2021-07-09T20:49:15,688 Created temporary directory: /tmp/pip-ephem-wheel-cache-9m_l8s70 2021-07-09T20:49:15,691 Created temporary directory: /tmp/pip-req-tracker-jmcq30di 2021-07-09T20:49:15,691 Initialized build tracking at /tmp/pip-req-tracker-jmcq30di 2021-07-09T20:49:15,692 Created build tracker: /tmp/pip-req-tracker-jmcq30di 2021-07-09T20:49:15,692 Entered build tracker: /tmp/pip-req-tracker-jmcq30di 2021-07-09T20:49:15,692 Created temporary directory: /tmp/pip-wheel-hj7jxewv 2021-07-09T20:49:15,726 1 location(s) to search for versions of khmer: 2021-07-09T20:49:15,726 * https://pypi.org/simple/khmer/ 2021-07-09T20:49:15,726 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2021-07-09T20:49:15,727 Getting page https://pypi.org/simple/khmer/ 2021-07-09T20:49:15,728 Found index url https://pypi.org/simple 2021-07-09T20:49:15,833 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/) 2021-07-09T20:49:15,833 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/) 2021-07-09T20:49:15,834 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 2021-07-09T20:49:15,834 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 2021-07-09T20:49:15,850 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/) 2021-07-09T20:49:15,851 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 2021-07-09T20:49:15,851 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/) 2021-07-09T20:49:15,851 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 2021-07-09T20:49:15,852 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/) 2021-07-09T20:49:15,852 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 2021-07-09T20:49:15,853 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/) 2021-07-09T20:49:15,853 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 2021-07-09T20:49:15,853 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/) 2021-07-09T20:49:15,854 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 2021-07-09T20:49:15,854 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 2021-07-09T20:49:15,855 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/) 2021-07-09T20:49:15,855 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 2021-07-09T20:49:15,855 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/) 2021-07-09T20:49:15,856 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 2021-07-09T20:49:15,856 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/) 2021-07-09T20:49:15,856 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 2021-07-09T20:49:15,857 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/) 2021-07-09T20:49:15,857 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/) 2021-07-09T20:49:15,858 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 2021-07-09T20:49:15,858 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/) 2021-07-09T20:49:15,858 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/) 2021-07-09T20:49:15,859 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/) 2021-07-09T20:49:15,859 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/) 2021-07-09T20:49:15,860 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 2021-07-09T20:49:15,860 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 2021-07-09T20:49:15,860 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/) 2021-07-09T20:49:15,861 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 2021-07-09T20:49:15,861 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/) 2021-07-09T20:49:15,862 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/) 2021-07-09T20:49:15,862 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/) 2021-07-09T20:49:15,863 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/) 2021-07-09T20:49:15,863 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/) 2021-07-09T20:49:15,863 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 2021-07-09T20:49:15,864 Skipping link: not a file: https://pypi.org/simple/khmer/ 2021-07-09T20:49:15,867 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2021-07-09T20:49:15,884 Collecting khmer==0.8 2021-07-09T20:49:15,886 Created temporary directory: /tmp/pip-unpack-br_gtr52 2021-07-09T20:49:16,891 Downloading khmer-0.8.tar.gz (18.9 MB) 2021-07-09T20:49:21,934 Added khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz#sha256=3fc678c7c7987a2e203ee053270e9565d1fc845ff472851e52c93efa19887c46 to build tracker '/tmp/pip-req-tracker-jmcq30di' 2021-07-09T20:49:21,935 Running setup.py (path:/tmp/pip-wheel-hj7jxewv/khmer_7dd91339b5fe464fac7d69b92c5a2289/setup.py) egg_info for package khmer 2021-07-09T20:49:21,936 Created temporary directory: /tmp/pip-pip-egg-info-1yjqbrmh 2021-07-09T20:49:21,937 Running command python setup.py egg_info 2021-07-09T20:49:57,596 running egg_info 2021-07-09T20:49:57,598 creating /tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info 2021-07-09T20:49:57,599 writing /tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info/PKG-INFO 2021-07-09T20:49:57,602 writing dependency_links to /tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info/dependency_links.txt 2021-07-09T20:49:57,604 writing requirements to /tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info/requires.txt 2021-07-09T20:49:57,605 writing top-level names to /tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info/top_level.txt 2021-07-09T20:49:57,607 writing manifest file '/tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info/SOURCES.txt' 2021-07-09T20:49:57,785 reading manifest file '/tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info/SOURCES.txt' 2021-07-09T20:49:57,787 reading manifest template 'MANIFEST.in' 2021-07-09T20:49:59,832 no previously-included directories found matching 'doc/doxygen' 2021-07-09T20:49:59,835 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T20:49:59,862 writing manifest file '/tmp/pip-pip-egg-info-1yjqbrmh/khmer.egg-info/SOURCES.txt' 2021-07-09T20:49:59,937 Source in /tmp/pip-wheel-hj7jxewv/khmer_7dd91339b5fe464fac7d69b92c5a2289 has version 0.8, which satisfies requirement khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz#sha256=3fc678c7c7987a2e203ee053270e9565d1fc845ff472851e52c93efa19887c46 2021-07-09T20:49:59,938 Removed khmer==0.8 from https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz#sha256=3fc678c7c7987a2e203ee053270e9565d1fc845ff472851e52c93efa19887c46 from build tracker '/tmp/pip-req-tracker-jmcq30di' 2021-07-09T20:49:59,943 Created temporary directory: /tmp/pip-unpack-oxw_sr2q 2021-07-09T20:49:59,943 Building wheels for collected packages: khmer 2021-07-09T20:49:59,948 Created temporary directory: /tmp/pip-wheel-3wcdnf6e 2021-07-09T20:49:59,948 Building wheel for khmer (setup.py): started 2021-07-09T20:49:59,948 Destination directory: /tmp/pip-wheel-3wcdnf6e 2021-07-09T20:49:59,948 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-hj7jxewv/khmer_7dd91339b5fe464fac7d69b92c5a2289/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-hj7jxewv/khmer_7dd91339b5fe464fac7d69b92c5a2289/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-3wcdnf6e 2021-07-09T20:50:02,351 running bdist_wheel 2021-07-09T20:50:02,354 running build 2021-07-09T20:50:02,355 got version from file /tmp/pip-wheel-hj7jxewv/khmer_7dd91339b5fe464fac7d69b92c5a2289/khmer/_version.py {'version': '0.8', 'full': 'fd0d19f81d7a627bdffe3ab44658928074fb5acb'} 2021-07-09T20:50:02,355 running build_py 2021-07-09T20:50:02,500 creating build 2021-07-09T20:50:02,500 creating build/lib.linux-armv7l-3.9 2021-07-09T20:50:02,501 creating build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,502 copying khmer/threading_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,504 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,506 copying khmer/_version.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,507 copying khmer/load_pe.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,509 copying khmer/thread_utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,511 copying khmer/counting_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,513 copying khmer/khmer_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,516 copying khmer/utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,517 copying khmer/__init__.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:02,519 running egg_info 2021-07-09T20:50:02,522 creating khmer.egg-info 2021-07-09T20:50:02,522 writing khmer.egg-info/PKG-INFO 2021-07-09T20:50:02,525 writing dependency_links to khmer.egg-info/dependency_links.txt 2021-07-09T20:50:02,527 writing requirements to khmer.egg-info/requires.txt 2021-07-09T20:50:02,528 writing top-level names to khmer.egg-info/top_level.txt 2021-07-09T20:50:02,530 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T20:50:02,537 reading manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T20:50:02,539 reading manifest template 'MANIFEST.in' 2021-07-09T20:50:04,684 no previously-included directories found matching 'doc/doxygen' 2021-07-09T20:50:04,686 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T20:50:04,728 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T20:50:04,745 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T20:50:04,753 running build_ext 2021-07-09T20:50:04,769 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2021-07-09T20:50:05,046 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2021-07-09T20:50:05,181 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2021-07-09T20:50:05,560 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2021-07-09T20:50:06,504 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2021-07-09T20:50:06,632 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2021-07-09T20:50:07,988 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2021-07-09T20:50:09,221 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2021-07-09T20:50:09,372 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2021-07-09T20:50:10,869 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2021-07-09T20:50:11,614 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2021-07-09T20:50:12,044 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2021-07-09T20:50:12,485 ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 2021-07-09T20:50:12,574 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2021-07-09T20:50:13,320 blocksort.c: In function ‘mainSort’: 2021-07-09T20:50:13,320 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T20:50:13,321 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T20:50:13,321 | ^~~~~~~ 2021-07-09T20:50:13,321 blocksort.c:514:18: note: called from here 2021-07-09T20:50:13,321 514 | while ( mainGtU ( 2021-07-09T20:50:13,321 | ^~~~~~~~~ 2021-07-09T20:50:13,321 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T20:50:13,321 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:13,321 516 | ) ) { 2021-07-09T20:50:13,322 | ~ 2021-07-09T20:50:13,322 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T20:50:13,322 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T20:50:13,322 | ^~~~~~~ 2021-07-09T20:50:13,322 blocksort.c:528:18: note: called from here 2021-07-09T20:50:13,322 528 | while ( mainGtU ( 2021-07-09T20:50:13,322 | ^~~~~~~~~ 2021-07-09T20:50:13,323 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T20:50:13,323 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:13,323 530 | ) ) { 2021-07-09T20:50:13,323 | ~ 2021-07-09T20:50:13,323 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T20:50:13,323 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T20:50:13,323 | ^~~~~~~ 2021-07-09T20:50:13,323 blocksort.c:542:18: note: called from here 2021-07-09T20:50:13,324 542 | while ( mainGtU ( 2021-07-09T20:50:13,324 | ^~~~~~~~~ 2021-07-09T20:50:13,324 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T20:50:13,324 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:13,324 544 | ) ) { 2021-07-09T20:50:13,324 | ~ 2021-07-09T20:50:14,023 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2021-07-09T20:50:14,428 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2021-07-09T20:50:14,556 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2021-07-09T20:50:14,684 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2021-07-09T20:50:18,535 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2021-07-09T20:50:20,795 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2021-07-09T20:50:22,440 #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 2021-07-09T20:50:22,443 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2021-07-09T20:50:22,445 #rm -f libbz2.so.1.0 2021-07-09T20:50:22,448 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2021-07-09T20:50:22,458 building 'khmer._khmermodule' extension 2021-07-09T20:50:22,459 creating build/temp.linux-armv7l-3.9 2021-07-09T20:50:22,460 creating build/temp.linux-armv7l-3.9/khmer 2021-07-09T20:50:22,461 creating build/temp.linux-armv7l-3.9/lib 2021-07-09T20:50:22,462 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=0.8 -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.9 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-3.9/khmer/_khmermodule.o -O3 2021-07-09T20:50:24,725 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2021-07-09T20:50:24,725 khmer/_khmermodule.cc:85:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2021-07-09T20:50:24,725 85 | tobj.ob_size = 0; 2021-07-09T20:50:24,725 | ^~~~~~~ 2021-07-09T20:50:24,726 khmer/_khmermodule.cc:86:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T20:50:24,726 86 | tobj.ob_type = &PyType_Type; 2021-07-09T20:50:24,726 | ^~~~~~~ 2021-07-09T20:50:24,731 khmer/_khmermodule.cc: At global scope: 2021-07-09T20:50:24,731 khmer/_khmermodule.cc:206:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:24,732 206 | "Config", sizeof(khmer_ConfigObject), 2021-07-09T20:50:24,732 | ^~~~~~~~ 2021-07-09T20:50:24,732 | | 2021-07-09T20:50:24,732 | const char* 2021-07-09T20:50:24,732 khmer/_khmermodule.cc:208:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:24,733 208 | khmer_config_dealloc, /*tp_dealloc*/ 2021-07-09T20:50:24,733 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,733 | | 2021-07-09T20:50:24,733 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T20:50:24,733 khmer/_khmermodule.cc:210:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T20:50:24,733 210 | khmer_config_getattr, /*tp_getattr*/ 2021-07-09T20:50:24,733 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,734 | | 2021-07-09T20:50:24,734 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T20:50:24,735 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T20:50:24,735 from /usr/include/python3.9/Python.h:85, 2021-07-09T20:50:24,735 from khmer/_khmermodule.cc:12: 2021-07-09T20:50:24,735 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T20:50:24,735 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T20:50:24,735 | ~~~ 2021-07-09T20:50:24,736 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T20:50:24,736 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,736 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T20:50:24,736 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T20:50:24,736 | | 2021-07-09T20:50:24,736 | long unsigned int 2021-07-09T20:50:24,736 353 | 0) 2021-07-09T20:50:24,736 | ~~ 2021-07-09T20:50:24,736 khmer/_khmermodule.cc:223:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T20:50:24,737 223 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T20:50:24,737 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,737 khmer/_khmermodule.cc:224:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T20:50:24,737 224 | "config object", /* tp_doc */ 2021-07-09T20:50:24,737 | ^~~~~~~~~~~~~~~ 2021-07-09T20:50:24,737 | | 2021-07-09T20:50:24,737 | const char* 2021-07-09T20:50:24,747 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2021-07-09T20:50:24,748 khmer/_khmermodule.cc:312:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T20:50:24,748 312 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2021-07-09T20:50:24,748 | ^~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,748 | PyLong_FromSize_t 2021-07-09T20:50:24,758 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2021-07-09T20:50:24,758 khmer/_khmermodule.cc:370:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T20:50:24,758 370 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2021-07-09T20:50:24,758 | ^~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,758 | PyLong_FromSize_t 2021-07-09T20:50:24,768 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2021-07-09T20:50:24,768 khmer/_khmermodule.cc:399:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T20:50:24,768 399 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2021-07-09T20:50:24,768 | ^~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,768 | PyLong_FromSize_t 2021-07-09T20:50:24,779 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2021-07-09T20:50:24,779 khmer/_khmermodule.cc:466:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T20:50:24,779 466 | return Py_FindMethod(khmer_config_methods, obj, name); 2021-07-09T20:50:24,779 | ^~~~~~~~~~~~~ 2021-07-09T20:50:24,780 | PyCMethod 2021-07-09T20:50:24,790 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2021-07-09T20:50:24,790 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T20:50:24,790 504 | PyString_FromString( \ 2021-07-09T20:50:24,790 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,791 khmer/_khmermodule.cc:513:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T20:50:24,791 513 | return KHMER_READ_STRING_GETTER( self, name ); 2021-07-09T20:50:24,791 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,801 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2021-07-09T20:50:24,801 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T20:50:24,801 504 | PyString_FromString( \ 2021-07-09T20:50:24,801 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,801 khmer/_khmermodule.cc:521:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T20:50:24,801 521 | return KHMER_READ_STRING_GETTER( self, sequence ); 2021-07-09T20:50:24,801 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,811 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2021-07-09T20:50:24,811 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T20:50:24,812 504 | PyString_FromString( \ 2021-07-09T20:50:24,812 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,812 khmer/_khmermodule.cc:529:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T20:50:24,812 529 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2021-07-09T20:50:24,812 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,822 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2021-07-09T20:50:24,822 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T20:50:24,822 504 | PyString_FromString( \ 2021-07-09T20:50:24,822 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,822 khmer/_khmermodule.cc:537:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T20:50:24,823 537 | return KHMER_READ_STRING_GETTER( self, annotations ); 2021-07-09T20:50:24,823 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,848 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2021-07-09T20:50:24,849 khmer/_khmermodule.cc:874:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:24,849 874 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2021-07-09T20:50:24,849 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:24,849 | PyLong_FromLong 2021-07-09T20:50:24,861 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2021-07-09T20:50:24,862 khmer/_khmermodule.cc:1024:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T20:50:24,862 1024 | return PyString_FromString(_revhash(val, ktable->ksize()).c_str()); 2021-07-09T20:50:24,862 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,862 | PyLong_FromString 2021-07-09T20:50:24,870 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2021-07-09T20:50:24,871 khmer/_khmermodule.cc:1050:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:24,871 1050 | return PyInt_FromLong(1); 2021-07-09T20:50:24,871 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:24,871 | PyLong_FromLong 2021-07-09T20:50:24,881 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2021-07-09T20:50:24,881 khmer/_khmermodule.cc:1078:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T20:50:24,881 1078 | return PyInt_FromSize_t(n_consumed); 2021-07-09T20:50:24,881 | ^~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,881 | PyLong_FromSize_t 2021-07-09T20:50:24,888 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2021-07-09T20:50:24,888 khmer/_khmermodule.cc:1097:16: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T20:50:24,888 1097 | } else if (PyInt_Check(arg)) { 2021-07-09T20:50:24,888 | ^~~~~~~~~~~ 2021-07-09T20:50:24,889 | PySet_Check 2021-07-09T20:50:24,896 khmer/_khmermodule.cc:1098:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T20:50:24,896 1098 | long pos = PyInt_AsLong(arg); 2021-07-09T20:50:24,896 | ^~~~~~~~~~~~ 2021-07-09T20:50:24,896 | PyLong_AsLong 2021-07-09T20:50:24,905 khmer/_khmermodule.cc:1100:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T20:50:24,905 1100 | } else if (PyString_Check(arg)) { 2021-07-09T20:50:24,905 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:24,905 | PyMapping_Check 2021-07-09T20:50:24,916 khmer/_khmermodule.cc:1101:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T20:50:24,916 1101 | std::string s = PyString_AsString(arg); 2021-07-09T20:50:24,916 | ^~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,928 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2021-07-09T20:50:24,928 khmer/_khmermodule.cc:1123:23: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T20:50:24,928 1123 | char * kmer_str = PyString_AsString( val ); 2021-07-09T20:50:24,928 | ^~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,935 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2021-07-09T20:50:24,935 khmer/_khmermodule.cc:1143:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T20:50:24,935 1143 | if (PyInt_Check(arg)) { 2021-07-09T20:50:24,935 | ^~~~~~~~~~~ 2021-07-09T20:50:24,935 | PySet_Check 2021-07-09T20:50:24,943 khmer/_khmermodule.cc:1144:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T20:50:24,943 1144 | long pos = PyInt_AsLong(arg); 2021-07-09T20:50:24,943 | ^~~~~~~~~~~~ 2021-07-09T20:50:24,943 | PyLong_AsLong 2021-07-09T20:50:24,951 khmer/_khmermodule.cc:1146:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T20:50:24,952 1146 | } else if (PyString_Check(arg)) { 2021-07-09T20:50:24,952 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:24,952 | PyMapping_Check 2021-07-09T20:50:24,962 khmer/_khmermodule.cc:1147:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T20:50:24,963 1147 | std::string s = PyString_AsString(arg); 2021-07-09T20:50:24,963 | ^~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,972 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2021-07-09T20:50:24,972 khmer/_khmermodule.cc:1195:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:24,972 1195 | return PyInt_FromLong(ktable->ksize()); 2021-07-09T20:50:24,973 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:24,973 | PyLong_FromLong 2021-07-09T20:50:24,983 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2021-07-09T20:50:24,984 khmer/_khmermodule.cc:1242:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T20:50:24,984 1242 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2021-07-09T20:50:24,984 | ^~~~~~~~~~~~~ 2021-07-09T20:50:24,984 | PyCMethod 2021-07-09T20:50:24,985 khmer/_khmermodule.cc: At global scope: 2021-07-09T20:50:24,985 khmer/_khmermodule.cc:1265:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:24,985 1265 | "KTable", sizeof(khmer_KTableObject), 2021-07-09T20:50:24,985 | ^~~~~~~~ 2021-07-09T20:50:24,986 | | 2021-07-09T20:50:24,986 | const char* 2021-07-09T20:50:24,986 khmer/_khmermodule.cc:1267:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:24,986 1267 | khmer_ktable_dealloc, /*tp_dealloc*/ 2021-07-09T20:50:24,986 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,986 | | 2021-07-09T20:50:24,987 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T20:50:24,987 khmer/_khmermodule.cc:1269:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T20:50:24,987 1269 | khmer_ktable_getattr, /*tp_getattr*/ 2021-07-09T20:50:24,987 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,987 | | 2021-07-09T20:50:24,987 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T20:50:24,987 khmer/_khmermodule.cc:1274:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2021-07-09T20:50:24,987 1274 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2021-07-09T20:50:24,988 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,988 | | 2021-07-09T20:50:24,988 | PySequenceMethods* 2021-07-09T20:50:24,989 khmer/_khmermodule.cc:1405:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:24,989 1405 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2021-07-09T20:50:24,989 | ^~~~~~~~~ 2021-07-09T20:50:24,989 | | 2021-07-09T20:50:24,989 | const char* 2021-07-09T20:50:24,990 khmer/_khmermodule.cc:1407:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:24,990 1407 | khmer_subset_dealloc, /*tp_dealloc*/ 2021-07-09T20:50:24,990 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,990 | | 2021-07-09T20:50:24,990 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T20:50:24,990 khmer/_khmermodule.cc:1409:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T20:50:24,991 1409 | khmer_subset_getattr, /*tp_getattr*/ 2021-07-09T20:50:24,991 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,991 | | 2021-07-09T20:50:24,991 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T20:50:24,991 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T20:50:24,991 from /usr/include/python3.9/Python.h:85, 2021-07-09T20:50:24,991 from khmer/_khmermodule.cc:12: 2021-07-09T20:50:24,991 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T20:50:24,992 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T20:50:24,992 | ~~~ 2021-07-09T20:50:24,992 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T20:50:24,992 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,992 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T20:50:24,993 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T20:50:24,993 | | 2021-07-09T20:50:24,993 | long unsigned int 2021-07-09T20:50:24,993 353 | 0) 2021-07-09T20:50:24,993 | ~~ 2021-07-09T20:50:24,993 khmer/_khmermodule.cc:1422:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T20:50:24,993 1422 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T20:50:24,993 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:24,994 khmer/_khmermodule.cc:1423:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T20:50:24,994 1423 | "subset object", /* tp_doc */ 2021-07-09T20:50:24,994 | ^~~~~~~~~~~~~~~ 2021-07-09T20:50:24,994 | | 2021-07-09T20:50:24,994 | const char* 2021-07-09T20:50:25,000 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2021-07-09T20:50:25,001 khmer/_khmermodule.cc:1519:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,001 1519 | return PyInt_FromLong(1); 2021-07-09T20:50:25,001 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,001 | PyLong_FromLong 2021-07-09T20:50:25,009 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2021-07-09T20:50:25,009 khmer/_khmermodule.cc:1536:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,010 1536 | return PyInt_FromLong(0); 2021-07-09T20:50:25,010 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,010 | PyLong_FromLong 2021-07-09T20:50:25,020 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2021-07-09T20:50:25,020 khmer/_khmermodule.cc:1624:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,020 1624 | return PyInt_FromLong(n_consumed); 2021-07-09T20:50:25,021 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,021 | PyLong_FromLong 2021-07-09T20:50:25,029 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2021-07-09T20:50:25,029 khmer/_khmermodule.cc:1656:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,029 1656 | return PyInt_FromLong(n_consumed); 2021-07-09T20:50:25,029 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,029 | PyLong_FromLong 2021-07-09T20:50:25,037 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2021-07-09T20:50:25,038 khmer/_khmermodule.cc:1679:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,038 1679 | return PyInt_FromLong(N); 2021-07-09T20:50:25,038 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,038 | PyLong_FromLong 2021-07-09T20:50:25,046 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2021-07-09T20:50:25,046 khmer/_khmermodule.cc:1702:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,046 1702 | return PyInt_FromLong(N); 2021-07-09T20:50:25,047 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,047 | PyLong_FromLong 2021-07-09T20:50:25,055 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2021-07-09T20:50:25,056 khmer/_khmermodule.cc:1805:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T20:50:25,056 1805 | if (PyInt_Check(arg)) { 2021-07-09T20:50:25,056 | ^~~~~~~~~~~ 2021-07-09T20:50:25,056 | PySet_Check 2021-07-09T20:50:25,063 khmer/_khmermodule.cc:1806:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T20:50:25,063 1806 | long pos = PyInt_AsLong(arg); 2021-07-09T20:50:25,063 | ^~~~~~~~~~~~ 2021-07-09T20:50:25,063 | PyLong_AsLong 2021-07-09T20:50:25,071 khmer/_khmermodule.cc:1808:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T20:50:25,071 1808 | } else if (PyString_Check(arg)) { 2021-07-09T20:50:25,071 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,071 | PyMapping_Check 2021-07-09T20:50:25,081 khmer/_khmermodule.cc:1809:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T20:50:25,082 1809 | std::string s = PyString_AsString(arg); 2021-07-09T20:50:25,082 | ^~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,089 khmer/_khmermodule.cc:1813:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,089 1813 | return PyInt_FromLong(count); 2021-07-09T20:50:25,090 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,090 | PyLong_FromLong 2021-07-09T20:50:25,098 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2021-07-09T20:50:25,098 khmer/_khmermodule.cc:1829:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,098 1829 | return PyInt_FromLong(count); 2021-07-09T20:50:25,098 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,098 | PyLong_FromLong 2021-07-09T20:50:25,109 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2021-07-09T20:50:25,109 khmer/_khmermodule.cc:1853:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T20:50:25,109 1853 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T20:50:25,109 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,109 | PyBytes_FromStringAndSize 2021-07-09T20:50:25,120 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2021-07-09T20:50:25,120 khmer/_khmermodule.cc:1883:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T20:50:25,120 1883 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T20:50:25,120 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,121 | PyBytes_FromStringAndSize 2021-07-09T20:50:25,132 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2021-07-09T20:50:25,133 khmer/_khmermodule.cc:2024:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,133 2024 | return PyInt_FromLong(k); 2021-07-09T20:50:25,133 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,133 | PyLong_FromLong 2021-07-09T20:50:25,148 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2021-07-09T20:50:25,148 khmer/_khmermodule.cc:2136:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T20:50:25,149 2136 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T20:50:25,149 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,149 | PyLong_FromVoidPtr 2021-07-09T20:50:25,161 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2021-07-09T20:50:25,161 khmer/_khmermodule.cc:2242:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T20:50:25,161 2242 | return Py_FindMethod(khmer_counting_methods, obj, name); 2021-07-09T20:50:25,161 | ^~~~~~~~~~~~~ 2021-07-09T20:50:25,162 | PyCMethod 2021-07-09T20:50:25,162 khmer/_khmermodule.cc: At global scope: 2021-07-09T20:50:25,162 khmer/_khmermodule.cc:2252:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,162 2252 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2021-07-09T20:50:25,162 | ^~~~~~~~~~~~~~~ 2021-07-09T20:50:25,162 | | 2021-07-09T20:50:25,162 | const char* 2021-07-09T20:50:25,163 khmer/_khmermodule.cc:2254:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,163 2254 | khmer_counting_dealloc, /*tp_dealloc*/ 2021-07-09T20:50:25,163 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,163 | | 2021-07-09T20:50:25,163 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T20:50:25,163 khmer/_khmermodule.cc:2256:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T20:50:25,163 2256 | khmer_counting_getattr, /*tp_getattr*/ 2021-07-09T20:50:25,163 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,164 | | 2021-07-09T20:50:25,164 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T20:50:25,164 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T20:50:25,164 from /usr/include/python3.9/Python.h:85, 2021-07-09T20:50:25,164 from khmer/_khmermodule.cc:12: 2021-07-09T20:50:25,164 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T20:50:25,165 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T20:50:25,165 | ~~~ 2021-07-09T20:50:25,165 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T20:50:25,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,165 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T20:50:25,165 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T20:50:25,165 | | 2021-07-09T20:50:25,165 | long unsigned int 2021-07-09T20:50:25,166 353 | 0) 2021-07-09T20:50:25,166 | ~~ 2021-07-09T20:50:25,166 khmer/_khmermodule.cc:2269:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T20:50:25,166 2269 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T20:50:25,166 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,166 khmer/_khmermodule.cc:2270:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T20:50:25,166 2270 | "counting hash object", /* tp_doc */ 2021-07-09T20:50:25,167 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,167 | | 2021-07-09T20:50:25,167 | const char* 2021-07-09T20:50:25,167 khmer/_khmermodule.cc:2350:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,167 2350 | "Hashbits", sizeof(khmer_KHashbitsObject), 2021-07-09T20:50:25,167 | ^~~~~~~~~~ 2021-07-09T20:50:25,167 | | 2021-07-09T20:50:25,168 | const char* 2021-07-09T20:50:25,168 khmer/_khmermodule.cc:2352:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,168 2352 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2021-07-09T20:50:25,168 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,168 | | 2021-07-09T20:50:25,168 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T20:50:25,168 khmer/_khmermodule.cc:2354:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T20:50:25,168 2354 | khmer_hashbits_getattr, /*tp_getattr*/ 2021-07-09T20:50:25,169 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,169 | | 2021-07-09T20:50:25,169 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T20:50:25,169 khmer/_khmermodule.cc:2367:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T20:50:25,169 2367 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2021-07-09T20:50:25,169 khmer/_khmermodule.cc:2368:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T20:50:25,169 2368 | "hashbits object", /* tp_doc */ 2021-07-09T20:50:25,170 | ^~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,170 | | 2021-07-09T20:50:25,170 | const char* 2021-07-09T20:50:25,179 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2021-07-09T20:50:25,179 khmer/_khmermodule.cc:2541:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,180 2541 | return PyInt_FromLong(hashbits->n_tags()); 2021-07-09T20:50:25,180 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,180 | PyLong_FromLong 2021-07-09T20:50:25,188 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2021-07-09T20:50:25,188 khmer/_khmermodule.cc:2563:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,188 2563 | return PyInt_FromLong(1); 2021-07-09T20:50:25,188 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,188 | PyLong_FromLong 2021-07-09T20:50:25,196 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2021-07-09T20:50:25,197 khmer/_khmermodule.cc:2586:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,197 2586 | return PyInt_FromLong(n_consumed); 2021-07-09T20:50:25,197 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,197 | PyLong_FromLong 2021-07-09T20:50:25,212 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2021-07-09T20:50:25,212 khmer/_khmermodule.cc:2693:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,212 2693 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2021-07-09T20:50:25,212 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,213 | PyLong_AsVoidPtr 2021-07-09T20:50:25,220 khmer/_khmermodule.cc:2703:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,220 2703 | return PyInt_FromLong(next_largest); 2021-07-09T20:50:25,220 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,220 | PyLong_FromLong 2021-07-09T20:50:25,226 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2021-07-09T20:50:25,227 khmer/_khmermodule.cc:2719:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T20:50:25,227 2719 | if (PyInt_Check(arg)) { 2021-07-09T20:50:25,227 | ^~~~~~~~~~~ 2021-07-09T20:50:25,227 | PySet_Check 2021-07-09T20:50:25,234 khmer/_khmermodule.cc:2720:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T20:50:25,234 2720 | long pos = PyInt_AsLong(arg); 2021-07-09T20:50:25,234 | ^~~~~~~~~~~~ 2021-07-09T20:50:25,234 | PyLong_AsLong 2021-07-09T20:50:25,242 khmer/_khmermodule.cc:2722:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T20:50:25,242 2722 | } else if (PyString_Check(arg)) { 2021-07-09T20:50:25,242 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,242 | PyMapping_Check 2021-07-09T20:50:25,252 khmer/_khmermodule.cc:2723:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T20:50:25,253 2723 | std::string s = PyString_AsString(arg); 2021-07-09T20:50:25,253 | ^~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,261 khmer/_khmermodule.cc:2730:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,261 2730 | return PyInt_FromLong(count); 2021-07-09T20:50:25,261 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,261 | PyLong_FromLong 2021-07-09T20:50:25,270 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2021-07-09T20:50:25,270 khmer/_khmermodule.cc:2772:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,270 2772 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2021-07-09T20:50:25,270 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,271 | PyLong_FromLong 2021-07-09T20:50:25,281 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2021-07-09T20:50:25,281 khmer/_khmermodule.cc:2793:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T20:50:25,281 2793 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T20:50:25,281 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,282 | PyBytes_FromStringAndSize 2021-07-09T20:50:25,305 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2021-07-09T20:50:25,305 khmer/_khmermodule.cc:2868:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T20:50:25,305 2868 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T20:50:25,305 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,306 | PyLong_FromVoidPtr 2021-07-09T20:50:25,315 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2021-07-09T20:50:25,315 khmer/_khmermodule.cc:2896:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T20:50:25,315 2896 | if (!PyCObject_Check(subset_obj)) { 2021-07-09T20:50:25,315 | ^~~~~~~~~~~~~~~ 2021-07-09T20:50:25,316 | PyODict_Check 2021-07-09T20:50:25,327 khmer/_khmermodule.cc:2902:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,327 2902 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T20:50:25,327 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,327 | PyLong_AsVoidPtr 2021-07-09T20:50:25,347 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2021-07-09T20:50:25,347 khmer/_khmermodule.cc:3166:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T20:50:25,348 3166 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T20:50:25,348 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,348 | PyLong_FromVoidPtr 2021-07-09T20:50:25,356 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2021-07-09T20:50:25,357 khmer/_khmermodule.cc:3179:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T20:50:25,357 3179 | if (!PyCObject_Check(ppi_obj)) { 2021-07-09T20:50:25,357 | ^~~~~~~~~~~~~~~ 2021-07-09T20:50:25,357 | PyODict_Check 2021-07-09T20:50:25,368 khmer/_khmermodule.cc:3185:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,369 3185 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2021-07-09T20:50:25,369 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,369 | PyLong_AsVoidPtr 2021-07-09T20:50:25,376 khmer/_khmermodule.cc:3191:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,377 3191 | return PyInt_FromLong(p); 2021-07-09T20:50:25,377 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,377 | PyLong_FromLong 2021-07-09T20:50:25,389 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2021-07-09T20:50:25,390 khmer/_khmermodule.cc:3306:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,390 3306 | return PyInt_FromLong(n_partitions); 2021-07-09T20:50:25,390 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,390 | PyLong_FromLong 2021-07-09T20:50:25,398 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2021-07-09T20:50:25,399 khmer/_khmermodule.cc:3337:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,399 3337 | return PyInt_FromLong(n_singletons); 2021-07-09T20:50:25,399 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,399 | PyLong_FromLong 2021-07-09T20:50:25,413 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2021-07-09T20:50:25,414 khmer/_khmermodule.cc:3436:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,414 3436 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T20:50:25,414 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,414 | PyLong_AsVoidPtr 2021-07-09T20:50:25,426 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2021-07-09T20:50:25,426 khmer/_khmermodule.cc:3453:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,426 3453 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T20:50:25,426 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,426 | PyLong_AsVoidPtr 2021-07-09T20:50:25,468 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T20:50:25,468 khmer/_khmermodule.cc:3564:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,468 3564 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T20:50:25,468 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,468 | PyLong_AsVoidPtr 2021-07-09T20:50:25,481 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T20:50:25,481 khmer/_khmermodule.cc:3595:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T20:50:25,481 3595 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T20:50:25,481 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,481 | PyLong_FromVoidPtr 2021-07-09T20:50:25,490 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2021-07-09T20:50:25,490 khmer/_khmermodule.cc:3624:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,490 3624 | return PyInt_FromLong(d); 2021-07-09T20:50:25,490 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,490 | PyLong_FromLong 2021-07-09T20:50:25,502 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2021-07-09T20:50:25,502 khmer/_khmermodule.cc:3640:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,502 3640 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T20:50:25,502 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,503 | PyLong_AsVoidPtr 2021-07-09T20:50:25,514 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2021-07-09T20:50:25,514 khmer/_khmermodule.cc:3666:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,515 3666 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T20:50:25,515 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,515 | PyLong_AsVoidPtr 2021-07-09T20:50:25,527 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T20:50:25,527 khmer/_khmermodule.cc:3687:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T20:50:25,527 3687 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T20:50:25,527 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,528 | PyLong_AsVoidPtr 2021-07-09T20:50:25,536 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2021-07-09T20:50:25,536 khmer/_khmermodule.cc:3723:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,537 3723 | return PyInt_FromLong(p1); 2021-07-09T20:50:25,537 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,537 | PyLong_FromLong 2021-07-09T20:50:25,545 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2021-07-09T20:50:25,545 khmer/_khmermodule.cc:3740:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,545 3740 | return PyInt_FromLong(partition_id); 2021-07-09T20:50:25,545 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,545 | PyLong_FromLong 2021-07-09T20:50:25,558 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2021-07-09T20:50:25,558 khmer/_khmermodule.cc:3882:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,558 3882 | return PyInt_FromLong(k); 2021-07-09T20:50:25,558 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,558 | PyLong_FromLong 2021-07-09T20:50:25,580 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T20:50:25,580 from /usr/include/python3.9/Python.h:106, 2021-07-09T20:50:25,580 from khmer/_khmermodule.cc:12: 2021-07-09T20:50:25,580 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2021-07-09T20:50:25,580 khmer/_khmermodule.cc:3926:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T20:50:25,580 3926 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2021-07-09T20:50:25,581 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,581 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T20:50:25,581 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T20:50:25,581 | ^ 2021-07-09T20:50:25,593 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2021-07-09T20:50:25,594 khmer/_khmermodule.cc:4033:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T20:50:25,594 4033 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2021-07-09T20:50:25,594 | ^~~~~~~~~~~~~ 2021-07-09T20:50:25,594 | PyCMethod 2021-07-09T20:50:25,634 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2021-07-09T20:50:25,634 khmer/_khmermodule.cc:4260:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T20:50:25,634 4260 | return Py_FindMethod(khmer_subset_methods, obj, name); 2021-07-09T20:50:25,634 | ^~~~~~~~~~~~~ 2021-07-09T20:50:25,635 | PyCMethod 2021-07-09T20:50:25,662 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2021-07-09T20:50:25,662 khmer/_khmermodule.cc:4612:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T20:50:25,662 4612 | return PyInt_FromLong(labelhash->n_labels()); 2021-07-09T20:50:25,662 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,663 | PyLong_FromLong 2021-07-09T20:50:25,663 khmer/_khmermodule.cc: At global scope: 2021-07-09T20:50:25,663 khmer/_khmermodule.cc:4631:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,663 4631 | "_LabelHash", /* tp_name */ 2021-07-09T20:50:25,663 | ^~~~~~~~~~~~ 2021-07-09T20:50:25,664 | | 2021-07-09T20:50:25,664 | const char* 2021-07-09T20:50:25,664 khmer/_khmermodule.cc:4634:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,664 4634 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2021-07-09T20:50:25,664 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,664 | | 2021-07-09T20:50:25,665 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T20:50:25,665 khmer/_khmermodule.cc:4649:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T20:50:25,665 4649 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2021-07-09T20:50:25,665 khmer/_khmermodule.cc:4657:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2021-07-09T20:50:25,665 4657 | khmer_labelhash_methods, /* tp_methods */ 2021-07-09T20:50:25,665 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,665 | | 2021-07-09T20:50:25,665 | PyMethodDef* 2021-07-09T20:50:25,678 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2021-07-09T20:50:25,679 khmer/_khmermodule.cc:4740:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T20:50:25,679 4740 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2021-07-09T20:50:25,679 | ^~~~~~~~~~~~~ 2021-07-09T20:50:25,679 | PyCMethod 2021-07-09T20:50:25,679 khmer/_khmermodule.cc: At global scope: 2021-07-09T20:50:25,679 khmer/_khmermodule.cc:4758:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,680 4758 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2021-07-09T20:50:25,680 | ^~~~~~~~~~~~~ 2021-07-09T20:50:25,680 | | 2021-07-09T20:50:25,680 | const char* 2021-07-09T20:50:25,680 khmer/_khmermodule.cc:4760:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T20:50:25,680 4760 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2021-07-09T20:50:25,680 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,680 | | 2021-07-09T20:50:25,681 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T20:50:25,681 khmer/_khmermodule.cc:4762:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T20:50:25,681 4762 | khmer_readaligner_getattr, /*tp_getattr*/ 2021-07-09T20:50:25,681 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,681 | | 2021-07-09T20:50:25,681 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T20:50:25,681 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T20:50:25,682 from /usr/include/python3.9/Python.h:85, 2021-07-09T20:50:25,682 from khmer/_khmermodule.cc:12: 2021-07-09T20:50:25,682 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T20:50:25,682 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T20:50:25,682 | ~~~ 2021-07-09T20:50:25,682 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T20:50:25,682 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,683 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T20:50:25,683 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T20:50:25,683 | | 2021-07-09T20:50:25,683 | long unsigned int 2021-07-09T20:50:25,683 353 | 0) 2021-07-09T20:50:25,683 | ~~ 2021-07-09T20:50:25,683 khmer/_khmermodule.cc:4775:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T20:50:25,683 4775 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T20:50:25,684 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,684 khmer/_khmermodule.cc:4776:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T20:50:25,684 4776 | "ReadAligner object", /* tp_doc */ 2021-07-09T20:50:25,684 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,684 | | 2021-07-09T20:50:25,684 | const char* 2021-07-09T20:50:25,688 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2021-07-09T20:50:25,688 khmer/_khmermodule.cc:4917:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2021-07-09T20:50:25,688 4917 | self->ob_type->tp_free((PyObject*)obj); 2021-07-09T20:50:25,688 | ^~~~~~~ 2021-07-09T20:50:25,699 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2021-07-09T20:50:25,699 khmer/_khmermodule.cc:4992:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T20:50:25,700 4992 | return PyString_FromString(_revhash(val, ksize).c_str()); 2021-07-09T20:50:25,700 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:25,700 | PyLong_FromString 2021-07-09T20:50:25,701 khmer/_khmermodule.cc: At global scope: 2021-07-09T20:50:25,701 khmer/_khmermodule.cc:5072:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2021-07-09T20:50:25,701 5072 | init_khmer(void) 2021-07-09T20:50:25,701 | ^~~~~~~~~~ 2021-07-09T20:50:25,701 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2021-07-09T20:50:25,701 33 | void init_khmer(); 2021-07-09T20:50:25,701 | ^~~~~~~~~~ 2021-07-09T20:50:25,702 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2021-07-09T20:50:25,702 khmer/_khmermodule.cc:5076:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T20:50:25,702 5076 | khmer_ConfigType.ob_type = &PyType_Type; 2021-07-09T20:50:25,702 | ^~~~~~~ 2021-07-09T20:50:25,702 khmer/_khmermodule.cc:5077:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T20:50:25,702 5077 | khmer_KTableType.ob_type = &PyType_Type; 2021-07-09T20:50:25,703 | ^~~~~~~ 2021-07-09T20:50:25,703 khmer/_khmermodule.cc:5078:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T20:50:25,703 5078 | khmer_KCountingHashType.ob_type = &PyType_Type; 2021-07-09T20:50:25,703 | ^~~~~~~ 2021-07-09T20:50:25,703 khmer/_khmermodule.cc:5085:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T20:50:25,703 5085 | return; 2021-07-09T20:50:25,703 | ^~~~~~ 2021-07-09T20:50:25,704 khmer/_khmermodule.cc:5092:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T20:50:25,704 5092 | return; 2021-07-09T20:50:25,704 | ^~~~~~ 2021-07-09T20:50:25,712 khmer/_khmermodule.cc:5096:9: error: ‘Py_InitModule3’ was not declared in this scope 2021-07-09T20:50:25,713 5096 | m = Py_InitModule3( "_khmer", KhmerMethods, 2021-07-09T20:50:25,713 | ^~~~~~~~~~~~~~ 2021-07-09T20:50:25,713 khmer/_khmermodule.cc:5099:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T20:50:25,713 5099 | return; 2021-07-09T20:50:25,713 | ^~~~~~ 2021-07-09T20:50:25,713 khmer/_khmermodule.cc:5104:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T20:50:25,714 5104 | return; 2021-07-09T20:50:25,714 | ^~~~~~ 2021-07-09T20:50:25,714 khmer/_khmermodule.cc:5111:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T20:50:25,714 5111 | return; 2021-07-09T20:50:25,714 | ^~~~~~ 2021-07-09T20:50:25,714 khmer/_khmermodule.cc:5117:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T20:50:25,715 5117 | return; 2021-07-09T20:50:25,715 | ^~~~~~ 2021-07-09T20:50:25,715 khmer/_khmermodule.cc:5120:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T20:50:25,715 5120 | return; 2021-07-09T20:50:25,715 | ^~~~~~ 2021-07-09T20:50:26,465 khmer/_khmermodule.cc:5130:23: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-09T20:50:26,465 5130 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2021-07-09T20:50:26,465 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T20:50:26,559 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T20:50:26,639 Building wheel for khmer (setup.py): finished with status 'error' 2021-07-09T20:50:26,639 ERROR: Failed building wheel for khmer 2021-07-09T20:50:26,640 Running setup.py clean for khmer 2021-07-09T20:50:26,640 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-hj7jxewv/khmer_7dd91339b5fe464fac7d69b92c5a2289/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-hj7jxewv/khmer_7dd91339b5fe464fac7d69b92c5a2289/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 2021-07-09T20:50:28,964 running clean 2021-07-09T20:50:28,965 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T20:50:28,967 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T20:50:28,971 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T20:50:28,972 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T20:50:28,972 removing 'build' 2021-07-09T20:50:29,035 Failed to build khmer 2021-07-09T20:50:29,035 ERROR: Failed to build one or more wheels 2021-07-09T20:50:29,036 Exception information: 2021-07-09T20:50:29,036 Traceback (most recent call last): 2021-07-09T20:50:29,036 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T20:50:29,036 status = self.run(options, args) 2021-07-09T20:50:29,036 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T20:50:29,036 return func(self, options, args) 2021-07-09T20:50:29,036 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T20:50:29,036 raise CommandError( 2021-07-09T20:50:29,036 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T20:50:29,039 Removed build tracker: '/tmp/pip-req-tracker-jmcq30di'