc:466:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:30:51,354 466 | return Py_FindMethod(khmer_config_methods, obj, name); 2023-09-08T15:30:51,355 | ^~~~~~~~~~~~~ 2023-09-08T15:30:51,356 | PyCMethod 2023-09-08T15:30:51,380 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2023-09-08T15:30:51,381 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:30:51,381 504 | PyString_FromString( \ 2023-09-08T15:30:51,382 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,383 khmer/_khmermodule.cc:513:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:30:51,383 513 | return KHMER_READ_STRING_GETTER( self, name ); 2023-09-08T15:30:51,384 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,407 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2023-09-08T15:30:51,407 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:30:51,408 504 | PyString_FromString( \ 2023-09-08T15:30:51,408 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,409 khmer/_khmermodule.cc:521:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:30:51,410 521 | return KHMER_READ_STRING_GETTER( self, sequence ); 2023-09-08T15:30:51,411 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,433 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2023-09-08T15:30:51,434 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:30:51,435 504 | PyString_FromString( \ 2023-09-08T15:30:51,435 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,436 khmer/_khmermodule.cc:529:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:30:51,437 529 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2023-09-08T15:30:51,437 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,460 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2023-09-08T15:30:51,460 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:30:51,461 504 | PyString_FromString( \ 2023-09-08T15:30:51,462 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,462 khmer/_khmermodule.cc:537:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:30:51,463 537 | return KHMER_READ_STRING_GETTER( self, annotations ); 2023-09-08T15:30:51,464 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,506 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2023-09-08T15:30:51,507 khmer/_khmermodule.cc:874:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,508 874 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2023-09-08T15:30:51,508 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,509 | PyLong_FromLong 2023-09-08T15:30:51,510 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:30:51,511 khmer/_khmermodule.cc:987:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,512 987 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2023-09-08T15:30:51,513 | ^~~~~~~~~ 2023-09-08T15:30:51,513 | | 2023-09-08T15:30:51,514 | const char* 2023-09-08T15:30:51,515 khmer/_khmermodule.cc:989:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,515 989 | khmer_subset_dealloc, /*tp_dealloc*/ 2023-09-08T15:30:51,516 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,517 | | 2023-09-08T15:30:51,517 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:30:51,518 khmer/_khmermodule.cc:991:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:30:51,518 991 | khmer_subset_getattr, /*tp_getattr*/ 2023-09-08T15:30:51,519 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,519 | | 2023-09-08T15:30:51,520 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:30:51,520 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:30:51,521 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:30:51,521 | ~~~ 2023-09-08T15:30:51,522 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:30:51,523 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:30:51,523 | | 2023-09-08T15:30:51,524 | int 2023-09-08T15:30:51,524 424 | 0) 2023-09-08T15:30:51,525 | ~~ 2023-09-08T15:30:51,526 khmer/_khmermodule.cc:1004:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:30:51,526 1004 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:30:51,527 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,527 khmer/_khmermodule.cc:1005:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:30:51,528 1005 | "subset object", /* tp_doc */ 2023-09-08T15:30:51,529 | ^~~~~~~~~~~~~~~ 2023-09-08T15:30:51,529 | | 2023-09-08T15:30:51,530 | const char* 2023-09-08T15:30:51,539 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2023-09-08T15:30:51,540 khmer/_khmermodule.cc:1101:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,540 1101 | return PyInt_FromLong(1); 2023-09-08T15:30:51,541 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,542 | PyLong_FromLong 2023-09-08T15:30:51,561 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2023-09-08T15:30:51,562 khmer/_khmermodule.cc:1118:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,563 1118 | return PyInt_FromLong(0); 2023-09-08T15:30:51,563 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,564 | PyLong_FromLong 2023-09-08T15:30:51,587 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2023-09-08T15:30:51,588 khmer/_khmermodule.cc:1206:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,588 1206 | return PyInt_FromLong(n_consumed); 2023-09-08T15:30:51,589 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,590 | PyLong_FromLong 2023-09-08T15:30:51,610 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2023-09-08T15:30:51,611 khmer/_khmermodule.cc:1238:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,612 1238 | return PyInt_FromLong(n_consumed); 2023-09-08T15:30:51,612 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,613 | PyLong_FromLong 2023-09-08T15:30:51,633 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2023-09-08T15:30:51,634 khmer/_khmermodule.cc:1261:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,634 1261 | return PyInt_FromLong(N); 2023-09-08T15:30:51,635 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,635 | PyLong_FromLong 2023-09-08T15:30:51,656 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2023-09-08T15:30:51,657 khmer/_khmermodule.cc:1284:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,657 1284 | return PyInt_FromLong(N); 2023-09-08T15:30:51,658 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,658 | PyLong_FromLong 2023-09-08T15:30:51,678 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2023-09-08T15:30:51,679 khmer/_khmermodule.cc:1387:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:30:51,680 1387 | if (PyInt_Check(arg)) { 2023-09-08T15:30:51,680 | ^~~~~~~~~~~ 2023-09-08T15:30:51,681 | PySet_Check 2023-09-08T15:30:51,698 khmer/_khmermodule.cc:1388:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:30:51,698 1388 | long pos = PyInt_AsLong(arg); 2023-09-08T15:30:51,699 | ^~~~~~~~~~~~ 2023-09-08T15:30:51,700 | PyLong_AsLong 2023-09-08T15:30:51,720 khmer/_khmermodule.cc:1390:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:30:51,721 1390 | } else if (PyString_Check(arg)) { 2023-09-08T15:30:51,722 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,723 | PyMapping_Check 2023-09-08T15:30:51,747 khmer/_khmermodule.cc:1391:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:30:51,748 1391 | std::string s = PyString_AsString(arg); 2023-09-08T15:30:51,749 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,769 khmer/_khmermodule.cc:1395:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,770 1395 | return PyInt_FromLong(count); 2023-09-08T15:30:51,771 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,771 | PyLong_FromLong 2023-09-08T15:30:51,792 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2023-09-08T15:30:51,792 khmer/_khmermodule.cc:1411:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,793 1411 | return PyInt_FromLong(count); 2023-09-08T15:30:51,794 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,795 | PyLong_FromLong 2023-09-08T15:30:51,820 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2023-09-08T15:30:51,821 khmer/_khmermodule.cc:1435:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:30:51,821 1435 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:30:51,822 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,823 | PyBytes_FromStringAndSize 2023-09-08T15:30:51,849 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2023-09-08T15:30:51,850 khmer/_khmermodule.cc:1465:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:30:51,850 1465 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:30:51,851 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,851 | PyBytes_FromStringAndSize 2023-09-08T15:30:51,877 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2023-09-08T15:30:51,878 khmer/_khmermodule.cc:1606:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:51,878 1606 | return PyInt_FromLong(k); 2023-09-08T15:30:51,879 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:51,879 | PyLong_FromLong 2023-09-08T15:30:51,911 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2023-09-08T15:30:51,912 khmer/_khmermodule.cc:1718:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:30:51,912 1718 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T15:30:51,913 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,913 | PyLong_FromVoidPtr 2023-09-08T15:30:51,939 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2023-09-08T15:30:51,940 khmer/_khmermodule.cc:1824:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:30:51,940 1824 | return Py_FindMethod(khmer_counting_methods, obj, name); 2023-09-08T15:30:51,941 | ^~~~~~~~~~~~~ 2023-09-08T15:30:51,942 | PyCMethod 2023-09-08T15:30:51,942 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:30:51,943 khmer/_khmermodule.cc:1834:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,944 1834 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2023-09-08T15:30:51,945 | ^~~~~~~~~~~~~~~ 2023-09-08T15:30:51,946 | | 2023-09-08T15:30:51,947 | const char* 2023-09-08T15:30:51,947 khmer/_khmermodule.cc:1836:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,948 1836 | khmer_counting_dealloc, /*tp_dealloc*/ 2023-09-08T15:30:51,949 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,950 | | 2023-09-08T15:30:51,951 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:30:51,951 khmer/_khmermodule.cc:1838:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:30:51,952 1838 | khmer_counting_getattr, /*tp_getattr*/ 2023-09-08T15:30:51,952 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,953 | | 2023-09-08T15:30:51,953 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:30:51,954 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:30:51,954 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:30:51,955 | ~~~ 2023-09-08T15:30:51,955 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:30:51,956 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:30:51,957 | | 2023-09-08T15:30:51,957 | int 2023-09-08T15:30:51,958 424 | 0) 2023-09-08T15:30:51,959 | ~~ 2023-09-08T15:30:51,959 khmer/_khmermodule.cc:1851:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:30:51,960 1851 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:30:51,960 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,961 khmer/_khmermodule.cc:1852:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:30:51,961 1852 | "counting hash object", /* tp_doc */ 2023-09-08T15:30:51,962 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,962 | | 2023-09-08T15:30:51,963 | const char* 2023-09-08T15:30:51,964 khmer/_khmermodule.cc: In function ‘PyObject* _new_counting_hash(PyObject*, PyObject*)’: 2023-09-08T15:30:51,964 khmer/_khmermodule.cc:1903:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:30:51,965 1903 | if (PyInt_Check(size_o)) { 2023-09-08T15:30:51,965 | ^~~~~~~~~~~ 2023-09-08T15:30:51,966 | PySet_Check 2023-09-08T15:30:51,982 khmer/_khmermodule.cc:1904:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:30:51,983 1904 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:30:51,983 | ^~~~~~~~~~~~ 2023-09-08T15:30:51,984 | PyLong_AsLong 2023-09-08T15:30:51,985 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:30:51,985 khmer/_khmermodule.cc:1940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,986 1940 | "Hashbits", sizeof(khmer_KHashbitsObject), 2023-09-08T15:30:51,987 | ^~~~~~~~~~ 2023-09-08T15:30:51,988 | | 2023-09-08T15:30:51,989 | const char* 2023-09-08T15:30:51,990 khmer/_khmermodule.cc:1942:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:51,991 1942 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2023-09-08T15:30:51,992 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,992 | | 2023-09-08T15:30:51,993 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:30:51,994 khmer/_khmermodule.cc:1944:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:30:51,995 1944 | khmer_hashbits_getattr, /*tp_getattr*/ 2023-09-08T15:30:51,996 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:51,996 | | 2023-09-08T15:30:51,997 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:30:51,998 khmer/_khmermodule.cc:1957:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:30:51,998 1957 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2023-09-08T15:30:51,999 khmer/_khmermodule.cc:1958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:30:52,000 1958 | "hashbits object", /* tp_doc */ 2023-09-08T15:30:52,000 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,001 | | 2023-09-08T15:30:52,002 | const char* 2023-09-08T15:30:52,019 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2023-09-08T15:30:52,020 khmer/_khmermodule.cc:2131:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:30:52,020 2131 | return PyInt_FromSize_t(hashbits->n_tags()); 2023-09-08T15:30:52,021 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,022 | PyLong_FromSize_t 2023-09-08T15:30:52,042 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2023-09-08T15:30:52,042 khmer/_khmermodule.cc:2153:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,043 2153 | return PyInt_FromLong(1); 2023-09-08T15:30:52,043 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,044 | PyLong_FromLong 2023-09-08T15:30:52,064 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2023-09-08T15:30:52,065 khmer/_khmermodule.cc:2176:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,066 2176 | return PyInt_FromLong(n_consumed); 2023-09-08T15:30:52,066 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,067 | PyLong_FromLong 2023-09-08T15:30:52,098 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2023-09-08T15:30:52,099 khmer/_khmermodule.cc:2283:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,100 2283 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2023-09-08T15:30:52,100 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,101 | PyLong_AsVoidPtr 2023-09-08T15:30:52,120 khmer/_khmermodule.cc:2293:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,121 2293 | return PyInt_FromLong(next_largest); 2023-09-08T15:30:52,122 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,122 | PyLong_FromLong 2023-09-08T15:30:52,138 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2023-09-08T15:30:52,139 khmer/_khmermodule.cc:2309:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:30:52,140 2309 | if (PyInt_Check(arg)) { 2023-09-08T15:30:52,140 | ^~~~~~~~~~~ 2023-09-08T15:30:52,141 | PySet_Check 2023-09-08T15:30:52,158 khmer/_khmermodule.cc:2310:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:30:52,158 2310 | long pos = PyInt_AsLong(arg); 2023-09-08T15:30:52,159 | ^~~~~~~~~~~~ 2023-09-08T15:30:52,160 | PyLong_AsLong 2023-09-08T15:30:52,181 khmer/_khmermodule.cc:2312:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:30:52,181 2312 | } else if (PyString_Check(arg)) { 2023-09-08T15:30:52,182 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,183 | PyMapping_Check 2023-09-08T15:30:52,208 khmer/_khmermodule.cc:2313:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:30:52,208 2313 | std::string s = PyString_AsString(arg); 2023-09-08T15:30:52,209 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,230 khmer/_khmermodule.cc:2320:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,230 2320 | return PyInt_FromLong(count); 2023-09-08T15:30:52,231 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,232 | PyLong_FromLong 2023-09-08T15:30:52,253 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2023-09-08T15:30:52,254 khmer/_khmermodule.cc:2362:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,255 2362 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2023-09-08T15:30:52,256 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,256 | PyLong_FromLong 2023-09-08T15:30:52,282 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2023-09-08T15:30:52,282 khmer/_khmermodule.cc:2383:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:30:52,283 2383 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:30:52,283 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,284 | PyBytes_FromStringAndSize 2023-09-08T15:30:52,325 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2023-09-08T15:30:52,325 khmer/_khmermodule.cc:2458:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:30:52,326 2458 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T15:30:52,327 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,328 | PyLong_FromVoidPtr 2023-09-08T15:30:52,351 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2023-09-08T15:30:52,352 khmer/_khmermodule.cc:2486:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T15:30:52,352 2486 | if (!PyCObject_Check(subset_obj)) { 2023-09-08T15:30:52,353 | ^~~~~~~~~~~~~~~ 2023-09-08T15:30:52,354 | PyODict_Check 2023-09-08T15:30:52,380 khmer/_khmermodule.cc:2492:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,381 2492 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:30:52,382 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,382 | PyLong_AsVoidPtr 2023-09-08T15:30:52,422 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2023-09-08T15:30:52,422 khmer/_khmermodule.cc:2756:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:30:52,423 2756 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T15:30:52,424 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,425 | PyLong_FromVoidPtr 2023-09-08T15:30:52,447 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2023-09-08T15:30:52,448 khmer/_khmermodule.cc:2769:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T15:30:52,449 2769 | if (!PyCObject_Check(ppi_obj)) { 2023-09-08T15:30:52,450 | ^~~~~~~~~~~~~~~ 2023-09-08T15:30:52,450 | PyODict_Check 2023-09-08T15:30:52,476 khmer/_khmermodule.cc:2775:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,477 2775 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2023-09-08T15:30:52,478 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,479 | PyLong_AsVoidPtr 2023-09-08T15:30:52,498 khmer/_khmermodule.cc:2781:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,499 2781 | return PyInt_FromLong(p); 2023-09-08T15:30:52,500 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,500 | PyLong_FromLong 2023-09-08T15:30:52,527 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2023-09-08T15:30:52,528 khmer/_khmermodule.cc:2896:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,529 2896 | return PyInt_FromLong(n_partitions); 2023-09-08T15:30:52,529 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,530 | PyLong_FromLong 2023-09-08T15:30:52,550 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2023-09-08T15:30:52,551 khmer/_khmermodule.cc:2927:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,551 2927 | return PyInt_FromLong(n_singletons); 2023-09-08T15:30:52,552 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,552 | PyLong_FromLong 2023-09-08T15:30:52,584 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2023-09-08T15:30:52,584 khmer/_khmermodule.cc:3026:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,585 3026 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:30:52,586 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,586 | PyLong_AsVoidPtr 2023-09-08T15:30:52,614 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2023-09-08T15:30:52,614 khmer/_khmermodule.cc:3043:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,615 3043 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:30:52,615 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,616 | PyLong_AsVoidPtr 2023-09-08T15:30:52,672 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:30:52,672 khmer/_khmermodule.cc:3154:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,673 3154 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:30:52,674 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,675 | PyLong_AsVoidPtr 2023-09-08T15:30:52,703 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:30:52,704 khmer/_khmermodule.cc:3185:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:30:52,705 3185 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T15:30:52,705 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,706 | PyLong_FromVoidPtr 2023-09-08T15:30:52,726 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2023-09-08T15:30:52,727 khmer/_khmermodule.cc:3214:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,728 3214 | return PyInt_FromLong(d); 2023-09-08T15:30:52,729 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,729 | PyLong_FromLong 2023-09-08T15:30:52,756 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2023-09-08T15:30:52,757 khmer/_khmermodule.cc:3230:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,757 3230 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T15:30:52,758 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,759 | PyLong_AsVoidPtr 2023-09-08T15:30:52,786 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2023-09-08T15:30:52,787 khmer/_khmermodule.cc:3256:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,788 3256 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T15:30:52,788 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,789 | PyLong_AsVoidPtr 2023-09-08T15:30:52,816 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:30:52,817 khmer/_khmermodule.cc:3277:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:30:52,817 3277 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:30:52,818 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,819 | PyLong_AsVoidPtr 2023-09-08T15:30:52,840 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2023-09-08T15:30:52,840 khmer/_khmermodule.cc:3313:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,841 3313 | return PyInt_FromLong(p1); 2023-09-08T15:30:52,842 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,843 | PyLong_FromLong 2023-09-08T15:30:52,862 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2023-09-08T15:30:52,863 khmer/_khmermodule.cc:3330:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,864 3330 | return PyInt_FromLong(partition_id); 2023-09-08T15:30:52,865 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,865 | PyLong_FromLong 2023-09-08T15:30:52,891 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2023-09-08T15:30:52,892 khmer/_khmermodule.cc:3472:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:30:52,892 3472 | return PyInt_FromLong(k); 2023-09-08T15:30:52,893 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,894 | PyLong_FromLong 2023-09-08T15:30:52,931 In file included from /usr/include/python3.11/Python.h:38: 2023-09-08T15:30:52,932 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2023-09-08T15:30:52,933 khmer/_khmermodule.cc:3516:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:30:52,933 3516 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T15:30:52,934 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:52,934 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T15:30:52,935 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T15:30:52,936 | ^~~~ 2023-09-08T15:30:52,936 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T15:30:52,937 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T15:30:52,937 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:52,938 khmer/_khmermodule.cc:3516:9: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T15:30:52,939 3516 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T15:30:52,940 | ^~~~~~~~~~~~~~~ 2023-09-08T15:30:52,960 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2023-09-08T15:30:52,961 khmer/_khmermodule.cc:3623:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:30:52,962 3623 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2023-09-08T15:30:52,964 | ^~~~~~~~~~~~~ 2023-09-08T15:30:52,964 | PyCMethod 2023-09-08T15:30:52,979 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_new(PyTypeObject*, PyObject*, PyObject*)’: 2023-09-08T15:30:52,981 khmer/_khmermodule.cc:3648:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:30:52,981 3648 | if (PyInt_Check(size_o)) { 2023-09-08T15:30:52,982 | ^~~~~~~~~~~ 2023-09-08T15:30:52,983 | PySet_Check 2023-09-08T15:30:52,999 khmer/_khmermodule.cc:3649:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:30:53,000 3649 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:30:53,000 | ^~~~~~~~~~~~ 2023-09-08T15:30:53,001 | PyLong_AsLong 2023-09-08T15:30:53,060 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2023-09-08T15:30:53,061 khmer/_khmermodule.cc:3859:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:30:53,061 3859 | return Py_FindMethod(khmer_subset_methods, obj, name); 2023-09-08T15:30:53,062 | ^~~~~~~~~~~~~ 2023-09-08T15:30:53,063 | PyCMethod 2023-09-08T15:30:53,079 khmer/_khmermodule.cc: In function ‘PyObject* khmer_labelhash_new(PyTypeObject*, PyObject*, PyObject*)’: 2023-09-08T15:30:53,080 khmer/_khmermodule.cc:3915:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:30:53,081 3915 | if (PyInt_Check(size_o)) { 2023-09-08T15:30:53,082 | ^~~~~~~~~~~ 2023-09-08T15:30:53,083 | PySet_Check 2023-09-08T15:30:53,099 khmer/_khmermodule.cc:3916:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:30:53,100 3916 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:30:53,101 | ^~~~~~~~~~~~ 2023-09-08T15:30:53,102 | PyLong_AsLong 2023-09-08T15:30:53,147 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2023-09-08T15:30:53,148 khmer/_khmermodule.cc:4221:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:30:53,148 4221 | return PyInt_FromSize_t(labelhash->n_labels()); 2023-09-08T15:30:53,149 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,150 | PyLong_FromSize_t 2023-09-08T15:30:53,150 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:30:53,151 khmer/_khmermodule.cc:4240:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:53,152 4240 | "_LabelHash", /* tp_name */ 2023-09-08T15:30:53,152 | ^~~~~~~~~~~~ 2023-09-08T15:30:53,153 | | 2023-09-08T15:30:53,154 | const char* 2023-09-08T15:30:53,155 khmer/_khmermodule.cc:4243:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:53,155 4243 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2023-09-08T15:30:53,156 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,157 | | 2023-09-08T15:30:53,158 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:30:53,159 khmer/_khmermodule.cc:4258:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:30:53,159 4258 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2023-09-08T15:30:53,160 khmer/_khmermodule.cc:4266:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2023-09-08T15:30:53,161 4266 | khmer_labelhash_methods, /* tp_methods */ 2023-09-08T15:30:53,161 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,162 | | 2023-09-08T15:30:53,163 | PyMethodDef* 2023-09-08T15:30:53,181 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2023-09-08T15:30:53,182 khmer/_khmermodule.cc:4349:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:30:53,182 4349 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2023-09-08T15:30:53,183 | ^~~~~~~~~~~~~ 2023-09-08T15:30:53,184 | PyCMethod 2023-09-08T15:30:53,184 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:30:53,185 khmer/_khmermodule.cc:4367:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:53,186 4367 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2023-09-08T15:30:53,187 | ^~~~~~~~~~~~~ 2023-09-08T15:30:53,187 | | 2023-09-08T15:30:53,188 | const char* 2023-09-08T15:30:53,188 khmer/_khmermodule.cc:4369:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:30:53,189 4369 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2023-09-08T15:30:53,190 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,191 | | 2023-09-08T15:30:53,192 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:30:53,192 khmer/_khmermodule.cc:4371:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:30:53,193 4371 | khmer_readaligner_getattr, /*tp_getattr*/ 2023-09-08T15:30:53,194 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,195 | | 2023-09-08T15:30:53,195 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:30:53,196 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:30:53,197 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:30:53,197 | ~~~ 2023-09-08T15:30:53,198 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:30:53,199 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:30:53,199 | | 2023-09-08T15:30:53,200 | int 2023-09-08T15:30:53,200 424 | 0) 2023-09-08T15:30:53,201 | ~~ 2023-09-08T15:30:53,201 khmer/_khmermodule.cc:4384:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:30:53,202 4384 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:30:53,203 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,203 khmer/_khmermodule.cc:4385:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:30:53,204 4385 | "ReadAligner object", /* tp_doc */ 2023-09-08T15:30:53,205 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,205 | | 2023-09-08T15:30:53,206 | const char* 2023-09-08T15:30:53,207 khmer/_khmermodule.cc: In function ‘PyObject* _new_hashbits(PyObject*, PyObject*)’: 2023-09-08T15:30:53,208 khmer/_khmermodule.cc:4445:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:30:53,209 4445 | if (PyInt_Check(size_o)) { 2023-09-08T15:30:53,210 | ^~~~~~~~~~~ 2023-09-08T15:30:53,210 | PySet_Check 2023-09-08T15:30:53,226 khmer/_khmermodule.cc:4446:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:30:53,227 4446 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:30:53,228 | ^~~~~~~~~~~~ 2023-09-08T15:30:53,228 | PyLong_AsLong 2023-09-08T15:30:53,233 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2023-09-08T15:30:53,234 khmer/_khmermodule.cc:4536:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2023-09-08T15:30:53,235 4536 | self->ob_type->tp_free((PyObject*)obj); 2023-09-08T15:30:53,236 | ^~~~~~~ 2023-09-08T15:30:53,263 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2023-09-08T15:30:53,263 khmer/_khmermodule.cc:4611:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:30:53,264 4611 | return PyString_FromString(_revhash(val, ksize).c_str()); 2023-09-08T15:30:53,264 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:53,265 | PyLong_FromString 2023-09-08T15:30:53,265 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:30:53,266 khmer/_khmermodule.cc:4687:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2023-09-08T15:30:53,267 4687 | init_khmer(void) 2023-09-08T15:30:53,268 | ^~~~~~~~~~ 2023-09-08T15:30:53,268 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2023-09-08T15:30:53,269 33 | void init_khmer(); 2023-09-08T15:30:53,270 | ^~~~~~~~~~ 2023-09-08T15:30:53,271 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2023-09-08T15:30:53,272 khmer/_khmermodule.cc:4691:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:30:53,272 4691 | khmer_ConfigType.ob_type = &PyType_Type; 2023-09-08T15:30:53,273 | ^~~~~~~ 2023-09-08T15:30:53,274 khmer/_khmermodule.cc:4692:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:30:53,275 4692 | khmer_KCountingHashType.ob_type = &PyType_Type; 2023-09-08T15:30:53,276 | ^~~~~~~ 2023-09-08T15:30:53,276 khmer/_khmermodule.cc:4699:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:30:53,277 4699 | return; 2023-09-08T15:30:53,277 | ^~~~~~ 2023-09-08T15:30:53,278 khmer/_khmermodule.cc:4706:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:30:53,278 4706 | return; 2023-09-08T15:30:53,279 | ^~~~~~ 2023-09-08T15:30:53,293 khmer/_khmermodule.cc:4710:9: error: ‘Py_InitModule3’ was not declared in this scope 2023-09-08T15:30:53,293 4710 | m = Py_InitModule3( "_khmer", KhmerMethods, 2023-09-08T15:30:53,294 | ^~~~~~~~~~~~~~ 2023-09-08T15:30:53,295 khmer/_khmermodule.cc:4713:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:30:53,295 4713 | return; 2023-09-08T15:30:53,296 | ^~~~~~ 2023-09-08T15:30:53,297 khmer/_khmermodule.cc:4718:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:30:53,298 4718 | return; 2023-09-08T15:30:53,298 | ^~~~~~ 2023-09-08T15:30:53,299 khmer/_khmermodule.cc:4725:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:30:53,300 4725 | return; 2023-09-08T15:30:53,301 | ^~~~~~ 2023-09-08T15:30:53,301 khmer/_khmermodule.cc:4731:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:30:53,302 4731 | return; 2023-09-08T15:30:53,302 | ^~~~~~ 2023-09-08T15:30:53,303 khmer/_khmermodule.cc:4734:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:30:53,304 4734 | return; 2023-09-08T15:30:53,304 | ^~~~~~ 2023-09-08T15:30:54,274 khmer/_khmermodule.cc:4744:23: warning: control reaches end of non-void function [-Wreturn-type] 2023-09-08T15:30:54,275 4744 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2023-09-08T15:30:54,275 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:30:54,374 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T15:30:54,525 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T15:30:54,538 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T15:30:54,538 exec(compile('"'"''"'"''"'"' 2023-09-08T15:30:54,538 # This is -- a caller that pip uses to run setup.py 2023-09-08T15:30:54,538 # 2023-09-08T15:30:54,538 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T15:30:54,538 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T15:30:54,538 # - It provides a clear error message when setuptools is not installed. 2023-09-08T15:30:54,538 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T15:30:54,538 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T15:30:54,538 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T15:30:54,538 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T15:30:54,538 import os, sys, tokenize 2023-09-08T15:30:54,538 2023-09-08T15:30:54,538 try: 2023-09-08T15:30:54,538 import setuptools 2023-09-08T15:30:54,538 except ImportError as error: 2023-09-08T15:30:54,538 print( 2023-09-08T15:30:54,538 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T15:30:54,538 "the build environment.", 2023-09-08T15:30:54,538 file=sys.stderr, 2023-09-08T15:30:54,538 ) 2023-09-08T15:30:54,538 sys.exit(1) 2023-09-08T15:30:54,538 2023-09-08T15:30:54,538 __file__ = %r 2023-09-08T15:30:54,538 sys.argv[0] = __file__ 2023-09-08T15:30:54,538 2023-09-08T15:30:54,538 if os.path.exists(__file__): 2023-09-08T15:30:54,538 filename = __file__ 2023-09-08T15:30:54,538 with tokenize.open(__file__) as f: 2023-09-08T15:30:54,538 setup_py_code = f.read() 2023-09-08T15:30:54,538 else: 2023-09-08T15:30:54,538 filename = "" 2023-09-08T15:30:54,538 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T15:30:54,538 2023-09-08T15:30:54,538 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T15:30:54,538 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-krd2gyzo/khmer_583a5c043eb54b749d7bc8a3285014ac/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-tksvqms5[/] 2023-09-08T15:30:54,539 [bold magenta]cwd[/]: /tmp/pip-wheel-krd2gyzo/khmer_583a5c043eb54b749d7bc8a3285014ac/ 2023-09-08T15:30:54,540 Building wheel for khmer (setup.py): finished with status 'error' 2023-09-08T15:30:54,541 ERROR: Failed building wheel for khmer 2023-09-08T15:30:54,542 Running setup.py clean for khmer 2023-09-08T15:30:54,544 Running command python setup.py clean 2023-09-08T15:30:55,436 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T15:30:55,436 !! 2023-09-08T15:30:55,437 ******************************************************************************** 2023-09-08T15:30:55,437 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T15:30:55,438 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T15:30:55,439 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T15:30:55,439 or your builds will no longer be supported. 2023-09-08T15:30:55,440 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T15:30:55,441 ******************************************************************************** 2023-09-08T15:30:55,442 !! 2023-09-08T15:30:55,442 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T15:30:55,619 running clean 2023-09-08T15:30:55,643 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T15:30:55,645 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T15:30:55,649 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-08T15:30:55,649 'build/scripts-3.11' does not exist -- can't clean it 2023-09-08T15:30:55,650 removing 'build' 2023-09-08T15:30:55,762 Failed to build khmer 2023-09-08T15:30:55,764 ERROR: Failed to build one or more wheels 2023-09-08T15:30:55,765 Exception information: 2023-09-08T15:30:55,765 Traceback (most recent call last): 2023-09-08T15:30:55,765 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T15:30:55,765 status = run_func(*args) 2023-09-08T15:30:55,765 ^^^^^^^^^^^^^^^ 2023-09-08T15:30:55,765 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T15:30:55,765 return func(self, options, args) 2023-09-08T15:30:55,765 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T15:30:55,765 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T15:30:55,765 raise CommandError("Failed to build one or more wheels") 2023-09-08T15:30:55,765 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T15:30:55,768 Removed build tracker: '/tmp/pip-build-tracker-rlvxxff1'