2021-07-09T21:30:56,721 Created temporary directory: /tmp/pip-ephem-wheel-cache-0izm5ypa 2021-07-09T21:30:56,724 Created temporary directory: /tmp/pip-req-tracker-4ux7av27 2021-07-09T21:30:56,724 Initialized build tracking at /tmp/pip-req-tracker-4ux7av27 2021-07-09T21:30:56,725 Created build tracker: /tmp/pip-req-tracker-4ux7av27 2021-07-09T21:30:56,725 Entered build tracker: /tmp/pip-req-tracker-4ux7av27 2021-07-09T21:30:56,726 Created temporary directory: /tmp/pip-wheel-ql1wtyha 2021-07-09T21:30:56,760 1 location(s) to search for versions of khmer: 2021-07-09T21:30:56,760 * https://pypi.org/simple/khmer/ 2021-07-09T21:30:56,760 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2021-07-09T21:30:56,761 Getting page https://pypi.org/simple/khmer/ 2021-07-09T21:30:56,762 Found index url https://pypi.org/simple 2021-07-09T21:30:56,869 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg#sha256=ebc63236f68de37edb1895fbe6507c0db3fcbc2b1fd54ea2952c28bcf26e23e6 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,869 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg#sha256=6dfaaca9076162129b1c3b2b7015ce267590784e20646082cf46e6f964564478 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,869 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz#sha256=b3aecbfb7465e5e6d7963513e40fa77bb63d3918fc47deba82102f13a69517ff (from https://pypi.org/simple/khmer/), version: 0.6 2021-07-09T21:30:56,870 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz#sha256=f552d041d1ac69077844e1a0303b5db9c123e28397b1bf9011ecdce010159f07 (from https://pypi.org/simple/khmer/), version: 0.6.1 2021-07-09T21:30:56,885 Skipping link: none of the wheel's tags (cp27-none-macosx_10_8_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl#sha256=0535143a6c2399efcddcc35dae42b2ad6042309debcd4c39c1a27faeb6273473 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,886 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz#sha256=5a8a45cbd59fe5de27cb1372d2817a4ab22460fa9591ad04780a8a4026cce2f9 (from https://pypi.org/simple/khmer/), version: 0.7 2021-07-09T21:30:56,886 Skipping link: none of the wheel's tags (cp27-none-macosx_10_8_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl#sha256=a23be5a2a74f0967b9669579c3253978a7516d59c96485113b009ec07cf31d42 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,887 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz#sha256=08f7b20fc7f4405bbe27145d47e710e61d50639f79ab4763f685780f24935ddd (from https://pypi.org/simple/khmer/), version: 0.7.1 2021-07-09T21:30:56,887 Skipping link: none of the wheel's tags (cp27-none-macosx_10_9_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl#sha256=e43f87d4f2a34197c74fe0b6eb52d31e9ed3d569652544de8d12d7f1a887f0b0 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,887 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz#sha256=3fc678c7c7987a2e203ee053270e9565d1fc845ff472851e52c93efa19887c46 (from https://pypi.org/simple/khmer/), version: 0.8 2021-07-09T21:30:56,888 Skipping link: none of the wheel's tags (cp27-none-macosx_10_9_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl#sha256=b2323e7f1252e51dffabf75001588c47d9d5516fb852bc7a07ec76248a645467 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,888 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz#sha256=05de0be6826aa4dda0a58eb6657b5928c769b6d1b433f8e7d78310fbdc8026ff (from https://pypi.org/simple/khmer/), version: 1.0 2021-07-09T21:30:56,889 Skipping link: none of the wheel's tags (cp27-none-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl#sha256=2618d646a155290fde19ad81846f94d7b2fccb5d87f602aef53cbb978caf0a3e (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,889 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz#sha256=9ab86b43de964265f94cb535ea9de41bc3868710561c5daa29e540e8237c27a0 (from https://pypi.org/simple/khmer/), version: 1.0.1 2021-07-09T21:30:56,889 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz#sha256=05f5cf4a8f634c3c2f77a2e65fcc5dfa7887d4cf12c519af141a13ae84c9dd1d (from https://pypi.org/simple/khmer/), version: 1.1 2021-07-09T21:30:56,890 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl#sha256=83a8adf4ec51f327ac6eb2836b3f7c778593bab1d4bad55e5fe1ae5b6f8f7a62 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,890 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz#sha256=8734414fdd2adf7e96b291243061d2066cf52a5dce7e3091db088ffa03db772f (from https://pypi.org/simple/khmer/), version: 1.2 2021-07-09T21:30:56,890 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl#sha256=4c8bed026fac3c74ecae93b6e22f4e7dada585f4006984bce7dec527fdc8b574 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,891 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz#sha256=6a878df7a9e10f3c40c730d7deb860f3150662526c469a87dbfb2451a03cf20f (from https://pypi.org/simple/khmer/), version: 1.3 2021-07-09T21:30:56,891 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl#sha256=2cc862a13ce1a9acf58633de51f5491fe8415992566a0bb2186bff15d608c61e (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,891 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz#sha256=f51c7db2a8eb29a51b8bc7342b524324663116a61dc7f24692cb04863b2dda41 (from https://pypi.org/simple/khmer/), version: 1.4 2021-07-09T21:30:56,892 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl#sha256=15522aa0f1c0ea082dfcc00f5525c48f4b1e1bd4fe91688688b7c05d8fc5a7d1 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,892 Skipping link: none of the wheel's tags (cp27-none-macosx_10_6_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl#sha256=ba5ea34ce63a0834cc9b1b3f4ac0b6ea8aabbfbe675cd60761bf9247793a4327 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,893 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz#sha256=1d42851ce5d4088b807509413af2a54c88f06091e2b03bd408b26a8056936650 (from https://pypi.org/simple/khmer/), version: 1.4.1 2021-07-09T21:30:56,893 Skipping link: none of the wheel's tags (cp27-none-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl#sha256=9443cb21d5b2c81acc39b4030ec1d3d34b7dc693ad9eea439c2f09309d666692 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,894 Skipping link: none of the wheel's tags (cp33-cp33m-macosx_10_6_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl#sha256=c8b768ed0f6dd9fd83a2ba04dc7b1d240512adba18512552a35989d54e369bf4 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,894 Skipping link: none of the wheel's tags (cp34-cp34m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl#sha256=4eade77bd6d1dc3d366594fd73d0db2ffc4e8a770654dfea9f2b224991e95aea (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,894 Skipping link: none of the wheel's tags (cp35-cp35m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl#sha256=d5ccb50aac89563ba5fb2ac93e1b9ab426e083fd6e03abf1a423caeaeb85b844 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,895 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz#sha256=6a8c6809b50adaf2d7d7307eefcca173f4b536329562530400fb1c88a12e6071 (from https://pypi.org/simple/khmer/), version: 2.0 2021-07-09T21:30:56,895 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz#sha256=baef38d2d577cb666002a70ac8eca5d247593758ac1357bb17c066bea251e77a (from https://pypi.org/simple/khmer/), version: 2.1rc3 2021-07-09T21:30:56,895 Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_12_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl#sha256=bb2f957f6776a8553033015a20dcd41a6a20bc447c1756541d2318bd907b5d47 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,896 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz#sha256=43c741b44911fa8c79f549433f996e7fc90a58c6db06b5602adc8d8d1df5f3d6 (from https://pypi.org/simple/khmer/), version: 2.1 2021-07-09T21:30:56,896 Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=4a62de0eaafc3dbf4ea01006504a3e98853f4a0b8b37e72c9e93082181f0f2c5 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,897 Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=10d448f3131303c5c4745aecad7473f6e35ac5737d6fa2a7b731aedeea874e77 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,897 Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=deef940b791731d1af110cc1973c4ee5f437701181fc16537b468f857a62a2fa (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,898 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=06a1e981744c3aea2e74fdc668914afb13e36bce96f12777852fa9b9b14d9658 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,898 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=6b5548c457aa506bc43962c36d4fa2ffcd5a0762b862d18e915041e3adba8737 (from https://pypi.org/simple/khmer/) 2021-07-09T21:30:56,898 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz#sha256=a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24 (from https://pypi.org/simple/khmer/), version: 2.1.1 2021-07-09T21:30:56,899 Skipping link: not a file: https://pypi.org/simple/khmer/ 2021-07-09T21:30:56,902 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2021-07-09T21:30:56,919 Collecting khmer==1.0 2021-07-09T21:30:56,920 Created temporary directory: /tmp/pip-unpack-lwkecigp 2021-07-09T21:31:00,298 Downloading khmer-1.0.tar.gz (43.5 MB) 2021-07-09T21:32:11,049 Added khmer==1.0 from https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz#sha256=05de0be6826aa4dda0a58eb6657b5928c769b6d1b433f8e7d78310fbdc8026ff to build tracker '/tmp/pip-req-tracker-4ux7av27' 2021-07-09T21:32:11,050 Running setup.py (path:/tmp/pip-wheel-ql1wtyha/khmer_114b5526d8df4ac084f60e2b754642e1/setup.py) egg_info for package khmer 2021-07-09T21:32:11,051 Created temporary directory: /tmp/pip-pip-egg-info-wbqrx8gx 2021-07-09T21:32:11,051 Running command python setup.py egg_info 2021-07-09T21:32:12,092 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead 2021-07-09T21:32:12,092 warnings.warn( 2021-07-09T21:32:12,134 running egg_info 2021-07-09T21:32:12,136 creating /tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info 2021-07-09T21:32:12,137 writing /tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info/PKG-INFO 2021-07-09T21:32:12,140 writing dependency_links to /tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info/dependency_links.txt 2021-07-09T21:32:12,142 writing requirements to /tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info/requires.txt 2021-07-09T21:32:12,143 writing top-level names to /tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info/top_level.txt 2021-07-09T21:32:12,145 writing manifest file '/tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info/SOURCES.txt' 2021-07-09T21:32:12,301 reading manifest file '/tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info/SOURCES.txt' 2021-07-09T21:32:12,303 reading manifest template 'MANIFEST.in' 2021-07-09T21:32:14,349 no previously-included directories found matching 'doc/doxygen' 2021-07-09T21:32:14,352 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T21:32:14,378 writing manifest file '/tmp/pip-pip-egg-info-wbqrx8gx/khmer.egg-info/SOURCES.txt' 2021-07-09T21:32:14,455 Source in /tmp/pip-wheel-ql1wtyha/khmer_114b5526d8df4ac084f60e2b754642e1 has version 1.0, which satisfies requirement khmer==1.0 from https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz#sha256=05de0be6826aa4dda0a58eb6657b5928c769b6d1b433f8e7d78310fbdc8026ff 2021-07-09T21:32:14,456 Removed khmer==1.0 from https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz#sha256=05de0be6826aa4dda0a58eb6657b5928c769b6d1b433f8e7d78310fbdc8026ff from build tracker '/tmp/pip-req-tracker-4ux7av27' 2021-07-09T21:32:14,461 Created temporary directory: /tmp/pip-unpack-so56hoj3 2021-07-09T21:32:14,461 Building wheels for collected packages: khmer 2021-07-09T21:32:14,465 Created temporary directory: /tmp/pip-wheel-4zec5ups 2021-07-09T21:32:14,465 Building wheel for khmer (setup.py): started 2021-07-09T21:32:14,466 Destination directory: /tmp/pip-wheel-4zec5ups 2021-07-09T21:32:14,466 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ql1wtyha/khmer_114b5526d8df4ac084f60e2b754642e1/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ql1wtyha/khmer_114b5526d8df4ac084f60e2b754642e1/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-4zec5ups 2021-07-09T21:32:15,372 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead 2021-07-09T21:32:15,373 warnings.warn( 2021-07-09T21:32:15,430 running bdist_wheel 2021-07-09T21:32:15,434 running build 2021-07-09T21:32:15,435 got version from file /tmp/pip-wheel-ql1wtyha/khmer_114b5526d8df4ac084f60e2b754642e1/khmer/_version.py {'version': '1.0', 'full': '4c1e91f063bf0da81f6e6ea41de038b966eb9ff2'} 2021-07-09T21:32:15,435 running build_py 2021-07-09T21:32:15,576 creating build 2021-07-09T21:32:15,576 creating build/lib.linux-armv7l-3.9 2021-07-09T21:32:15,577 creating build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,578 copying khmer/khmer_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,581 copying khmer/_version.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,583 copying khmer/thread_utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,585 copying khmer/load_pe.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,587 copying khmer/utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,589 copying khmer/__init__.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,591 copying khmer/file.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,593 copying khmer/threading_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:15,595 running egg_info 2021-07-09T21:32:15,606 creating khmer.egg-info 2021-07-09T21:32:15,607 writing khmer.egg-info/PKG-INFO 2021-07-09T21:32:15,610 writing dependency_links to khmer.egg-info/dependency_links.txt 2021-07-09T21:32:15,612 writing requirements to khmer.egg-info/requires.txt 2021-07-09T21:32:15,613 writing top-level names to khmer.egg-info/top_level.txt 2021-07-09T21:32:15,615 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T21:32:15,625 reading manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T21:32:15,627 reading manifest template 'MANIFEST.in' 2021-07-09T21:32:17,617 no previously-included directories found matching 'doc/doxygen' 2021-07-09T21:32:17,620 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T21:32:17,644 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T21:32:17,657 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:32:17,664 running build_ext 2021-07-09T21:32:17,664 bash -c cd lib/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC 2021-07-09T21:32:17,854 Checking for gcc... 2021-07-09T21:32:18,165 Building static library libz.a version 1.2.8 with gcc. 2021-07-09T21:32:18,293 Checking for off64_t... Yes. 2021-07-09T21:32:18,301 Checking for fseeko... Yes. 2021-07-09T21:32:18,542 Checking for strerror... Yes. 2021-07-09T21:32:18,566 cp: cannot stat 'zconf.h.in': No such file or directory 2021-07-09T21:32:18,741 Checking for unistd.h... Yes. 2021-07-09T21:32:18,889 Checking for stdarg.h... Yes. 2021-07-09T21:32:19,061 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). 2021-07-09T21:32:19,303 Checking for vsnprintf() in stdio.h... Yes. 2021-07-09T21:32:19,441 Checking for return value of vsnprintf()... Yes. 2021-07-09T21:32:19,557 Checking for attribute(visibility) support... Yes. 2021-07-09T21:32:19,612 ./configure: line 806: zlib.pc.in: No such file or directory 2021-07-09T21:32:19,697 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c 2021-07-09T21:32:20,035 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c 2021-07-09T21:32:20,447 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c 2021-07-09T21:32:22,205 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c 2021-07-09T21:32:22,982 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c 2021-07-09T21:32:23,433 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c 2021-07-09T21:32:25,133 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c 2021-07-09T21:32:25,636 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c 2021-07-09T21:32:26,897 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c 2021-07-09T21:32:27,099 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c 2021-07-09T21:32:27,263 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c 2021-07-09T21:32:27,417 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c 2021-07-09T21:32:27,604 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c 2021-07-09T21:32:28,047 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c 2021-07-09T21:32:28,581 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c 2021-07-09T21:32:29,115 bash -c cd lib/bzip2 && make -f Makefile-libbz2_so all 2021-07-09T21:32:29,140 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2021-07-09T21:32:29,892 blocksort.c: In function ‘mainSort’: 2021-07-09T21:32:29,892 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T21:32:29,892 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T21:32:29,892 | ^~~~~~~ 2021-07-09T21:32:29,893 blocksort.c:514:18: note: called from here 2021-07-09T21:32:29,893 514 | while ( mainGtU ( 2021-07-09T21:32:29,893 | ^~~~~~~~~ 2021-07-09T21:32:29,893 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T21:32:29,893 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:29,893 516 | ) ) { 2021-07-09T21:32:29,894 | ~ 2021-07-09T21:32:29,894 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T21:32:29,894 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T21:32:29,894 | ^~~~~~~ 2021-07-09T21:32:29,895 blocksort.c:528:18: note: called from here 2021-07-09T21:32:29,895 528 | while ( mainGtU ( 2021-07-09T21:32:29,895 | ^~~~~~~~~ 2021-07-09T21:32:29,895 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T21:32:29,895 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:29,895 530 | ) ) { 2021-07-09T21:32:29,895 | ~ 2021-07-09T21:32:29,896 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T21:32:29,896 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T21:32:29,896 | ^~~~~~~ 2021-07-09T21:32:29,896 blocksort.c:542:18: note: called from here 2021-07-09T21:32:29,896 542 | while ( mainGtU ( 2021-07-09T21:32:29,897 | ^~~~~~~~~ 2021-07-09T21:32:29,897 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T21:32:29,897 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:29,897 544 | ) ) { 2021-07-09T21:32:29,897 | ~ 2021-07-09T21:32:30,587 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2021-07-09T21:32:30,994 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2021-07-09T21:32:31,127 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2021-07-09T21:32:31,260 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2021-07-09T21:32:35,121 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2021-07-09T21:32:37,379 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2021-07-09T21:32:39,024 #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 2021-07-09T21:32:39,026 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2021-07-09T21:32:39,029 #rm -f libbz2.so.1.0 2021-07-09T21:32:39,032 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2021-07-09T21:32:39,044 building 'khmer._khmermodule' extension 2021-07-09T21:32:39,045 creating build/temp.linux-armv7l-3.9 2021-07-09T21:32:39,045 creating build/temp.linux-armv7l-3.9/khmer 2021-07-09T21:32:39,046 creating build/temp.linux-armv7l-3.9/lib 2021-07-09T21:32:39,047 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.0 -UNO_UNIQUE_RC -Ilib -Ilib/zlib -Ilib/bzip2 -I/usr/include/python3.9 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-3.9/khmer/_khmermodule.o -O3 2021-07-09T21:32:41,319 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2021-07-09T21:32:41,319 khmer/_khmermodule.cc:85:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2021-07-09T21:32:41,319 85 | tobj.ob_size = 0; 2021-07-09T21:32:41,320 | ^~~~~~~ 2021-07-09T21:32:41,320 khmer/_khmermodule.cc:86:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T21:32:41,320 86 | tobj.ob_type = &PyType_Type; 2021-07-09T21:32:41,320 | ^~~~~~~ 2021-07-09T21:32:41,324 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:32:41,324 khmer/_khmermodule.cc:206:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,325 206 | "Config", sizeof(khmer_ConfigObject), 2021-07-09T21:32:41,325 | ^~~~~~~~ 2021-07-09T21:32:41,325 | | 2021-07-09T21:32:41,325 | const char* 2021-07-09T21:32:41,325 khmer/_khmermodule.cc:208:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,325 208 | khmer_config_dealloc, /*tp_dealloc*/ 2021-07-09T21:32:41,326 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,326 | | 2021-07-09T21:32:41,326 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:32:41,326 khmer/_khmermodule.cc:210:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:32:41,326 210 | khmer_config_getattr, /*tp_getattr*/ 2021-07-09T21:32:41,326 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,327 | | 2021-07-09T21:32:41,327 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:32:41,327 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:32:41,327 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:32:41,327 from khmer/_khmermodule.cc:13: 2021-07-09T21:32:41,327 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:32:41,328 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:32:41,328 | ~~~ 2021-07-09T21:32:41,328 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:32:41,328 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,328 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:32:41,328 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:32:41,328 | | 2021-07-09T21:32:41,328 | long unsigned int 2021-07-09T21:32:41,328 353 | 0) 2021-07-09T21:32:41,329 | ~~ 2021-07-09T21:32:41,329 khmer/_khmermodule.cc:223:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:32:41,329 223 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:32:41,329 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,329 khmer/_khmermodule.cc:224:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:32:41,329 224 | "config object", /* tp_doc */ 2021-07-09T21:32:41,329 | ^~~~~~~~~~~~~~~ 2021-07-09T21:32:41,329 | | 2021-07-09T21:32:41,330 | const char* 2021-07-09T21:32:41,335 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2021-07-09T21:32:41,335 khmer/_khmermodule.cc:312:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:32:41,336 312 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2021-07-09T21:32:41,336 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,336 | PyLong_FromSize_t 2021-07-09T21:32:41,345 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2021-07-09T21:32:41,345 khmer/_khmermodule.cc:370:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:32:41,345 370 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2021-07-09T21:32:41,346 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,346 | PyLong_FromSize_t 2021-07-09T21:32:41,354 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2021-07-09T21:32:41,355 khmer/_khmermodule.cc:399:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:32:41,355 399 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2021-07-09T21:32:41,355 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,355 | PyLong_FromSize_t 2021-07-09T21:32:41,365 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2021-07-09T21:32:41,365 khmer/_khmermodule.cc:466:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:32:41,365 466 | return Py_FindMethod(khmer_config_methods, obj, name); 2021-07-09T21:32:41,365 | ^~~~~~~~~~~~~ 2021-07-09T21:32:41,365 | PyCMethod 2021-07-09T21:32:41,375 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2021-07-09T21:32:41,375 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:32:41,375 504 | PyString_FromString( \ 2021-07-09T21:32:41,376 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,376 khmer/_khmermodule.cc:513:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:32:41,376 513 | return KHMER_READ_STRING_GETTER( self, name ); 2021-07-09T21:32:41,376 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,384 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2021-07-09T21:32:41,385 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:32:41,385 504 | PyString_FromString( \ 2021-07-09T21:32:41,385 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,385 khmer/_khmermodule.cc:521:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:32:41,386 521 | return KHMER_READ_STRING_GETTER( self, sequence ); 2021-07-09T21:32:41,386 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,394 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2021-07-09T21:32:41,394 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:32:41,395 504 | PyString_FromString( \ 2021-07-09T21:32:41,395 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,395 khmer/_khmermodule.cc:529:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:32:41,395 529 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2021-07-09T21:32:41,395 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,404 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2021-07-09T21:32:41,404 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:32:41,404 504 | PyString_FromString( \ 2021-07-09T21:32:41,404 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,404 khmer/_khmermodule.cc:537:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:32:41,404 537 | return KHMER_READ_STRING_GETTER( self, annotations ); 2021-07-09T21:32:41,405 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,429 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2021-07-09T21:32:41,429 khmer/_khmermodule.cc:874:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,429 874 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2021-07-09T21:32:41,429 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,429 | PyLong_FromLong 2021-07-09T21:32:41,431 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:32:41,432 khmer/_khmermodule.cc:987:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,432 987 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2021-07-09T21:32:41,432 | ^~~~~~~~~ 2021-07-09T21:32:41,432 | | 2021-07-09T21:32:41,432 | const char* 2021-07-09T21:32:41,432 khmer/_khmermodule.cc:989:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,433 989 | khmer_subset_dealloc, /*tp_dealloc*/ 2021-07-09T21:32:41,433 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,433 | | 2021-07-09T21:32:41,433 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:32:41,433 khmer/_khmermodule.cc:991:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:32:41,433 991 | khmer_subset_getattr, /*tp_getattr*/ 2021-07-09T21:32:41,433 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,434 | | 2021-07-09T21:32:41,434 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:32:41,434 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:32:41,434 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:32:41,434 from khmer/_khmermodule.cc:13: 2021-07-09T21:32:41,434 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:32:41,434 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:32:41,434 | ~~~ 2021-07-09T21:32:41,435 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:32:41,435 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,435 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:32:41,435 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:32:41,435 | | 2021-07-09T21:32:41,436 | long unsigned int 2021-07-09T21:32:41,436 353 | 0) 2021-07-09T21:32:41,436 | ~~ 2021-07-09T21:32:41,436 khmer/_khmermodule.cc:1004:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:32:41,436 1004 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:32:41,436 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,436 khmer/_khmermodule.cc:1005:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:32:41,436 1005 | "subset object", /* tp_doc */ 2021-07-09T21:32:41,436 | ^~~~~~~~~~~~~~~ 2021-07-09T21:32:41,437 | | 2021-07-09T21:32:41,437 | const char* 2021-07-09T21:32:41,442 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2021-07-09T21:32:41,443 khmer/_khmermodule.cc:1101:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,443 1101 | return PyInt_FromLong(1); 2021-07-09T21:32:41,443 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,443 | PyLong_FromLong 2021-07-09T21:32:41,451 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2021-07-09T21:32:41,451 khmer/_khmermodule.cc:1118:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,451 1118 | return PyInt_FromLong(0); 2021-07-09T21:32:41,451 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,452 | PyLong_FromLong 2021-07-09T21:32:41,461 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2021-07-09T21:32:41,461 khmer/_khmermodule.cc:1206:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,461 1206 | return PyInt_FromLong(n_consumed); 2021-07-09T21:32:41,462 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,462 | PyLong_FromLong 2021-07-09T21:32:41,470 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2021-07-09T21:32:41,470 khmer/_khmermodule.cc:1238:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,470 1238 | return PyInt_FromLong(n_consumed); 2021-07-09T21:32:41,470 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,471 | PyLong_FromLong 2021-07-09T21:32:41,478 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2021-07-09T21:32:41,479 khmer/_khmermodule.cc:1261:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,479 1261 | return PyInt_FromLong(N); 2021-07-09T21:32:41,479 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,479 | PyLong_FromLong 2021-07-09T21:32:41,487 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2021-07-09T21:32:41,487 khmer/_khmermodule.cc:1284:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,487 1284 | return PyInt_FromLong(N); 2021-07-09T21:32:41,488 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,488 | PyLong_FromLong 2021-07-09T21:32:41,496 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2021-07-09T21:32:41,497 khmer/_khmermodule.cc:1387:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:32:41,497 1387 | if (PyInt_Check(arg)) { 2021-07-09T21:32:41,497 | ^~~~~~~~~~~ 2021-07-09T21:32:41,497 | PySet_Check 2021-07-09T21:32:41,503 khmer/_khmermodule.cc:1388:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:32:41,504 1388 | long pos = PyInt_AsLong(arg); 2021-07-09T21:32:41,504 | ^~~~~~~~~~~~ 2021-07-09T21:32:41,504 | PyLong_AsLong 2021-07-09T21:32:41,511 khmer/_khmermodule.cc:1390:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T21:32:41,512 1390 | } else if (PyString_Check(arg)) { 2021-07-09T21:32:41,512 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,512 | PyMapping_Check 2021-07-09T21:32:41,522 khmer/_khmermodule.cc:1391:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T21:32:41,523 1391 | std::string s = PyString_AsString(arg); 2021-07-09T21:32:41,523 | ^~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,530 khmer/_khmermodule.cc:1395:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,530 1395 | return PyInt_FromLong(count); 2021-07-09T21:32:41,530 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,531 | PyLong_FromLong 2021-07-09T21:32:41,538 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2021-07-09T21:32:41,539 khmer/_khmermodule.cc:1411:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,539 1411 | return PyInt_FromLong(count); 2021-07-09T21:32:41,539 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,539 | PyLong_FromLong 2021-07-09T21:32:41,549 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2021-07-09T21:32:41,550 khmer/_khmermodule.cc:1435:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T21:32:41,550 1435 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T21:32:41,550 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,550 | PyBytes_FromStringAndSize 2021-07-09T21:32:41,560 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2021-07-09T21:32:41,561 khmer/_khmermodule.cc:1465:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T21:32:41,561 1465 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T21:32:41,561 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,561 | PyBytes_FromStringAndSize 2021-07-09T21:32:41,573 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2021-07-09T21:32:41,573 khmer/_khmermodule.cc:1606:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,573 1606 | return PyInt_FromLong(k); 2021-07-09T21:32:41,574 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,574 | PyLong_FromLong 2021-07-09T21:32:41,589 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2021-07-09T21:32:41,589 khmer/_khmermodule.cc:1718:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:32:41,589 1718 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T21:32:41,589 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,590 | PyLong_FromVoidPtr 2021-07-09T21:32:41,601 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2021-07-09T21:32:41,602 khmer/_khmermodule.cc:1824:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:32:41,602 1824 | return Py_FindMethod(khmer_counting_methods, obj, name); 2021-07-09T21:32:41,602 | ^~~~~~~~~~~~~ 2021-07-09T21:32:41,602 | PyCMethod 2021-07-09T21:32:41,602 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:32:41,602 khmer/_khmermodule.cc:1834:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,603 1834 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2021-07-09T21:32:41,603 | ^~~~~~~~~~~~~~~ 2021-07-09T21:32:41,603 | | 2021-07-09T21:32:41,603 | const char* 2021-07-09T21:32:41,603 khmer/_khmermodule.cc:1836:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,603 1836 | khmer_counting_dealloc, /*tp_dealloc*/ 2021-07-09T21:32:41,603 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,604 | | 2021-07-09T21:32:41,604 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:32:41,604 khmer/_khmermodule.cc:1838:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:32:41,604 1838 | khmer_counting_getattr, /*tp_getattr*/ 2021-07-09T21:32:41,604 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,604 | | 2021-07-09T21:32:41,605 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:32:41,605 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:32:41,605 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:32:41,605 from khmer/_khmermodule.cc:13: 2021-07-09T21:32:41,605 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:32:41,605 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:32:41,606 | ~~~ 2021-07-09T21:32:41,606 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:32:41,606 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,606 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:32:41,606 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:32:41,606 | | 2021-07-09T21:32:41,606 | long unsigned int 2021-07-09T21:32:41,606 353 | 0) 2021-07-09T21:32:41,607 | ~~ 2021-07-09T21:32:41,607 khmer/_khmermodule.cc:1851:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:32:41,607 1851 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:32:41,607 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,607 khmer/_khmermodule.cc:1852:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:32:41,607 1852 | "counting hash object", /* tp_doc */ 2021-07-09T21:32:41,607 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,608 | | 2021-07-09T21:32:41,608 | const char* 2021-07-09T21:32:41,610 khmer/_khmermodule.cc: In function ‘PyObject* _new_counting_hash(PyObject*, PyObject*)’: 2021-07-09T21:32:41,611 khmer/_khmermodule.cc:1903:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:32:41,611 1903 | if (PyInt_Check(size_o)) { 2021-07-09T21:32:41,611 | ^~~~~~~~~~~ 2021-07-09T21:32:41,611 | PySet_Check 2021-07-09T21:32:41,617 khmer/_khmermodule.cc:1904:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:32:41,618 1904 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:32:41,618 | ^~~~~~~~~~~~ 2021-07-09T21:32:41,618 | PyLong_AsLong 2021-07-09T21:32:41,619 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:32:41,619 khmer/_khmermodule.cc:1940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,620 1940 | "Hashbits", sizeof(khmer_KHashbitsObject), 2021-07-09T21:32:41,620 | ^~~~~~~~~~ 2021-07-09T21:32:41,620 | | 2021-07-09T21:32:41,620 | const char* 2021-07-09T21:32:41,620 khmer/_khmermodule.cc:1942:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:41,620 1942 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2021-07-09T21:32:41,621 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,621 | | 2021-07-09T21:32:41,621 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:32:41,621 khmer/_khmermodule.cc:1944:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:32:41,621 1944 | khmer_hashbits_getattr, /*tp_getattr*/ 2021-07-09T21:32:41,621 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,621 | | 2021-07-09T21:32:41,622 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:32:41,622 khmer/_khmermodule.cc:1957:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:32:41,622 1957 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2021-07-09T21:32:41,622 khmer/_khmermodule.cc:1958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:32:41,622 1958 | "hashbits object", /* tp_doc */ 2021-07-09T21:32:41,622 | ^~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,622 | | 2021-07-09T21:32:41,623 | const char* 2021-07-09T21:32:41,634 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2021-07-09T21:32:41,634 khmer/_khmermodule.cc:2131:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:32:41,634 2131 | return PyInt_FromSize_t(hashbits->n_tags()); 2021-07-09T21:32:41,635 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,635 | PyLong_FromSize_t 2021-07-09T21:32:41,642 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2021-07-09T21:32:41,643 khmer/_khmermodule.cc:2153:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,643 2153 | return PyInt_FromLong(1); 2021-07-09T21:32:41,643 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,643 | PyLong_FromLong 2021-07-09T21:32:41,651 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2021-07-09T21:32:41,651 khmer/_khmermodule.cc:2176:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,651 2176 | return PyInt_FromLong(n_consumed); 2021-07-09T21:32:41,652 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,652 | PyLong_FromLong 2021-07-09T21:32:41,666 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2021-07-09T21:32:41,667 khmer/_khmermodule.cc:2283:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,667 2283 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2021-07-09T21:32:41,667 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,667 | PyLong_AsVoidPtr 2021-07-09T21:32:41,674 khmer/_khmermodule.cc:2293:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,675 2293 | return PyInt_FromLong(next_largest); 2021-07-09T21:32:41,675 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,675 | PyLong_FromLong 2021-07-09T21:32:41,681 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2021-07-09T21:32:41,681 khmer/_khmermodule.cc:2309:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:32:41,681 2309 | if (PyInt_Check(arg)) { 2021-07-09T21:32:41,681 | ^~~~~~~~~~~ 2021-07-09T21:32:41,682 | PySet_Check 2021-07-09T21:32:41,688 khmer/_khmermodule.cc:2310:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:32:41,688 2310 | long pos = PyInt_AsLong(arg); 2021-07-09T21:32:41,689 | ^~~~~~~~~~~~ 2021-07-09T21:32:41,689 | PyLong_AsLong 2021-07-09T21:32:41,696 khmer/_khmermodule.cc:2312:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T21:32:41,696 2312 | } else if (PyString_Check(arg)) { 2021-07-09T21:32:41,697 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,697 | PyMapping_Check 2021-07-09T21:32:41,707 khmer/_khmermodule.cc:2313:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T21:32:41,707 2313 | std::string s = PyString_AsString(arg); 2021-07-09T21:32:41,707 | ^~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,715 khmer/_khmermodule.cc:2320:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,715 2320 | return PyInt_FromLong(count); 2021-07-09T21:32:41,715 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,716 | PyLong_FromLong 2021-07-09T21:32:41,724 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2021-07-09T21:32:41,724 khmer/_khmermodule.cc:2362:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,725 2362 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2021-07-09T21:32:41,725 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,725 | PyLong_FromLong 2021-07-09T21:32:41,735 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2021-07-09T21:32:41,735 khmer/_khmermodule.cc:2383:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T21:32:41,736 2383 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T21:32:41,736 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,736 | PyBytes_FromStringAndSize 2021-07-09T21:32:41,765 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2021-07-09T21:32:41,765 khmer/_khmermodule.cc:2458:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:32:41,765 2458 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T21:32:41,766 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,766 | PyLong_FromVoidPtr 2021-07-09T21:32:41,775 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2021-07-09T21:32:41,775 khmer/_khmermodule.cc:2486:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T21:32:41,775 2486 | if (!PyCObject_Check(subset_obj)) { 2021-07-09T21:32:41,776 | ^~~~~~~~~~~~~~~ 2021-07-09T21:32:41,776 | PyODict_Check 2021-07-09T21:32:41,787 khmer/_khmermodule.cc:2492:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,787 2492 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:32:41,787 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,787 | PyLong_AsVoidPtr 2021-07-09T21:32:41,807 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2021-07-09T21:32:41,807 khmer/_khmermodule.cc:2756:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:32:41,808 2756 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T21:32:41,808 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,808 | PyLong_FromVoidPtr 2021-07-09T21:32:41,816 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2021-07-09T21:32:41,817 khmer/_khmermodule.cc:2769:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T21:32:41,817 2769 | if (!PyCObject_Check(ppi_obj)) { 2021-07-09T21:32:41,817 | ^~~~~~~~~~~~~~~ 2021-07-09T21:32:41,817 | PyODict_Check 2021-07-09T21:32:41,828 khmer/_khmermodule.cc:2775:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,828 2775 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2021-07-09T21:32:41,829 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,829 | PyLong_AsVoidPtr 2021-07-09T21:32:41,836 khmer/_khmermodule.cc:2781:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,836 2781 | return PyInt_FromLong(p); 2021-07-09T21:32:41,837 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,837 | PyLong_FromLong 2021-07-09T21:32:41,849 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2021-07-09T21:32:41,849 khmer/_khmermodule.cc:2896:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,849 2896 | return PyInt_FromLong(n_partitions); 2021-07-09T21:32:41,849 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,850 | PyLong_FromLong 2021-07-09T21:32:41,858 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2021-07-09T21:32:41,858 khmer/_khmermodule.cc:2927:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,858 2927 | return PyInt_FromLong(n_singletons); 2021-07-09T21:32:41,858 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,859 | PyLong_FromLong 2021-07-09T21:32:41,873 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2021-07-09T21:32:41,873 khmer/_khmermodule.cc:3026:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,873 3026 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:32:41,874 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,874 | PyLong_AsVoidPtr 2021-07-09T21:32:41,885 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2021-07-09T21:32:41,885 khmer/_khmermodule.cc:3043:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,886 3043 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:32:41,886 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,886 | PyLong_AsVoidPtr 2021-07-09T21:32:41,921 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T21:32:41,921 khmer/_khmermodule.cc:3154:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,922 3154 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:32:41,922 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,922 | PyLong_AsVoidPtr 2021-07-09T21:32:41,934 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T21:32:41,934 khmer/_khmermodule.cc:3185:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:32:41,935 3185 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T21:32:41,935 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,935 | PyLong_FromVoidPtr 2021-07-09T21:32:41,943 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2021-07-09T21:32:41,943 khmer/_khmermodule.cc:3214:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,943 3214 | return PyInt_FromLong(d); 2021-07-09T21:32:41,944 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,944 | PyLong_FromLong 2021-07-09T21:32:41,955 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2021-07-09T21:32:41,955 khmer/_khmermodule.cc:3230:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,956 3230 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T21:32:41,956 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,956 | PyLong_AsVoidPtr 2021-07-09T21:32:41,968 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2021-07-09T21:32:41,968 khmer/_khmermodule.cc:3256:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,968 3256 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T21:32:41,968 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,968 | PyLong_AsVoidPtr 2021-07-09T21:32:41,980 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T21:32:41,980 khmer/_khmermodule.cc:3277:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:32:41,981 3277 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:32:41,981 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:41,981 | PyLong_AsVoidPtr 2021-07-09T21:32:41,989 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2021-07-09T21:32:41,990 khmer/_khmermodule.cc:3313:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,990 3313 | return PyInt_FromLong(p1); 2021-07-09T21:32:41,990 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,990 | PyLong_FromLong 2021-07-09T21:32:41,998 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2021-07-09T21:32:41,998 khmer/_khmermodule.cc:3330:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:41,998 3330 | return PyInt_FromLong(partition_id); 2021-07-09T21:32:41,999 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:41,999 | PyLong_FromLong 2021-07-09T21:32:42,011 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2021-07-09T21:32:42,011 khmer/_khmermodule.cc:3472:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:32:42,011 3472 | return PyInt_FromLong(k); 2021-07-09T21:32:42,011 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:42,012 | PyLong_FromLong 2021-07-09T21:32:42,033 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T21:32:42,033 from /usr/include/python3.9/Python.h:106, 2021-07-09T21:32:42,033 from khmer/_khmermodule.cc:13: 2021-07-09T21:32:42,033 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2021-07-09T21:32:42,033 khmer/_khmermodule.cc:3516:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:32:42,034 3516 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2021-07-09T21:32:42,034 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,034 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T21:32:42,034 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T21:32:42,034 | ^ 2021-07-09T21:32:42,046 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2021-07-09T21:32:42,047 khmer/_khmermodule.cc:3623:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:32:42,047 3623 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2021-07-09T21:32:42,047 | ^~~~~~~~~~~~~ 2021-07-09T21:32:42,047 | PyCMethod 2021-07-09T21:32:42,053 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_new(PyTypeObject*, PyObject*, PyObject*)’: 2021-07-09T21:32:42,054 khmer/_khmermodule.cc:3648:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:32:42,054 3648 | if (PyInt_Check(size_o)) { 2021-07-09T21:32:42,054 | ^~~~~~~~~~~ 2021-07-09T21:32:42,054 | PySet_Check 2021-07-09T21:32:42,061 khmer/_khmermodule.cc:3649:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:32:42,061 3649 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:32:42,061 | ^~~~~~~~~~~~ 2021-07-09T21:32:42,061 | PyLong_AsLong 2021-07-09T21:32:42,101 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2021-07-09T21:32:42,101 khmer/_khmermodule.cc:3859:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:32:42,101 3859 | return Py_FindMethod(khmer_subset_methods, obj, name); 2021-07-09T21:32:42,101 | ^~~~~~~~~~~~~ 2021-07-09T21:32:42,102 | PyCMethod 2021-07-09T21:32:42,108 khmer/_khmermodule.cc: In function ‘PyObject* khmer_labelhash_new(PyTypeObject*, PyObject*, PyObject*)’: 2021-07-09T21:32:42,109 khmer/_khmermodule.cc:3915:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:32:42,109 3915 | if (PyInt_Check(size_o)) { 2021-07-09T21:32:42,109 | ^~~~~~~~~~~ 2021-07-09T21:32:42,109 | PySet_Check 2021-07-09T21:32:42,115 khmer/_khmermodule.cc:3916:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:32:42,116 3916 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:32:42,116 | ^~~~~~~~~~~~ 2021-07-09T21:32:42,116 | PyLong_AsLong 2021-07-09T21:32:42,144 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2021-07-09T21:32:42,144 khmer/_khmermodule.cc:4221:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:32:42,145 4221 | return PyInt_FromSize_t(labelhash->n_labels()); 2021-07-09T21:32:42,145 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,145 | PyLong_FromSize_t 2021-07-09T21:32:42,145 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:32:42,145 khmer/_khmermodule.cc:4240:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:42,146 4240 | "_LabelHash", /* tp_name */ 2021-07-09T21:32:42,146 | ^~~~~~~~~~~~ 2021-07-09T21:32:42,146 | | 2021-07-09T21:32:42,146 | const char* 2021-07-09T21:32:42,146 khmer/_khmermodule.cc:4243:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:42,146 4243 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2021-07-09T21:32:42,147 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,147 | | 2021-07-09T21:32:42,147 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:32:42,147 khmer/_khmermodule.cc:4258:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:32:42,147 4258 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2021-07-09T21:32:42,147 khmer/_khmermodule.cc:4266:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2021-07-09T21:32:42,147 4266 | khmer_labelhash_methods, /* tp_methods */ 2021-07-09T21:32:42,148 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,148 | | 2021-07-09T21:32:42,148 | PyMethodDef* 2021-07-09T21:32:42,161 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2021-07-09T21:32:42,161 khmer/_khmermodule.cc:4349:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:32:42,161 4349 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2021-07-09T21:32:42,161 | ^~~~~~~~~~~~~ 2021-07-09T21:32:42,161 | PyCMethod 2021-07-09T21:32:42,161 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:32:42,162 khmer/_khmermodule.cc:4367:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:42,162 4367 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2021-07-09T21:32:42,162 | ^~~~~~~~~~~~~ 2021-07-09T21:32:42,162 | | 2021-07-09T21:32:42,162 | const char* 2021-07-09T21:32:42,162 khmer/_khmermodule.cc:4369:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:32:42,162 4369 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2021-07-09T21:32:42,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,163 | | 2021-07-09T21:32:42,163 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:32:42,163 khmer/_khmermodule.cc:4371:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:32:42,163 4371 | khmer_readaligner_getattr, /*tp_getattr*/ 2021-07-09T21:32:42,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,163 | | 2021-07-09T21:32:42,164 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:32:42,164 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:32:42,164 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:32:42,164 from khmer/_khmermodule.cc:13: 2021-07-09T21:32:42,164 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:32:42,165 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:32:42,165 | ~~~ 2021-07-09T21:32:42,165 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:32:42,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,165 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:32:42,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:32:42,165 | | 2021-07-09T21:32:42,166 | long unsigned int 2021-07-09T21:32:42,166 353 | 0) 2021-07-09T21:32:42,166 | ~~ 2021-07-09T21:32:42,166 khmer/_khmermodule.cc:4384:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:32:42,166 4384 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:32:42,166 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,166 khmer/_khmermodule.cc:4385:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:32:42,166 4385 | "ReadAligner object", /* tp_doc */ 2021-07-09T21:32:42,167 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,167 | | 2021-07-09T21:32:42,167 | const char* 2021-07-09T21:32:42,170 khmer/_khmermodule.cc: In function ‘PyObject* _new_hashbits(PyObject*, PyObject*)’: 2021-07-09T21:32:42,171 khmer/_khmermodule.cc:4445:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:32:42,171 4445 | if (PyInt_Check(size_o)) { 2021-07-09T21:32:42,171 | ^~~~~~~~~~~ 2021-07-09T21:32:42,171 | PySet_Check 2021-07-09T21:32:42,177 khmer/_khmermodule.cc:4446:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:32:42,178 4446 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:32:42,178 | ^~~~~~~~~~~~ 2021-07-09T21:32:42,178 | PyLong_AsLong 2021-07-09T21:32:42,183 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2021-07-09T21:32:42,184 khmer/_khmermodule.cc:4536:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2021-07-09T21:32:42,184 4536 | self->ob_type->tp_free((PyObject*)obj); 2021-07-09T21:32:42,184 | ^~~~~~~ 2021-07-09T21:32:42,195 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2021-07-09T21:32:42,195 khmer/_khmermodule.cc:4611:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:32:42,195 4611 | return PyString_FromString(_revhash(val, ksize).c_str()); 2021-07-09T21:32:42,196 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:42,196 | PyLong_FromString 2021-07-09T21:32:42,196 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:32:42,197 khmer/_khmermodule.cc:4687:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2021-07-09T21:32:42,197 4687 | init_khmer(void) 2021-07-09T21:32:42,197 | ^~~~~~~~~~ 2021-07-09T21:32:42,197 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2021-07-09T21:32:42,197 33 | void init_khmer(); 2021-07-09T21:32:42,197 | ^~~~~~~~~~ 2021-07-09T21:32:42,197 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2021-07-09T21:32:42,198 khmer/_khmermodule.cc:4691:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T21:32:42,198 4691 | khmer_ConfigType.ob_type = &PyType_Type; 2021-07-09T21:32:42,198 | ^~~~~~~ 2021-07-09T21:32:42,198 khmer/_khmermodule.cc:4692:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T21:32:42,198 4692 | khmer_KCountingHashType.ob_type = &PyType_Type; 2021-07-09T21:32:42,199 | ^~~~~~~ 2021-07-09T21:32:42,199 khmer/_khmermodule.cc:4699:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:32:42,199 4699 | return; 2021-07-09T21:32:42,199 | ^~~~~~ 2021-07-09T21:32:42,199 khmer/_khmermodule.cc:4706:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:32:42,199 4706 | return; 2021-07-09T21:32:42,199 | ^~~~~~ 2021-07-09T21:32:42,208 khmer/_khmermodule.cc:4710:9: error: ‘Py_InitModule3’ was not declared in this scope 2021-07-09T21:32:42,208 4710 | m = Py_InitModule3( "_khmer", KhmerMethods, 2021-07-09T21:32:42,208 | ^~~~~~~~~~~~~~ 2021-07-09T21:32:42,208 khmer/_khmermodule.cc:4713:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:32:42,209 4713 | return; 2021-07-09T21:32:42,209 | ^~~~~~ 2021-07-09T21:32:42,209 khmer/_khmermodule.cc:4718:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:32:42,209 4718 | return; 2021-07-09T21:32:42,209 | ^~~~~~ 2021-07-09T21:32:42,209 khmer/_khmermodule.cc:4725:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:32:42,209 4725 | return; 2021-07-09T21:32:42,210 | ^~~~~~ 2021-07-09T21:32:42,210 khmer/_khmermodule.cc:4731:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:32:42,210 4731 | return; 2021-07-09T21:32:42,210 | ^~~~~~ 2021-07-09T21:32:42,210 khmer/_khmermodule.cc:4734:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:32:42,210 4734 | return; 2021-07-09T21:32:42,211 | ^~~~~~ 2021-07-09T21:32:42,971 khmer/_khmermodule.cc:4744:23: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-09T21:32:42,971 4744 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2021-07-09T21:32:42,971 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:32:43,062 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T21:32:43,149 Building wheel for khmer (setup.py): finished with status 'error' 2021-07-09T21:32:43,150 ERROR: Failed building wheel for khmer 2021-07-09T21:32:43,150 Running setup.py clean for khmer 2021-07-09T21:32:43,151 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ql1wtyha/khmer_114b5526d8df4ac084f60e2b754642e1/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ql1wtyha/khmer_114b5526d8df4ac084f60e2b754642e1/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2021-07-09T21:32:44,072 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead 2021-07-09T21:32:44,073 warnings.warn( 2021-07-09T21:32:44,107 running clean 2021-07-09T21:32:44,107 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T21:32:44,110 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T21:32:44,114 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T21:32:44,114 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T21:32:44,114 removing 'build' 2021-07-09T21:32:44,182 Failed to build khmer 2021-07-09T21:32:44,183 ERROR: Failed to build one or more wheels 2021-07-09T21:32:44,184 Exception information: 2021-07-09T21:32:44,184 Traceback (most recent call last): 2021-07-09T21:32:44,184 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T21:32:44,184 status = self.run(options, args) 2021-07-09T21:32:44,184 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T21:32:44,184 return func(self, options, args) 2021-07-09T21:32:44,184 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T21:32:44,184 raise CommandError( 2021-07-09T21:32:44,184 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T21:32:44,187 Removed build tracker: '/tmp/pip-req-tracker-4ux7av27'