2021-07-09T19:03:27,105 Created temporary directory: /tmp/pip-ephem-wheel-cache-6nzpj9nc 2021-07-09T19:03:27,108 Created temporary directory: /tmp/pip-req-tracker-q7es3d5y 2021-07-09T19:03:27,108 Initialized build tracking at /tmp/pip-req-tracker-q7es3d5y 2021-07-09T19:03:27,108 Created build tracker: /tmp/pip-req-tracker-q7es3d5y 2021-07-09T19:03:27,109 Entered build tracker: /tmp/pip-req-tracker-q7es3d5y 2021-07-09T19:03:27,109 Created temporary directory: /tmp/pip-wheel-4w1fpc62 2021-07-09T19:03:27,144 1 location(s) to search for versions of khmer: 2021-07-09T19:03:27,144 * https://pypi.org/simple/khmer/ 2021-07-09T19:03:27,144 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2021-07-09T19:03:27,145 Getting page https://pypi.org/simple/khmer/ 2021-07-09T19:03:27,146 Found index url https://pypi.org/simple 2021-07-09T19:03:27,342 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/) 2021-07-09T19:03:27,342 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/) 2021-07-09T19:03:27,343 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 2021-07-09T19:03:27,343 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 2021-07-09T19:03:27,359 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/) 2021-07-09T19:03:27,359 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 2021-07-09T19:03:27,360 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/) 2021-07-09T19:03:27,360 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 2021-07-09T19:03:27,361 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/) 2021-07-09T19:03:27,361 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 2021-07-09T19:03:27,361 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/) 2021-07-09T19:03:27,362 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 2021-07-09T19:03:27,362 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/) 2021-07-09T19:03:27,362 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 2021-07-09T19:03:27,363 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 2021-07-09T19:03:27,363 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/) 2021-07-09T19:03:27,363 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 2021-07-09T19:03:27,364 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/) 2021-07-09T19:03:27,364 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 2021-07-09T19:03:27,365 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/) 2021-07-09T19:03:27,365 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 2021-07-09T19:03:27,365 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/) 2021-07-09T19:03:27,366 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/) 2021-07-09T19:03:27,366 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 2021-07-09T19:03:27,367 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/) 2021-07-09T19:03:27,367 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/) 2021-07-09T19:03:27,367 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/) 2021-07-09T19:03:27,368 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/) 2021-07-09T19:03:27,368 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 2021-07-09T19:03:27,368 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 2021-07-09T19:03:27,369 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/) 2021-07-09T19:03:27,369 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 2021-07-09T19:03:27,370 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/) 2021-07-09T19:03:27,370 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/) 2021-07-09T19:03:27,371 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/) 2021-07-09T19:03:27,371 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/) 2021-07-09T19:03:27,372 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/) 2021-07-09T19:03:27,372 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 2021-07-09T19:03:27,372 Skipping link: not a file: https://pypi.org/simple/khmer/ 2021-07-09T19:03:27,375 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2021-07-09T19:03:27,392 Collecting khmer==0.6 2021-07-09T19:03:27,394 Created temporary directory: /tmp/pip-unpack-2w4kllx0 2021-07-09T19:03:28,472 Downloading khmer-0.6.tar.gz (19.2 MB) 2021-07-09T19:03:33,726 Added khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz#sha256=b3aecbfb7465e5e6d7963513e40fa77bb63d3918fc47deba82102f13a69517ff to build tracker '/tmp/pip-req-tracker-q7es3d5y' 2021-07-09T19:03:33,727 Running setup.py (path:/tmp/pip-wheel-4w1fpc62/khmer_d6cbbdec738843e1abdc45d122272304/setup.py) egg_info for package khmer 2021-07-09T19:03:33,728 Created temporary directory: /tmp/pip-pip-egg-info-q97egs75 2021-07-09T19:03:33,728 Running command python setup.py egg_info 2021-07-09T19:03:34,523 running egg_info 2021-07-09T19:03:34,526 creating /tmp/pip-pip-egg-info-q97egs75/khmer.egg-info 2021-07-09T19:03:34,527 writing /tmp/pip-pip-egg-info-q97egs75/khmer.egg-info/PKG-INFO 2021-07-09T19:03:34,529 writing dependency_links to /tmp/pip-pip-egg-info-q97egs75/khmer.egg-info/dependency_links.txt 2021-07-09T19:03:34,531 writing requirements to /tmp/pip-pip-egg-info-q97egs75/khmer.egg-info/requires.txt 2021-07-09T19:03:34,532 writing top-level names to /tmp/pip-pip-egg-info-q97egs75/khmer.egg-info/top_level.txt 2021-07-09T19:03:34,533 writing manifest file '/tmp/pip-pip-egg-info-q97egs75/khmer.egg-info/SOURCES.txt' 2021-07-09T19:03:34,687 reading manifest file '/tmp/pip-pip-egg-info-q97egs75/khmer.egg-info/SOURCES.txt' 2021-07-09T19:03:34,689 reading manifest template 'MANIFEST.in' 2021-07-09T19:03:34,690 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T19:03:34,693 writing manifest file '/tmp/pip-pip-egg-info-q97egs75/khmer.egg-info/SOURCES.txt' 2021-07-09T19:03:34,757 Source in /tmp/pip-wheel-4w1fpc62/khmer_d6cbbdec738843e1abdc45d122272304 has version 0.6, which satisfies requirement khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz#sha256=b3aecbfb7465e5e6d7963513e40fa77bb63d3918fc47deba82102f13a69517ff 2021-07-09T19:03:34,758 Removed khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz#sha256=b3aecbfb7465e5e6d7963513e40fa77bb63d3918fc47deba82102f13a69517ff from build tracker '/tmp/pip-req-tracker-q7es3d5y' 2021-07-09T19:03:34,763 Created temporary directory: /tmp/pip-unpack-hrug8zoi 2021-07-09T19:03:34,763 Building wheels for collected packages: khmer 2021-07-09T19:03:34,768 Created temporary directory: /tmp/pip-wheel-z4qm6hi3 2021-07-09T19:03:34,768 Building wheel for khmer (setup.py): started 2021-07-09T19:03:34,768 Destination directory: /tmp/pip-wheel-z4qm6hi3 2021-07-09T19:03:34,769 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-4w1fpc62/khmer_d6cbbdec738843e1abdc45d122272304/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-4w1fpc62/khmer_d6cbbdec738843e1abdc45d122272304/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-z4qm6hi3 2021-07-09T19:03:35,583 running bdist_wheel 2021-07-09T19:03:35,587 running build 2021-07-09T19:03:35,587 running build_py 2021-07-09T19:03:35,735 creating build 2021-07-09T19:03:35,735 creating build/lib.linux-armv7l-3.9 2021-07-09T19:03:35,736 creating build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,737 copying khmer/load_pe.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,739 copying khmer/__init__.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,741 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,743 copying khmer/thread_utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,745 copying khmer/counting_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,747 copying khmer/threading_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,749 copying khmer/utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,751 running egg_info 2021-07-09T19:03:35,764 writing khmer.egg-info/PKG-INFO 2021-07-09T19:03:35,766 writing dependency_links to khmer.egg-info/dependency_links.txt 2021-07-09T19:03:35,768 writing requirements to khmer.egg-info/requires.txt 2021-07-09T19:03:35,769 writing top-level names to khmer.egg-info/top_level.txt 2021-07-09T19:03:35,777 reading manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T19:03:35,865 reading manifest template 'MANIFEST.in' 2021-07-09T19:03:35,867 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T19:03:35,899 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T19:03:35,920 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:03:35,925 running build_ext 2021-07-09T19:03:36,005 Checking for gcc... 2021-07-09T19:03:36,112 Checking for shared library support... 2021-07-09T19:03:36,304 Building shared library libz.so.1.2.3 with gcc. 2021-07-09T19:03:36,420 Checking for unistd.h... Yes. 2021-07-09T19:03:36,552 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf() 2021-07-09T19:03:36,794 Checking for vsnprintf() in stdio.h... Yes. 2021-07-09T19:03:36,908 Checking for return value of vsnprintf()... Yes. 2021-07-09T19:03:37,003 Checking for errno.h... Yes. 2021-07-09T19:03:37,118 Checking for mmap support... Yes. 2021-07-09T19:03:37,191 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2021-07-09T19:03:37,486 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2021-07-09T19:03:37,624 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2021-07-09T19:03:38,008 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2021-07-09T19:03:38,945 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2021-07-09T19:03:39,075 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2021-07-09T19:03:40,420 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2021-07-09T19:03:41,663 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2021-07-09T19:03:41,815 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2021-07-09T19:03:43,311 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2021-07-09T19:03:44,052 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2021-07-09T19:03:44,470 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2021-07-09T19:03:44,907 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 2021-07-09T19:03:45,004 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2021-07-09T19:03:45,787 blocksort.c: In function ‘mainSort’: 2021-07-09T19:03:45,787 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T19:03:45,787 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T19:03:45,787 | ^~~~~~~ 2021-07-09T19:03:45,787 blocksort.c:514:18: note: called from here 2021-07-09T19:03:45,787 514 | while ( mainGtU ( 2021-07-09T19:03:45,788 | ^~~~~~~~~ 2021-07-09T19:03:45,788 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T19:03:45,788 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:45,788 516 | ) ) { 2021-07-09T19:03:45,788 | ~ 2021-07-09T19:03:45,788 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T19:03:45,788 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T19:03:45,789 | ^~~~~~~ 2021-07-09T19:03:45,789 blocksort.c:528:18: note: called from here 2021-07-09T19:03:45,789 528 | while ( mainGtU ( 2021-07-09T19:03:45,789 | ^~~~~~~~~ 2021-07-09T19:03:45,789 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T19:03:45,789 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:45,789 530 | ) ) { 2021-07-09T19:03:45,790 | ~ 2021-07-09T19:03:45,790 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T19:03:45,790 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T19:03:45,790 | ^~~~~~~ 2021-07-09T19:03:45,790 blocksort.c:542:18: note: called from here 2021-07-09T19:03:45,790 542 | while ( mainGtU ( 2021-07-09T19:03:45,790 | ^~~~~~~~~ 2021-07-09T19:03:45,790 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T19:03:45,791 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:45,791 544 | ) ) { 2021-07-09T19:03:45,791 | ~ 2021-07-09T19:03:46,482 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2021-07-09T19:03:46,887 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2021-07-09T19:03:47,020 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2021-07-09T19:03:47,152 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2021-07-09T19:03:51,017 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2021-07-09T19:03:53,252 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2021-07-09T19:03:54,892 #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 2021-07-09T19:03:54,895 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2021-07-09T19:03:54,897 #rm -f libbz2.so.1.0 2021-07-09T19:03:54,900 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2021-07-09T19:03:54,913 building 'khmer._khmermodule' extension 2021-07-09T19:03:54,914 creating build/temp.linux-armv7l-3.9 2021-07-09T19:03:54,915 creating build/temp.linux-armv7l-3.9/khmer 2021-07-09T19:03:54,916 creating build/temp.linux-armv7l-3.9/lib 2021-07-09T19:03:54,917 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 -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.9 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-3.9/khmer/_khmermodule.o -O3 2021-07-09T19:03:57,032 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2021-07-09T19:03:57,032 khmer/_khmermodule.cc:81:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2021-07-09T19:03:57,032 81 | tobj.ob_size = 0; 2021-07-09T19:03:57,032 | ^~~~~~~ 2021-07-09T19:03:57,032 khmer/_khmermodule.cc:82:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T19:03:57,033 82 | tobj.ob_type = &PyType_Type; 2021-07-09T19:03:57,033 | ^~~~~~~ 2021-07-09T19:03:57,037 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:03:57,037 khmer/_khmermodule.cc:198:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,037 198 | "Config", sizeof(khmer_ConfigObject), 2021-07-09T19:03:57,037 | ^~~~~~~~ 2021-07-09T19:03:57,038 | | 2021-07-09T19:03:57,038 | const char* 2021-07-09T19:03:57,038 khmer/_khmermodule.cc:200:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,038 200 | khmer_config_dealloc, /*tp_dealloc*/ 2021-07-09T19:03:57,038 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,038 | | 2021-07-09T19:03:57,039 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:03:57,039 khmer/_khmermodule.cc:202:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:03:57,039 202 | khmer_config_getattr, /*tp_getattr*/ 2021-07-09T19:03:57,039 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,040 | | 2021-07-09T19:03:57,040 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:03:57,040 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:03:57,040 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:03:57,040 from khmer/_khmermodule.cc:13: 2021-07-09T19:03:57,040 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:03:57,040 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:03:57,040 | ~~~ 2021-07-09T19:03:57,041 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:03:57,041 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,041 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:03:57,041 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:03:57,041 | | 2021-07-09T19:03:57,041 | long unsigned int 2021-07-09T19:03:57,041 353 | 0) 2021-07-09T19:03:57,041 | ~~ 2021-07-09T19:03:57,041 khmer/_khmermodule.cc:215:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:03:57,042 215 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:03:57,042 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,042 khmer/_khmermodule.cc:216:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:03:57,042 216 | "config object", /* tp_doc */ 2021-07-09T19:03:57,042 | ^~~~~~~~~~~~~~~ 2021-07-09T19:03:57,042 | | 2021-07-09T19:03:57,042 | const char* 2021-07-09T19:03:57,047 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2021-07-09T19:03:57,047 khmer/_khmermodule.cc:300:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T19:03:57,048 300 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2021-07-09T19:03:57,048 | ^~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,048 | PyLong_FromSize_t 2021-07-09T19:03:57,057 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2021-07-09T19:03:57,057 khmer/_khmermodule.cc:358:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T19:03:57,057 358 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2021-07-09T19:03:57,057 | ^~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,057 | PyLong_FromSize_t 2021-07-09T19:03:57,066 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2021-07-09T19:03:57,066 khmer/_khmermodule.cc:386:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T19:03:57,066 386 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2021-07-09T19:03:57,066 | ^~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,066 | PyLong_FromSize_t 2021-07-09T19:03:57,076 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2021-07-09T19:03:57,076 khmer/_khmermodule.cc:434:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:03:57,076 434 | return Py_FindMethod(khmer_config_methods, obj, name); 2021-07-09T19:03:57,076 | ^~~~~~~~~~~~~ 2021-07-09T19:03:57,077 | PyCMethod 2021-07-09T19:03:57,086 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2021-07-09T19:03:57,086 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:03:57,086 472 | PyString_FromString( \ 2021-07-09T19:03:57,087 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,087 khmer/_khmermodule.cc:480:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:03:57,087 480 | { return KHMER_READ_STRING_GETTER( self, name ); } 2021-07-09T19:03:57,087 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,095 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2021-07-09T19:03:57,096 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:03:57,096 472 | PyString_FromString( \ 2021-07-09T19:03:57,096 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,096 khmer/_khmermodule.cc:486:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:03:57,096 486 | { return KHMER_READ_STRING_GETTER( self, sequence ); } 2021-07-09T19:03:57,096 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,105 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2021-07-09T19:03:57,105 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:03:57,105 472 | PyString_FromString( \ 2021-07-09T19:03:57,105 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,106 khmer/_khmermodule.cc:492:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:03:57,106 492 | { return KHMER_READ_STRING_GETTER( self, accuracy ); } 2021-07-09T19:03:57,106 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,114 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2021-07-09T19:03:57,114 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:03:57,114 472 | PyString_FromString( \ 2021-07-09T19:03:57,115 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,115 khmer/_khmermodule.cc:498:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:03:57,115 498 | { return KHMER_READ_STRING_GETTER( self, annotations ); } 2021-07-09T19:03:57,115 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,138 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2021-07-09T19:03:57,139 khmer/_khmermodule.cc:816:2: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,139 816 | PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ) 2021-07-09T19:03:57,139 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,139 | PyLong_FromLong 2021-07-09T19:03:57,150 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2021-07-09T19:03:57,150 khmer/_khmermodule.cc:959:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:03:57,150 959 | return PyString_FromString(khmer::_revhash(val, ktable->ksize()).c_str()); 2021-07-09T19:03:57,151 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,151 | PyLong_FromString 2021-07-09T19:03:57,158 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2021-07-09T19:03:57,158 khmer/_khmermodule.cc:985:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,159 985 | return PyInt_FromLong(1); 2021-07-09T19:03:57,159 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,159 | PyLong_FromLong 2021-07-09T19:03:57,167 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2021-07-09T19:03:57,167 khmer/_khmermodule.cc:1013:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,167 1013 | return PyInt_FromLong(n_consumed); 2021-07-09T19:03:57,167 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,167 | PyLong_FromLong 2021-07-09T19:03:57,173 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2021-07-09T19:03:57,173 khmer/_khmermodule.cc:1032:14: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:03:57,174 1032 | } else if (PyInt_Check(arg)) { 2021-07-09T19:03:57,174 | ^~~~~~~~~~~ 2021-07-09T19:03:57,174 | PySet_Check 2021-07-09T19:03:57,180 khmer/_khmermodule.cc:1033:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:03:57,180 1033 | long pos = PyInt_AsLong(arg); 2021-07-09T19:03:57,181 | ^~~~~~~~~~~~ 2021-07-09T19:03:57,181 | PyLong_AsLong 2021-07-09T19:03:57,188 khmer/_khmermodule.cc:1035:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:03:57,188 1035 | } else if (PyString_Check(arg)) { 2021-07-09T19:03:57,189 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,189 | PyMapping_Check 2021-07-09T19:03:57,198 khmer/_khmermodule.cc:1036:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:03:57,199 1036 | std::string s = PyString_AsString(arg); 2021-07-09T19:03:57,199 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,206 khmer/_khmermodule.cc:1040:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,206 1040 | return PyInt_FromLong(count); 2021-07-09T19:03:57,207 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,207 | PyLong_FromLong 2021-07-09T19:03:57,214 khmer/_khmermodule.cc: In function ‘PyObject* ktable__getitem__(PyObject*, Py_ssize_t)’: 2021-07-09T19:03:57,214 khmer/_khmermodule.cc:1050:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,215 1050 | return PyInt_FromLong(count); 2021-07-09T19:03:57,215 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,215 | PyLong_FromLong 2021-07-09T19:03:57,225 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2021-07-09T19:03:57,225 khmer/_khmermodule.cc:1058:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:03:57,225 1058 | char * kmer_str = PyString_AsString( val ); 2021-07-09T19:03:57,226 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,231 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2021-07-09T19:03:57,232 khmer/_khmermodule.cc:1076:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:03:57,232 1076 | if (PyInt_Check(arg)) { 2021-07-09T19:03:57,232 | ^~~~~~~~~~~ 2021-07-09T19:03:57,232 | PySet_Check 2021-07-09T19:03:57,238 khmer/_khmermodule.cc:1077:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:03:57,239 1077 | long pos = PyInt_AsLong(arg); 2021-07-09T19:03:57,239 | ^~~~~~~~~~~~ 2021-07-09T19:03:57,239 | PyLong_AsLong 2021-07-09T19:03:57,246 khmer/_khmermodule.cc:1079:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:03:57,247 1079 | } else if (PyString_Check(arg)) { 2021-07-09T19:03:57,247 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,247 | PyMapping_Check 2021-07-09T19:03:57,257 khmer/_khmermodule.cc:1080:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:03:57,257 1080 | std::string s = PyString_AsString(arg); 2021-07-09T19:03:57,257 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,265 khmer/_khmermodule.cc: In function ‘PyObject* ktable_max_hash(PyObject*, PyObject*)’: 2021-07-09T19:03:57,265 khmer/_khmermodule.cc:1097:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,265 1097 | return PyInt_FromLong(ktable->max_hash()); 2021-07-09T19:03:57,266 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,266 | PyLong_FromLong 2021-07-09T19:03:57,273 khmer/_khmermodule.cc: In function ‘PyObject* ktable_n_entries(PyObject*, PyObject*)’: 2021-07-09T19:03:57,273 khmer/_khmermodule.cc:1109:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,273 1109 | return PyInt_FromLong(ktable->n_entries()); 2021-07-09T19:03:57,273 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,274 | PyLong_FromLong 2021-07-09T19:03:57,281 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2021-07-09T19:03:57,281 khmer/_khmermodule.cc:1129:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,281 1129 | return PyInt_FromLong(ktable->ksize()); 2021-07-09T19:03:57,282 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,282 | PyLong_FromLong 2021-07-09T19:03:57,291 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2021-07-09T19:03:57,292 khmer/_khmermodule.cc:1175:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:03:57,292 1175 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2021-07-09T19:03:57,292 | ^~~~~~~~~~~~~ 2021-07-09T19:03:57,292 | PyCMethod 2021-07-09T19:03:57,292 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:03:57,292 khmer/_khmermodule.cc:1196:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,293 1196 | "KTable", sizeof(khmer_KTableObject), 2021-07-09T19:03:57,293 | ^~~~~~~~ 2021-07-09T19:03:57,293 | | 2021-07-09T19:03:57,293 | const char* 2021-07-09T19:03:57,293 khmer/_khmermodule.cc:1198:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,293 1198 | khmer_ktable_dealloc, /*tp_dealloc*/ 2021-07-09T19:03:57,293 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,294 | | 2021-07-09T19:03:57,294 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:03:57,294 khmer/_khmermodule.cc:1200:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:03:57,294 1200 | khmer_ktable_getattr, /*tp_getattr*/ 2021-07-09T19:03:57,294 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,294 | | 2021-07-09T19:03:57,295 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:03:57,295 khmer/_khmermodule.cc:1205:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2021-07-09T19:03:57,295 1205 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2021-07-09T19:03:57,295 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,295 | | 2021-07-09T19:03:57,295 | PySequenceMethods* 2021-07-09T19:03:57,295 khmer/_khmermodule.cc:1314:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,296 1314 | "KHashbits", sizeof(khmer_KHashbitsObject), 2021-07-09T19:03:57,296 | ^~~~~~~~~~~ 2021-07-09T19:03:57,296 | | 2021-07-09T19:03:57,296 | const char* 2021-07-09T19:03:57,296 khmer/_khmermodule.cc:1316:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,296 1316 | khmer_hashbits_dealloc, /*tp_dealloc*/ 2021-07-09T19:03:57,296 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,297 | | 2021-07-09T19:03:57,297 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:03:57,297 khmer/_khmermodule.cc:1318:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:03:57,297 1318 | khmer_hashbits_getattr, /*tp_getattr*/ 2021-07-09T19:03:57,297 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,297 | | 2021-07-09T19:03:57,298 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:03:57,298 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:03:57,298 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:03:57,298 from khmer/_khmermodule.cc:13: 2021-07-09T19:03:57,298 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:03:57,298 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:03:57,299 | ~~~ 2021-07-09T19:03:57,299 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:03:57,299 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,299 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:03:57,299 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:03:57,299 | | 2021-07-09T19:03:57,299 | long unsigned int 2021-07-09T19:03:57,299 353 | 0) 2021-07-09T19:03:57,300 | ~~ 2021-07-09T19:03:57,300 khmer/_khmermodule.cc:1331:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:03:57,300 1331 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:03:57,300 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,300 khmer/_khmermodule.cc:1332:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:03:57,300 1332 | "hashbits object", /* tp_doc */ 2021-07-09T19:03:57,300 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,300 | | 2021-07-09T19:03:57,300 | const char* 2021-07-09T19:03:57,305 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_occupied(PyObject*, PyObject*)’: 2021-07-09T19:03:57,305 khmer/_khmermodule.cc:1389:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,305 1389 | return PyInt_FromLong(n); 2021-07-09T19:03:57,306 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,306 | PyLong_FromLong 2021-07-09T19:03:57,313 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_entries(PyObject*, PyObject*)’: 2021-07-09T19:03:57,313 khmer/_khmermodule.cc:1401:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,313 1401 | return PyInt_FromLong(counting->n_entries()); 2021-07-09T19:03:57,313 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,314 | PyLong_FromLong 2021-07-09T19:03:57,321 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2021-07-09T19:03:57,321 khmer/_khmermodule.cc:1423:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,322 1423 | return PyInt_FromLong(1); 2021-07-09T19:03:57,322 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,322 | PyLong_FromLong 2021-07-09T19:03:57,329 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2021-07-09T19:03:57,330 khmer/_khmermodule.cc:1440:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,330 1440 | return PyInt_FromLong(0); 2021-07-09T19:03:57,330 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,330 | PyLong_FromLong 2021-07-09T19:03:57,340 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2021-07-09T19:03:57,340 khmer/_khmermodule.cc:1526:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,340 1526 | return PyInt_FromLong(n_consumed); 2021-07-09T19:03:57,340 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,340 | PyLong_FromLong 2021-07-09T19:03:57,348 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2021-07-09T19:03:57,348 khmer/_khmermodule.cc:1558:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,349 1558 | return PyInt_FromLong(n_consumed); 2021-07-09T19:03:57,349 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,349 | PyLong_FromLong 2021-07-09T19:03:57,357 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2021-07-09T19:03:57,357 khmer/_khmermodule.cc:1581:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,357 1581 | return PyInt_FromLong(N); 2021-07-09T19:03:57,357 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,357 | PyLong_FromLong 2021-07-09T19:03:57,365 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2021-07-09T19:03:57,365 khmer/_khmermodule.cc:1604:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,366 1604 | return PyInt_FromLong(N); 2021-07-09T19:03:57,366 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,366 | PyLong_FromLong 2021-07-09T19:03:57,374 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2021-07-09T19:03:57,375 khmer/_khmermodule.cc:1707:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:03:57,375 1707 | if (PyInt_Check(arg)) { 2021-07-09T19:03:57,375 | ^~~~~~~~~~~ 2021-07-09T19:03:57,375 | PySet_Check 2021-07-09T19:03:57,382 khmer/_khmermodule.cc:1708:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:03:57,382 1708 | long pos = PyInt_AsLong(arg); 2021-07-09T19:03:57,382 | ^~~~~~~~~~~~ 2021-07-09T19:03:57,382 | PyLong_AsLong 2021-07-09T19:03:57,390 khmer/_khmermodule.cc:1710:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:03:57,390 1710 | } else if (PyString_Check(arg)) { 2021-07-09T19:03:57,390 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,390 | PyMapping_Check 2021-07-09T19:03:57,400 khmer/_khmermodule.cc:1711:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:03:57,401 1711 | std::string s = PyString_AsString(arg); 2021-07-09T19:03:57,401 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,408 khmer/_khmermodule.cc:1715:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,408 1715 | return PyInt_FromLong(count); 2021-07-09T19:03:57,408 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,409 | PyLong_FromLong 2021-07-09T19:03:57,416 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2021-07-09T19:03:57,416 khmer/_khmermodule.cc:1731:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,417 1731 | return PyInt_FromLong(count); 2021-07-09T19:03:57,417 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,417 | PyLong_FromLong 2021-07-09T19:03:57,427 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2021-07-09T19:03:57,427 khmer/_khmermodule.cc:1755:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:03:57,427 1755 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:03:57,428 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,428 | PyBytes_FromStringAndSize 2021-07-09T19:03:57,438 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2021-07-09T19:03:57,438 khmer/_khmermodule.cc:1782:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:03:57,438 1782 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:03:57,438 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,439 | PyBytes_FromStringAndSize 2021-07-09T19:03:57,447 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T19:03:57,447 from /usr/include/python3.9/Python.h:106, 2021-07-09T19:03:57,447 from khmer/_khmermodule.cc:13: 2021-07-09T19:03:57,448 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution(PyObject*, PyObject*)’: 2021-07-09T19:03:57,448 khmer/_khmermodule.cc:1814:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,448 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2021-07-09T19:03:57,448 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,448 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T19:03:57,448 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T19:03:57,449 | ^ 2021-07-09T19:03:57,456 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution_with_reads_parser(PyObject*, PyObject*)’: 2021-07-09T19:03:57,456 khmer/_khmermodule.cc:1850:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,456 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2021-07-09T19:03:57,456 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,457 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T19:03:57,457 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T19:03:57,457 | ^ 2021-07-09T19:03:57,465 khmer/_khmermodule.cc: In function ‘PyObject* hash_fasta_count_kmers_by_position(PyObject*, PyObject*)’: 2021-07-09T19:03:57,465 khmer/_khmermodule.cc:1880:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,465 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2021-07-09T19:03:57,465 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,465 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T19:03:57,465 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T19:03:57,466 | ^ 2021-07-09T19:03:57,476 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2021-07-09T19:03:57,476 khmer/_khmermodule.cc:1987:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,476 1987 | return PyInt_FromLong(k); 2021-07-09T19:03:57,477 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,477 | PyLong_FromLong 2021-07-09T19:03:57,485 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T19:03:57,485 from /usr/include/python3.9/Python.h:106, 2021-07-09T19:03:57,486 from khmer/_khmermodule.cc:13: 2021-07-09T19:03:57,486 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_hashsizes(PyObject*, PyObject*)’: 2021-07-09T19:03:57,486 khmer/_khmermodule.cc:2004:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,486 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2021-07-09T19:03:57,486 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,486 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T19:03:57,486 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T19:03:57,486 | ^ 2021-07-09T19:03:57,496 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2021-07-09T19:03:57,496 khmer/_khmermodule.cc:2052:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:03:57,496 2052 | return Py_FindMethod(khmer_counting_methods, obj, name); 2021-07-09T19:03:57,497 | ^~~~~~~~~~~~~ 2021-07-09T19:03:57,497 | PyCMethod 2021-07-09T19:03:57,497 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:03:57,497 khmer/_khmermodule.cc:2060:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,497 2060 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2021-07-09T19:03:57,497 | ^~~~~~~~~~~~~~~ 2021-07-09T19:03:57,498 | | 2021-07-09T19:03:57,498 | const char* 2021-07-09T19:03:57,498 khmer/_khmermodule.cc:2062:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,498 2062 | khmer_counting_dealloc, /*tp_dealloc*/ 2021-07-09T19:03:57,498 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,498 | | 2021-07-09T19:03:57,498 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:03:57,499 khmer/_khmermodule.cc:2064:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:03:57,499 2064 | khmer_counting_getattr, /*tp_getattr*/ 2021-07-09T19:03:57,499 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,499 | | 2021-07-09T19:03:57,499 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:03:57,499 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:03:57,500 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:03:57,500 from khmer/_khmermodule.cc:13: 2021-07-09T19:03:57,500 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:03:57,500 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:03:57,500 | ~~~ 2021-07-09T19:03:57,501 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:03:57,501 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,501 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:03:57,501 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:03:57,501 | | 2021-07-09T19:03:57,501 | long unsigned int 2021-07-09T19:03:57,501 353 | 0) 2021-07-09T19:03:57,501 | ~~ 2021-07-09T19:03:57,501 khmer/_khmermodule.cc:2077:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:03:57,502 2077 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:03:57,502 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,502 khmer/_khmermodule.cc:2078:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:03:57,502 2078 | "counting hash object", /* tp_doc */ 2021-07-09T19:03:57,502 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,502 | | 2021-07-09T19:03:57,502 | const char* 2021-07-09T19:03:57,507 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_unique_kmers(PyObject*, PyObject*)’: 2021-07-09T19:03:57,507 khmer/_khmermodule.cc:2147:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,508 2147 | return PyInt_FromLong(n); 2021-07-09T19:03:57,508 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,508 | PyLong_FromLong 2021-07-09T19:03:57,517 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_occupied(PyObject*, PyObject*)’: 2021-07-09T19:03:57,517 khmer/_khmermodule.cc:2209:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,518 2209 | return PyInt_FromLong(n); 2021-07-09T19:03:57,518 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,518 | PyLong_FromLong 2021-07-09T19:03:57,525 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2021-07-09T19:03:57,525 khmer/_khmermodule.cc:2221:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,526 2221 | return PyInt_FromLong(hashbits->n_tags()); 2021-07-09T19:03:57,526 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,526 | PyLong_FromLong 2021-07-09T19:03:57,533 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2021-07-09T19:03:57,534 khmer/_khmermodule.cc:2243:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,534 2243 | return PyInt_FromLong(1); 2021-07-09T19:03:57,534 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,534 | PyLong_FromLong 2021-07-09T19:03:57,542 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2021-07-09T19:03:57,542 khmer/_khmermodule.cc:2266:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,542 2266 | return PyInt_FromLong(n_consumed); 2021-07-09T19:03:57,543 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,543 | PyLong_FromLong 2021-07-09T19:03:57,557 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2021-07-09T19:03:57,557 khmer/_khmermodule.cc:2377:43: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,558 2377 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2021-07-09T19:03:57,558 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,558 | PyLong_AsVoidPtr 2021-07-09T19:03:57,565 khmer/_khmermodule.cc:2386:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,565 2386 | return PyInt_FromLong(next_largest); 2021-07-09T19:03:57,565 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,566 | PyLong_FromLong 2021-07-09T19:03:57,572 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2021-07-09T19:03:57,572 khmer/_khmermodule.cc:2423:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:03:57,573 2423 | if (PyInt_Check(arg)) { 2021-07-09T19:03:57,573 | ^~~~~~~~~~~ 2021-07-09T19:03:57,573 | PySet_Check 2021-07-09T19:03:57,579 khmer/_khmermodule.cc:2424:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:03:57,580 2424 | long pos = PyInt_AsLong(arg); 2021-07-09T19:03:57,580 | ^~~~~~~~~~~~ 2021-07-09T19:03:57,580 | PyLong_AsLong 2021-07-09T19:03:57,587 khmer/_khmermodule.cc:2426:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:03:57,588 2426 | } else if (PyString_Check(arg)) { 2021-07-09T19:03:57,588 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,588 | PyMapping_Check 2021-07-09T19:03:57,598 khmer/_khmermodule.cc:2427:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:03:57,598 2427 | std::string s = PyString_AsString(arg); 2021-07-09T19:03:57,599 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,606 khmer/_khmermodule.cc:2431:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,606 2431 | return PyInt_FromLong(count); 2021-07-09T19:03:57,606 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,606 | PyLong_FromLong 2021-07-09T19:03:57,614 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_calc_connected_graph_size(PyObject*, PyObject*)’: 2021-07-09T19:03:57,615 khmer/_khmermodule.cc:2459:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,615 2459 | return PyInt_FromLong(size); 2021-07-09T19:03:57,615 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,615 | PyLong_FromLong 2021-07-09T19:03:57,623 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2021-07-09T19:03:57,623 khmer/_khmermodule.cc:2474:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,623 2474 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2021-07-09T19:03:57,623 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,623 | PyLong_FromLong 2021-07-09T19:03:57,633 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_degree(PyObject*, PyObject*)’: 2021-07-09T19:03:57,634 khmer/_khmermodule.cc:2496:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:03:57,634 2496 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:03:57,634 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,634 | PyBytes_FromStringAndSize 2021-07-09T19:03:57,645 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_sodd(PyObject*, PyObject*)’: 2021-07-09T19:03:57,645 khmer/_khmermodule.cc:2522:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:03:57,645 2522 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:03:57,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,645 | PyBytes_FromStringAndSize 2021-07-09T19:03:57,656 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2021-07-09T19:03:57,656 khmer/_khmermodule.cc:2547:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:03:57,656 2547 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:03:57,656 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,656 | PyBytes_FromStringAndSize 2021-07-09T19:03:57,679 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2021-07-09T19:03:57,680 khmer/_khmermodule.cc:2625:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T19:03:57,680 2625 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T19:03:57,680 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,680 | PyLong_FromVoidPtr 2021-07-09T19:03:57,689 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2021-07-09T19:03:57,689 khmer/_khmermodule.cc:2654:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T19:03:57,690 2654 | if (!PyCObject_Check(subset_obj)) { 2021-07-09T19:03:57,690 | ^~~~~~~~~~~~~~~ 2021-07-09T19:03:57,690 | PyODict_Check 2021-07-09T19:03:57,701 khmer/_khmermodule.cc:2659:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,701 2659 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:03:57,701 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,701 | PyLong_AsVoidPtr 2021-07-09T19:03:57,722 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2021-07-09T19:03:57,722 khmer/_khmermodule.cc:2951:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T19:03:57,722 2951 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T19:03:57,723 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,723 | PyLong_FromVoidPtr 2021-07-09T19:03:57,731 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2021-07-09T19:03:57,731 khmer/_khmermodule.cc:2964:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T19:03:57,732 2964 | if (!PyCObject_Check(ppi_obj)) { 2021-07-09T19:03:57,732 | ^~~~~~~~~~~~~~~ 2021-07-09T19:03:57,732 | PyODict_Check 2021-07-09T19:03:57,743 khmer/_khmermodule.cc:2969:33: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,743 2969 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2021-07-09T19:03:57,743 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,744 | PyLong_AsVoidPtr 2021-07-09T19:03:57,751 khmer/_khmermodule.cc:2975:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,751 2975 | return PyInt_FromLong(p); 2021-07-09T19:03:57,751 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,751 | PyLong_FromLong 2021-07-09T19:03:57,763 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2021-07-09T19:03:57,763 khmer/_khmermodule.cc:3093:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,764 3093 | return PyInt_FromLong(n_partitions); 2021-07-09T19:03:57,764 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,764 | PyLong_FromLong 2021-07-09T19:03:57,772 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2021-07-09T19:03:57,772 khmer/_khmermodule.cc:3124:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,773 3124 | return PyInt_FromLong(n_singletons); 2021-07-09T19:03:57,773 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,773 | PyLong_FromLong 2021-07-09T19:03:57,787 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2021-07-09T19:03:57,787 khmer/_khmermodule.cc:3227:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,788 3227 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:03:57,788 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,788 | PyLong_AsVoidPtr 2021-07-09T19:03:57,799 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2021-07-09T19:03:57,800 khmer/_khmermodule.cc:3245:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,800 3245 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:03:57,800 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,800 | PyLong_AsVoidPtr 2021-07-09T19:03:57,835 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T19:03:57,836 khmer/_khmermodule.cc:3347:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,836 3347 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:03:57,836 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,836 | PyLong_AsVoidPtr 2021-07-09T19:03:57,848 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T19:03:57,849 khmer/_khmermodule.cc:3379:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T19:03:57,849 3379 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T19:03:57,849 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,849 | PyLong_FromVoidPtr 2021-07-09T19:03:57,857 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2021-07-09T19:03:57,857 khmer/_khmermodule.cc:3409:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,858 3409 | return PyInt_FromLong(d); 2021-07-09T19:03:57,858 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,858 | PyLong_FromLong 2021-07-09T19:03:57,869 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2021-07-09T19:03:57,870 khmer/_khmermodule.cc:3425:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,870 3425 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T19:03:57,870 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,870 | PyLong_AsVoidPtr 2021-07-09T19:03:57,882 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2021-07-09T19:03:57,882 khmer/_khmermodule.cc:3451:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,882 3451 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T19:03:57,882 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,882 | PyLong_AsVoidPtr 2021-07-09T19:03:57,894 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T19:03:57,894 khmer/_khmermodule.cc:3472:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:03:57,895 3472 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:03:57,895 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,895 | PyLong_AsVoidPtr 2021-07-09T19:03:57,903 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2021-07-09T19:03:57,903 khmer/_khmermodule.cc:3510:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,904 3510 | return PyInt_FromLong(p1); 2021-07-09T19:03:57,904 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,904 | PyLong_FromLong 2021-07-09T19:03:57,912 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2021-07-09T19:03:57,912 khmer/_khmermodule.cc:3527:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,912 3527 | return PyInt_FromLong(partition_id); 2021-07-09T19:03:57,912 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,912 | PyLong_FromLong 2021-07-09T19:03:57,927 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_density_explosion(PyObject*, PyObject*)’: 2021-07-09T19:03:57,927 khmer/_khmermodule.cc:3651:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:03:57,927 3651 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:03:57,927 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,927 | PyBytes_FromStringAndSize 2021-07-09T19:03:57,936 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2021-07-09T19:03:57,936 khmer/_khmermodule.cc:3696:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,936 3696 | return PyInt_FromLong(k); 2021-07-09T19:03:57,936 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,937 | PyLong_FromLong 2021-07-09T19:03:57,944 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T19:03:57,945 from /usr/include/python3.9/Python.h:106, 2021-07-09T19:03:57,945 from khmer/_khmermodule.cc:13: 2021-07-09T19:03:57,945 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_hashsizes(PyObject*, PyObject*)’: 2021-07-09T19:03:57,945 khmer/_khmermodule.cc:3713:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:03:57,945 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2021-07-09T19:03:57,945 | ^~~~~~~~~~~~~~ 2021-07-09T19:03:57,946 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T19:03:57,946 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T19:03:57,946 | ^ 2021-07-09T19:03:57,965 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2021-07-09T19:03:57,965 khmer/_khmermodule.cc:3736:27: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:03:57,965 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2021-07-09T19:03:57,965 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,966 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T19:03:57,966 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T19:03:57,966 | ^ 2021-07-09T19:03:57,978 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2021-07-09T19:03:57,979 khmer/_khmermodule.cc:3847:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:03:57,979 3847 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2021-07-09T19:03:57,979 | ^~~~~~~~~~~~~ 2021-07-09T19:03:57,979 | PyCMethod 2021-07-09T19:03:57,993 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2021-07-09T19:03:57,994 khmer/_khmermodule.cc:3922:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:03:57,994 3922 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2021-07-09T19:03:57,994 | ^~~~~~~~~~~~~ 2021-07-09T19:03:57,994 | PyCMethod 2021-07-09T19:03:57,994 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:03:57,994 khmer/_khmermodule.cc:3940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,994 3940 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2021-07-09T19:03:57,995 | ^~~~~~~~~~~~~ 2021-07-09T19:03:57,995 | | 2021-07-09T19:03:57,995 | const char* 2021-07-09T19:03:57,995 khmer/_khmermodule.cc:3942:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:03:57,995 3942 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2021-07-09T19:03:57,995 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,996 | | 2021-07-09T19:03:57,996 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:03:57,996 khmer/_khmermodule.cc:3944:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:03:57,996 3944 | khmer_readaligner_getattr, /*tp_getattr*/ 2021-07-09T19:03:57,996 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,996 | | 2021-07-09T19:03:57,996 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:03:57,997 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:03:57,997 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:03:57,997 from khmer/_khmermodule.cc:13: 2021-07-09T19:03:57,997 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:03:57,997 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:03:57,997 | ~~~ 2021-07-09T19:03:57,997 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:03:57,998 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,998 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:03:57,998 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:03:57,998 | | 2021-07-09T19:03:57,998 | long unsigned int 2021-07-09T19:03:57,998 353 | 0) 2021-07-09T19:03:57,998 | ~~ 2021-07-09T19:03:57,999 khmer/_khmermodule.cc:3957:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:03:57,999 3957 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:03:57,999 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,999 khmer/_khmermodule.cc:3958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:03:57,999 3958 | "ReadAligner object", /* tp_doc */ 2021-07-09T19:03:57,999 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:57,999 | | 2021-07-09T19:03:58,000 | const char* 2021-07-09T19:03:58,013 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2021-07-09T19:03:58,014 khmer/_khmermodule.cc:4139:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:03:58,014 4139 | return PyString_FromString(khmer::_revhash(val, ksize).c_str()); 2021-07-09T19:03:58,014 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:58,014 | PyLong_FromString 2021-07-09T19:03:58,015 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:03:58,015 khmer/_khmermodule.cc:4195:17: error: expected constructor, destructor, or type conversion before ‘init_khmer’ 2021-07-09T19:03:58,015 4195 | DL_EXPORT(void) init_khmer(void) 2021-07-09T19:03:58,015 | ^~~~~~~~~~ 2021-07-09T19:03:58,644 khmer/_khmermodule.cc:4162:20: warning: ‘KhmerMethods’ defined but not used [-Wunused-variable] 2021-07-09T19:03:58,644 4162 | static PyMethodDef KhmerMethods[] = { 2021-07-09T19:03:58,644 | ^~~~~~~~~~~~ 2021-07-09T19:03:58,644 khmer/_khmermodule.cc:845:1: warning: ‘void khmer::python::_init_ReadPairIterator_Type()’ defined but not used [-Wunused-function] 2021-07-09T19:03:58,645 845 | _init_ReadPairIterator_Type( ) 2021-07-09T19:03:58,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:58,645 khmer/_khmermodule.cc:789:1: warning: ‘void khmer::python::_init_ReadParser_Type()’ defined but not used [-Wunused-function] 2021-07-09T19:03:58,645 789 | _init_ReadParser_Type( ) 2021-07-09T19:03:58,645 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:03:58,645 khmer/_khmermodule.cc:525:1: warning: ‘void khmer::python::_init_Read_Type()’ defined but not used [-Wunused-function] 2021-07-09T19:03:58,645 525 | _init_Read_Type( ) 2021-07-09T19:03:58,645 | ^~~~~~~~~~~~~~~ 2021-07-09T19:03:58,646 khmer/_khmermodule.cc:134:18: warning: ‘KhmerError’ defined but not used [-Wunused-variable] 2021-07-09T19:03:58,646 134 | static PyObject *KhmerError; 2021-07-09T19:03:58,646 | ^~~~~~~~~~ 2021-07-09T19:03:58,663 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T19:03:58,737 Building wheel for khmer (setup.py): finished with status 'error' 2021-07-09T19:03:58,738 ERROR: Failed building wheel for khmer 2021-07-09T19:03:58,738 Running setup.py clean for khmer 2021-07-09T19:03:58,739 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-4w1fpc62/khmer_d6cbbdec738843e1abdc45d122272304/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-4w1fpc62/khmer_d6cbbdec738843e1abdc45d122272304/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 2021-07-09T19:03:59,518 running clean 2021-07-09T19:03:59,520 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T19:03:59,523 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T19:03:59,528 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T19:03:59,528 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T19:03:59,529 removing 'build' 2021-07-09T19:03:59,584 Failed to build khmer 2021-07-09T19:03:59,584 ERROR: Failed to build one or more wheels 2021-07-09T19:03:59,585 Exception information: 2021-07-09T19:03:59,585 Traceback (most recent call last): 2021-07-09T19:03:59,585 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T19:03:59,585 status = self.run(options, args) 2021-07-09T19:03:59,585 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T19:03:59,585 return func(self, options, args) 2021-07-09T19:03:59,585 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T19:03:59,585 raise CommandError( 2021-07-09T19:03:59,585 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T19:03:59,588 Removed build tracker: '/tmp/pip-req-tracker-q7es3d5y'