2021-07-09T19:34:38,245 Created temporary directory: /tmp/pip-ephem-wheel-cache-itex6t0_ 2021-07-09T19:34:38,248 Created temporary directory: /tmp/pip-req-tracker-k_fkf633 2021-07-09T19:34:38,248 Initialized build tracking at /tmp/pip-req-tracker-k_fkf633 2021-07-09T19:34:38,249 Created build tracker: /tmp/pip-req-tracker-k_fkf633 2021-07-09T19:34:38,249 Entered build tracker: /tmp/pip-req-tracker-k_fkf633 2021-07-09T19:34:38,250 Created temporary directory: /tmp/pip-wheel-yr_eqtjv 2021-07-09T19:34:38,286 1 location(s) to search for versions of khmer: 2021-07-09T19:34:38,286 * https://pypi.org/simple/khmer/ 2021-07-09T19:34:38,286 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2021-07-09T19:34:38,287 Getting page https://pypi.org/simple/khmer/ 2021-07-09T19:34:38,288 Found index url https://pypi.org/simple 2021-07-09T19:34:38,416 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/) 2021-07-09T19:34:38,416 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/) 2021-07-09T19:34:38,416 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 2021-07-09T19:34:38,417 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 2021-07-09T19:34:38,433 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/) 2021-07-09T19:34:38,433 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 2021-07-09T19:34:38,434 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/) 2021-07-09T19:34:38,434 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 2021-07-09T19:34:38,434 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/) 2021-07-09T19:34:38,435 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 2021-07-09T19:34:38,435 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/) 2021-07-09T19:34:38,435 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 2021-07-09T19:34:38,436 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/) 2021-07-09T19:34:38,436 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 2021-07-09T19:34:38,436 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 2021-07-09T19:34:38,437 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/) 2021-07-09T19:34:38,437 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 2021-07-09T19:34:38,438 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/) 2021-07-09T19:34:38,438 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 2021-07-09T19:34:38,438 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/) 2021-07-09T19:34:38,439 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 2021-07-09T19:34:38,439 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/) 2021-07-09T19:34:38,440 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/) 2021-07-09T19:34:38,440 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 2021-07-09T19:34:38,440 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/) 2021-07-09T19:34:38,441 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/) 2021-07-09T19:34:38,441 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/) 2021-07-09T19:34:38,442 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/) 2021-07-09T19:34:38,442 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 2021-07-09T19:34:38,442 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 2021-07-09T19:34:38,443 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/) 2021-07-09T19:34:38,443 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 2021-07-09T19:34:38,444 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/) 2021-07-09T19:34:38,444 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/) 2021-07-09T19:34:38,444 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/) 2021-07-09T19:34:38,445 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/) 2021-07-09T19:34:38,445 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/) 2021-07-09T19:34:38,446 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 2021-07-09T19:34:38,446 Skipping link: not a file: https://pypi.org/simple/khmer/ 2021-07-09T19:34:38,449 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2021-07-09T19:34:38,466 Collecting khmer==0.7.1 2021-07-09T19:34:38,468 Created temporary directory: /tmp/pip-unpack-j4d9zkxm 2021-07-09T19:34:42,261 Downloading khmer-0.7.1.tar.gz (18.9 MB) 2021-07-09T19:34:47,082 Added khmer==0.7.1 from https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz#sha256=08f7b20fc7f4405bbe27145d47e710e61d50639f79ab4763f685780f24935ddd to build tracker '/tmp/pip-req-tracker-k_fkf633' 2021-07-09T19:34:47,084 Running setup.py (path:/tmp/pip-wheel-yr_eqtjv/khmer_08f5253071f44e19ae81112e5536223f/setup.py) egg_info for package khmer 2021-07-09T19:34:47,084 Created temporary directory: /tmp/pip-pip-egg-info-mzl9ijzi 2021-07-09T19:34:47,085 Running command python setup.py egg_info 2021-07-09T19:35:22,435 running egg_info 2021-07-09T19:35:22,437 creating /tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info 2021-07-09T19:35:22,438 writing /tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info/PKG-INFO 2021-07-09T19:35:22,440 writing dependency_links to /tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info/dependency_links.txt 2021-07-09T19:35:22,442 writing requirements to /tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info/requires.txt 2021-07-09T19:35:22,443 writing top-level names to /tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info/top_level.txt 2021-07-09T19:35:22,444 writing manifest file '/tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info/SOURCES.txt' 2021-07-09T19:35:22,617 reading manifest file '/tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info/SOURCES.txt' 2021-07-09T19:35:22,618 reading manifest template 'MANIFEST.in' 2021-07-09T19:35:24,667 no previously-included directories found matching 'doc/doxygen' 2021-07-09T19:35:24,671 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T19:35:24,697 writing manifest file '/tmp/pip-pip-egg-info-mzl9ijzi/khmer.egg-info/SOURCES.txt' 2021-07-09T19:35:24,772 Source in /tmp/pip-wheel-yr_eqtjv/khmer_08f5253071f44e19ae81112e5536223f has version 0.7.1, which satisfies requirement khmer==0.7.1 from https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz#sha256=08f7b20fc7f4405bbe27145d47e710e61d50639f79ab4763f685780f24935ddd 2021-07-09T19:35:24,773 Removed khmer==0.7.1 from https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz#sha256=08f7b20fc7f4405bbe27145d47e710e61d50639f79ab4763f685780f24935ddd from build tracker '/tmp/pip-req-tracker-k_fkf633' 2021-07-09T19:35:24,777 Created temporary directory: /tmp/pip-unpack-abhz1hu8 2021-07-09T19:35:24,778 Building wheels for collected packages: khmer 2021-07-09T19:35:24,782 Created temporary directory: /tmp/pip-wheel-3h7kpy1q 2021-07-09T19:35:24,782 Building wheel for khmer (setup.py): started 2021-07-09T19:35:24,782 Destination directory: /tmp/pip-wheel-3h7kpy1q 2021-07-09T19:35:24,783 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-yr_eqtjv/khmer_08f5253071f44e19ae81112e5536223f/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-yr_eqtjv/khmer_08f5253071f44e19ae81112e5536223f/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-3h7kpy1q 2021-07-09T19:35:27,067 running bdist_wheel 2021-07-09T19:35:27,071 running build 2021-07-09T19:35:27,073 got version from file /tmp/pip-wheel-yr_eqtjv/khmer_08f5253071f44e19ae81112e5536223f/khmer/_version.py {'version': '0.7.1', 'full': '1307fa03d7f0f2657ff22a6acad474361a1120f7'} 2021-07-09T19:35:27,073 running build_py 2021-07-09T19:35:27,217 creating build 2021-07-09T19:35:27,217 creating build/lib.linux-armv7l-3.9 2021-07-09T19:35:27,218 creating build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,220 copying khmer/load_pe.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,222 copying khmer/__init__.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,224 copying khmer/hashbits_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,226 copying khmer/thread_utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,229 copying khmer/counting_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,231 copying khmer/threading_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,233 copying khmer/utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,235 copying khmer/_version.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:27,237 running egg_info 2021-07-09T19:35:27,240 creating khmer.egg-info 2021-07-09T19:35:27,241 writing khmer.egg-info/PKG-INFO 2021-07-09T19:35:27,244 writing dependency_links to khmer.egg-info/dependency_links.txt 2021-07-09T19:35:27,246 writing requirements to khmer.egg-info/requires.txt 2021-07-09T19:35:27,247 writing top-level names to khmer.egg-info/top_level.txt 2021-07-09T19:35:27,249 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T19:35:27,256 reading manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T19:35:27,258 reading manifest template 'MANIFEST.in' 2021-07-09T19:35:29,219 no previously-included directories found matching 'doc/doxygen' 2021-07-09T19:35:29,222 warning: no previously-included files found matching 'data/1m-filtered.fa' 2021-07-09T19:35:29,259 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T19:35:29,277 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T19:35:29,284 running build_ext 2021-07-09T19:35:29,301 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2021-07-09T19:35:29,580 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2021-07-09T19:35:29,710 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2021-07-09T19:35:30,090 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2021-07-09T19:35:31,026 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2021-07-09T19:35:31,155 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2021-07-09T19:35:32,505 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2021-07-09T19:35:33,730 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2021-07-09T19:35:33,880 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2021-07-09T19:35:35,376 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2021-07-09T19:35:36,115 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2021-07-09T19:35:36,541 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2021-07-09T19:35:36,982 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 2021-07-09T19:35:37,084 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2021-07-09T19:35:37,832 blocksort.c: In function ‘mainSort’: 2021-07-09T19:35:37,832 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T19:35:37,832 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T19:35:37,832 | ^~~~~~~ 2021-07-09T19:35:37,832 blocksort.c:514:18: note: called from here 2021-07-09T19:35:37,832 514 | while ( mainGtU ( 2021-07-09T19:35:37,832 | ^~~~~~~~~ 2021-07-09T19:35:37,833 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T19:35:37,833 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:37,833 516 | ) ) { 2021-07-09T19:35:37,833 | ~ 2021-07-09T19:35:37,833 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T19:35:37,833 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T19:35:37,833 | ^~~~~~~ 2021-07-09T19:35:37,834 blocksort.c:528:18: note: called from here 2021-07-09T19:35:37,834 528 | while ( mainGtU ( 2021-07-09T19:35:37,834 | ^~~~~~~~~ 2021-07-09T19:35:37,834 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T19:35:37,834 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:37,834 530 | ) ) { 2021-07-09T19:35:37,834 | ~ 2021-07-09T19:35:37,834 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T19:35:37,835 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T19:35:37,835 | ^~~~~~~ 2021-07-09T19:35:37,835 blocksort.c:542:18: note: called from here 2021-07-09T19:35:37,835 542 | while ( mainGtU ( 2021-07-09T19:35:37,835 | ^~~~~~~~~ 2021-07-09T19:35:37,835 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T19:35:37,835 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:37,835 544 | ) ) { 2021-07-09T19:35:37,835 | ~ 2021-07-09T19:35:38,527 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2021-07-09T19:35:38,927 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2021-07-09T19:35:39,062 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2021-07-09T19:35:39,192 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2021-07-09T19:35:43,029 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2021-07-09T19:35:45,264 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2021-07-09T19:35:46,899 #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 2021-07-09T19:35:46,901 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2021-07-09T19:35:46,904 #rm -f libbz2.so.1.0 2021-07-09T19:35:46,907 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2021-07-09T19:35:46,918 building 'khmer._khmermodule' extension 2021-07-09T19:35:46,920 creating build/temp.linux-armv7l-3.9 2021-07-09T19:35:46,920 creating build/temp.linux-armv7l-3.9/khmer 2021-07-09T19:35:46,921 creating build/temp.linux-armv7l-3.9/lib 2021-07-09T19:35:46,923 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=0.7.1 -UNO_UNIQUE_RC -Ilib -I/usr/include/python3.9 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-3.9/khmer/_khmermodule.o -O3 2021-07-09T19:35:49,058 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2021-07-09T19:35:49,058 khmer/_khmermodule.cc:83:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2021-07-09T19:35:49,058 83 | tobj.ob_size = 0; 2021-07-09T19:35:49,059 | ^~~~~~~ 2021-07-09T19:35:49,059 khmer/_khmermodule.cc:84:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T19:35:49,059 84 | tobj.ob_type = &PyType_Type; 2021-07-09T19:35:49,059 | ^~~~~~~ 2021-07-09T19:35:49,064 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:35:49,065 khmer/_khmermodule.cc:200:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,065 200 | "Config", sizeof(khmer_ConfigObject), 2021-07-09T19:35:49,065 | ^~~~~~~~ 2021-07-09T19:35:49,065 | | 2021-07-09T19:35:49,065 | const char* 2021-07-09T19:35:49,065 khmer/_khmermodule.cc:202:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,066 202 | khmer_config_dealloc, /*tp_dealloc*/ 2021-07-09T19:35:49,066 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,066 | | 2021-07-09T19:35:49,066 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:35:49,066 khmer/_khmermodule.cc:204:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:35:49,067 204 | khmer_config_getattr, /*tp_getattr*/ 2021-07-09T19:35:49,067 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,067 | | 2021-07-09T19:35:49,067 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:35:49,068 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:35:49,068 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:35:49,068 from khmer/_khmermodule.cc:12: 2021-07-09T19:35:49,068 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:35:49,068 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:35:49,069 | ~~~ 2021-07-09T19:35:49,069 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:35:49,069 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,069 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:35:49,069 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:35:49,069 | | 2021-07-09T19:35:49,069 | long unsigned int 2021-07-09T19:35:49,069 353 | 0) 2021-07-09T19:35:49,070 | ~~ 2021-07-09T19:35:49,070 khmer/_khmermodule.cc:217:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:35:49,070 217 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:35:49,070 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,070 khmer/_khmermodule.cc:218:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:35:49,070 218 | "config object", /* tp_doc */ 2021-07-09T19:35:49,071 | ^~~~~~~~~~~~~~~ 2021-07-09T19:35:49,071 | | 2021-07-09T19:35:49,071 | const char* 2021-07-09T19:35:49,079 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2021-07-09T19:35:49,079 khmer/_khmermodule.cc:304:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T19:35:49,080 304 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2021-07-09T19:35:49,080 | ^~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,080 | PyLong_FromSize_t 2021-07-09T19:35:49,091 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2021-07-09T19:35:49,091 khmer/_khmermodule.cc:360:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T19:35:49,091 360 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2021-07-09T19:35:49,091 | ^~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,092 | PyLong_FromSize_t 2021-07-09T19:35:49,102 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2021-07-09T19:35:49,102 khmer/_khmermodule.cc:387:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T19:35:49,102 387 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2021-07-09T19:35:49,102 | ^~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,103 | PyLong_FromSize_t 2021-07-09T19:35:49,112 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2021-07-09T19:35:49,112 khmer/_khmermodule.cc:434:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:35:49,113 434 | return Py_FindMethod(khmer_config_methods, obj, name); 2021-07-09T19:35:49,113 | ^~~~~~~~~~~~~ 2021-07-09T19:35:49,113 | PyCMethod 2021-07-09T19:35:49,122 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2021-07-09T19:35:49,123 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:35:49,123 472 | PyString_FromString( \ 2021-07-09T19:35:49,123 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,123 khmer/_khmermodule.cc:480:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:35:49,123 480 | { return KHMER_READ_STRING_GETTER( self, name ); } 2021-07-09T19:35:49,123 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,132 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2021-07-09T19:35:49,132 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:35:49,132 472 | PyString_FromString( \ 2021-07-09T19:35:49,133 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,133 khmer/_khmermodule.cc:486:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:35:49,133 486 | { return KHMER_READ_STRING_GETTER( self, sequence ); } 2021-07-09T19:35:49,133 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,141 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2021-07-09T19:35:49,142 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:35:49,142 472 | PyString_FromString( \ 2021-07-09T19:35:49,142 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,142 khmer/_khmermodule.cc:492:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:35:49,142 492 | { return KHMER_READ_STRING_GETTER( self, accuracy ); } 2021-07-09T19:35:49,143 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,151 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2021-07-09T19:35:49,151 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:35:49,151 472 | PyString_FromString( \ 2021-07-09T19:35:49,152 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,152 khmer/_khmermodule.cc:498:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T19:35:49,152 498 | { return KHMER_READ_STRING_GETTER( self, annotations ); } 2021-07-09T19:35:49,152 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,176 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2021-07-09T19:35:49,176 khmer/_khmermodule.cc:824:2: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,176 824 | PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ) 2021-07-09T19:35:49,176 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,176 | PyLong_FromLong 2021-07-09T19:35:49,187 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2021-07-09T19:35:49,188 khmer/_khmermodule.cc:965:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:35:49,188 965 | return PyString_FromString(khmer::_revhash(val, ktable->ksize()).c_str()); 2021-07-09T19:35:49,188 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,188 | PyLong_FromString 2021-07-09T19:35:49,196 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2021-07-09T19:35:49,196 khmer/_khmermodule.cc:991:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,196 991 | return PyInt_FromLong(1); 2021-07-09T19:35:49,196 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,196 | PyLong_FromLong 2021-07-09T19:35:49,205 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2021-07-09T19:35:49,205 khmer/_khmermodule.cc:1019:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T19:35:49,206 1019 | return PyInt_FromSize_t(n_consumed); 2021-07-09T19:35:49,206 | ^~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,206 | PyLong_FromSize_t 2021-07-09T19:35:49,212 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2021-07-09T19:35:49,212 khmer/_khmermodule.cc:1038:14: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:35:49,212 1038 | } else if (PyInt_Check(arg)) { 2021-07-09T19:35:49,212 | ^~~~~~~~~~~ 2021-07-09T19:35:49,213 | PySet_Check 2021-07-09T19:35:49,219 khmer/_khmermodule.cc:1039:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:35:49,219 1039 | long pos = PyInt_AsLong(arg); 2021-07-09T19:35:49,219 | ^~~~~~~~~~~~ 2021-07-09T19:35:49,220 | PyLong_AsLong 2021-07-09T19:35:49,227 khmer/_khmermodule.cc:1041:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:35:49,227 1041 | } else if (PyString_Check(arg)) { 2021-07-09T19:35:49,227 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,228 | PyMapping_Check 2021-07-09T19:35:49,237 khmer/_khmermodule.cc:1042:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:35:49,238 1042 | std::string s = PyString_AsString(arg); 2021-07-09T19:35:49,238 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,250 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2021-07-09T19:35:49,250 khmer/_khmermodule.cc:1064:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:35:49,250 1064 | char * kmer_str = PyString_AsString( val ); 2021-07-09T19:35:49,250 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,257 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2021-07-09T19:35:49,257 khmer/_khmermodule.cc:1082:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:35:49,257 1082 | if (PyInt_Check(arg)) { 2021-07-09T19:35:49,257 | ^~~~~~~~~~~ 2021-07-09T19:35:49,258 | PySet_Check 2021-07-09T19:35:49,264 khmer/_khmermodule.cc:1083:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:35:49,264 1083 | long pos = PyInt_AsLong(arg); 2021-07-09T19:35:49,265 | ^~~~~~~~~~~~ 2021-07-09T19:35:49,265 | PyLong_AsLong 2021-07-09T19:35:49,273 khmer/_khmermodule.cc:1085:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:35:49,273 1085 | } else if (PyString_Check(arg)) { 2021-07-09T19:35:49,273 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,273 | PyMapping_Check 2021-07-09T19:35:49,284 khmer/_khmermodule.cc:1086:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:35:49,284 1086 | std::string s = PyString_AsString(arg); 2021-07-09T19:35:49,284 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,293 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2021-07-09T19:35:49,294 khmer/_khmermodule.cc:1134:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,294 1134 | return PyInt_FromLong(ktable->ksize()); 2021-07-09T19:35:49,294 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,294 | PyLong_FromLong 2021-07-09T19:35:49,304 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2021-07-09T19:35:49,305 khmer/_khmermodule.cc:1179:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:35:49,305 1179 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2021-07-09T19:35:49,305 | ^~~~~~~~~~~~~ 2021-07-09T19:35:49,305 | PyCMethod 2021-07-09T19:35:49,306 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:35:49,306 khmer/_khmermodule.cc:1200:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,306 1200 | "KTable", sizeof(khmer_KTableObject), 2021-07-09T19:35:49,306 | ^~~~~~~~ 2021-07-09T19:35:49,306 | | 2021-07-09T19:35:49,307 | const char* 2021-07-09T19:35:49,307 khmer/_khmermodule.cc:1202:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,307 1202 | khmer_ktable_dealloc, /*tp_dealloc*/ 2021-07-09T19:35:49,307 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,307 | | 2021-07-09T19:35:49,308 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:35:49,308 khmer/_khmermodule.cc:1204:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:35:49,308 1204 | khmer_ktable_getattr, /*tp_getattr*/ 2021-07-09T19:35:49,308 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,309 | | 2021-07-09T19:35:49,309 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:35:49,309 khmer/_khmermodule.cc:1209:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2021-07-09T19:35:49,309 1209 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2021-07-09T19:35:49,309 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,310 | | 2021-07-09T19:35:49,310 | PySequenceMethods* 2021-07-09T19:35:49,310 khmer/_khmermodule.cc:1327:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,310 1327 | "KHashbits", sizeof(khmer_KHashbitsObject), 2021-07-09T19:35:49,310 | ^~~~~~~~~~~ 2021-07-09T19:35:49,311 | | 2021-07-09T19:35:49,311 | const char* 2021-07-09T19:35:49,311 khmer/_khmermodule.cc:1329:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,311 1329 | khmer_hashbits_dealloc, /*tp_dealloc*/ 2021-07-09T19:35:49,311 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,312 | | 2021-07-09T19:35:49,312 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:35:49,312 khmer/_khmermodule.cc:1331:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:35:49,312 1331 | khmer_hashbits_getattr, /*tp_getattr*/ 2021-07-09T19:35:49,313 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,313 | | 2021-07-09T19:35:49,313 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:35:49,313 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:35:49,314 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:35:49,314 from khmer/_khmermodule.cc:12: 2021-07-09T19:35:49,314 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:35:49,314 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:35:49,315 | ~~~ 2021-07-09T19:35:49,315 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:35:49,315 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,315 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:35:49,315 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:35:49,315 | | 2021-07-09T19:35:49,315 | long unsigned int 2021-07-09T19:35:49,316 353 | 0) 2021-07-09T19:35:49,316 | ~~ 2021-07-09T19:35:49,316 khmer/_khmermodule.cc:1344:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:35:49,316 1344 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:35:49,316 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,316 khmer/_khmermodule.cc:1345:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:35:49,316 1345 | "hashbits object", /* tp_doc */ 2021-07-09T19:35:49,317 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,317 | | 2021-07-09T19:35:49,317 | const char* 2021-07-09T19:35:49,322 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2021-07-09T19:35:49,322 khmer/_khmermodule.cc:1435:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,322 1435 | return PyInt_FromLong(1); 2021-07-09T19:35:49,322 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,323 | PyLong_FromLong 2021-07-09T19:35:49,331 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2021-07-09T19:35:49,331 khmer/_khmermodule.cc:1452:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,331 1452 | return PyInt_FromLong(0); 2021-07-09T19:35:49,331 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,332 | PyLong_FromLong 2021-07-09T19:35:49,342 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2021-07-09T19:35:49,342 khmer/_khmermodule.cc:1538:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,342 1538 | return PyInt_FromLong(n_consumed); 2021-07-09T19:35:49,342 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,343 | PyLong_FromLong 2021-07-09T19:35:49,351 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2021-07-09T19:35:49,351 khmer/_khmermodule.cc:1570:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,352 1570 | return PyInt_FromLong(n_consumed); 2021-07-09T19:35:49,352 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,352 | PyLong_FromLong 2021-07-09T19:35:49,360 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2021-07-09T19:35:49,361 khmer/_khmermodule.cc:1593:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,361 1593 | return PyInt_FromLong(N); 2021-07-09T19:35:49,361 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,361 | PyLong_FromLong 2021-07-09T19:35:49,369 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2021-07-09T19:35:49,370 khmer/_khmermodule.cc:1616:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,370 1616 | return PyInt_FromLong(N); 2021-07-09T19:35:49,370 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,370 | PyLong_FromLong 2021-07-09T19:35:49,380 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2021-07-09T19:35:49,380 khmer/_khmermodule.cc:1719:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:35:49,380 1719 | if (PyInt_Check(arg)) { 2021-07-09T19:35:49,381 | ^~~~~~~~~~~ 2021-07-09T19:35:49,381 | PySet_Check 2021-07-09T19:35:49,387 khmer/_khmermodule.cc:1720:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:35:49,388 1720 | long pos = PyInt_AsLong(arg); 2021-07-09T19:35:49,388 | ^~~~~~~~~~~~ 2021-07-09T19:35:49,388 | PyLong_AsLong 2021-07-09T19:35:49,396 khmer/_khmermodule.cc:1722:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:35:49,396 1722 | } else if (PyString_Check(arg)) { 2021-07-09T19:35:49,396 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,396 | PyMapping_Check 2021-07-09T19:35:49,406 khmer/_khmermodule.cc:1723:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:35:49,406 1723 | std::string s = PyString_AsString(arg); 2021-07-09T19:35:49,407 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,414 khmer/_khmermodule.cc:1727:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,414 1727 | return PyInt_FromLong(count); 2021-07-09T19:35:49,414 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,415 | PyLong_FromLong 2021-07-09T19:35:49,423 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2021-07-09T19:35:49,423 khmer/_khmermodule.cc:1743:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,423 1743 | return PyInt_FromLong(count); 2021-07-09T19:35:49,423 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,423 | PyLong_FromLong 2021-07-09T19:35:49,433 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2021-07-09T19:35:49,434 khmer/_khmermodule.cc:1767:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:35:49,434 1767 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:35:49,434 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,434 | PyBytes_FromStringAndSize 2021-07-09T19:35:49,445 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2021-07-09T19:35:49,445 khmer/_khmermodule.cc:1797:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:35:49,445 1797 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:35:49,445 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,445 | PyBytes_FromStringAndSize 2021-07-09T19:35:49,459 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2021-07-09T19:35:49,459 khmer/_khmermodule.cc:2013:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,460 2013 | return PyInt_FromLong(k); 2021-07-09T19:35:49,460 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,460 | PyLong_FromLong 2021-07-09T19:35:49,472 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2021-07-09T19:35:49,472 khmer/_khmermodule.cc:2078:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:35:49,472 2078 | return Py_FindMethod(khmer_counting_methods, obj, name); 2021-07-09T19:35:49,472 | ^~~~~~~~~~~~~ 2021-07-09T19:35:49,472 | PyCMethod 2021-07-09T19:35:49,472 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:35:49,473 khmer/_khmermodule.cc:2086:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,473 2086 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2021-07-09T19:35:49,473 | ^~~~~~~~~~~~~~~ 2021-07-09T19:35:49,473 | | 2021-07-09T19:35:49,473 | const char* 2021-07-09T19:35:49,473 khmer/_khmermodule.cc:2088:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,473 2088 | khmer_counting_dealloc, /*tp_dealloc*/ 2021-07-09T19:35:49,474 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,474 | | 2021-07-09T19:35:49,474 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:35:49,474 khmer/_khmermodule.cc:2090:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:35:49,474 2090 | khmer_counting_getattr, /*tp_getattr*/ 2021-07-09T19:35:49,474 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,474 | | 2021-07-09T19:35:49,475 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:35:49,475 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:35:49,475 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:35:49,475 from khmer/_khmermodule.cc:12: 2021-07-09T19:35:49,475 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:35:49,475 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:35:49,475 | ~~~ 2021-07-09T19:35:49,476 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:35:49,476 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,476 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:35:49,476 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:35:49,476 | | 2021-07-09T19:35:49,476 | long unsigned int 2021-07-09T19:35:49,476 353 | 0) 2021-07-09T19:35:49,477 | ~~ 2021-07-09T19:35:49,477 khmer/_khmermodule.cc:2103:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:35:49,477 2103 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:35:49,477 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,477 khmer/_khmermodule.cc:2104:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:35:49,477 2104 | "counting hash object", /* tp_doc */ 2021-07-09T19:35:49,477 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,477 | | 2021-07-09T19:35:49,478 | const char* 2021-07-09T19:35:49,486 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2021-07-09T19:35:49,486 khmer/_khmermodule.cc:2259:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,486 2259 | return PyInt_FromLong(hashbits->n_tags()); 2021-07-09T19:35:49,487 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,487 | PyLong_FromLong 2021-07-09T19:35:49,494 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2021-07-09T19:35:49,495 khmer/_khmermodule.cc:2281:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,495 2281 | return PyInt_FromLong(1); 2021-07-09T19:35:49,495 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,495 | PyLong_FromLong 2021-07-09T19:35:49,503 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2021-07-09T19:35:49,503 khmer/_khmermodule.cc:2304:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,503 2304 | return PyInt_FromLong(n_consumed); 2021-07-09T19:35:49,504 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,504 | PyLong_FromLong 2021-07-09T19:35:49,518 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2021-07-09T19:35:49,518 khmer/_khmermodule.cc:2410:43: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,519 2410 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2021-07-09T19:35:49,519 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,519 | PyLong_AsVoidPtr 2021-07-09T19:35:49,526 khmer/_khmermodule.cc:2419:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,526 2419 | return PyInt_FromLong(next_largest); 2021-07-09T19:35:49,527 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,527 | PyLong_FromLong 2021-07-09T19:35:49,533 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2021-07-09T19:35:49,534 khmer/_khmermodule.cc:2455:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T19:35:49,534 2455 | if (PyInt_Check(arg)) { 2021-07-09T19:35:49,534 | ^~~~~~~~~~~ 2021-07-09T19:35:49,534 | PySet_Check 2021-07-09T19:35:49,541 khmer/_khmermodule.cc:2456:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T19:35:49,541 2456 | long pos = PyInt_AsLong(arg); 2021-07-09T19:35:49,541 | ^~~~~~~~~~~~ 2021-07-09T19:35:49,541 | PyLong_AsLong 2021-07-09T19:35:49,549 khmer/_khmermodule.cc:2458:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T19:35:49,549 2458 | } else if (PyString_Check(arg)) { 2021-07-09T19:35:49,549 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,549 | PyMapping_Check 2021-07-09T19:35:49,559 khmer/_khmermodule.cc:2459:21: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T19:35:49,560 2459 | std::string s = PyString_AsString(arg); 2021-07-09T19:35:49,560 | ^~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,567 khmer/_khmermodule.cc:2463:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,568 2463 | return PyInt_FromLong(count); 2021-07-09T19:35:49,568 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,568 | PyLong_FromLong 2021-07-09T19:35:49,577 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2021-07-09T19:35:49,577 khmer/_khmermodule.cc:2506:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,577 2506 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2021-07-09T19:35:49,577 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,577 | PyLong_FromLong 2021-07-09T19:35:49,588 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_degree(PyObject*, PyObject*)’: 2021-07-09T19:35:49,588 khmer/_khmermodule.cc:2528:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:35:49,588 2528 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:35:49,588 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,588 | PyBytes_FromStringAndSize 2021-07-09T19:35:49,599 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_sodd(PyObject*, PyObject*)’: 2021-07-09T19:35:49,599 khmer/_khmermodule.cc:2557:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:35:49,599 2557 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:35:49,599 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,600 | PyBytes_FromStringAndSize 2021-07-09T19:35:49,610 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2021-07-09T19:35:49,610 khmer/_khmermodule.cc:2585:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:35:49,610 2585 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:35:49,611 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,611 | PyBytes_FromStringAndSize 2021-07-09T19:35:49,634 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2021-07-09T19:35:49,634 khmer/_khmermodule.cc:2666:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T19:35:49,634 2666 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T19:35:49,635 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,635 | PyLong_FromVoidPtr 2021-07-09T19:35:49,644 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2021-07-09T19:35:49,644 khmer/_khmermodule.cc:2694:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T19:35:49,644 2694 | if (!PyCObject_Check(subset_obj)) { 2021-07-09T19:35:49,645 | ^~~~~~~~~~~~~~~ 2021-07-09T19:35:49,645 | PyODict_Check 2021-07-09T19:35:49,656 khmer/_khmermodule.cc:2700:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,656 2700 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:35:49,656 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,656 | PyLong_AsVoidPtr 2021-07-09T19:35:49,677 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2021-07-09T19:35:49,677 khmer/_khmermodule.cc:2989:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T19:35:49,677 2989 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T19:35:49,677 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,678 | PyLong_FromVoidPtr 2021-07-09T19:35:49,686 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2021-07-09T19:35:49,686 khmer/_khmermodule.cc:3002:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T19:35:49,687 3002 | if (!PyCObject_Check(ppi_obj)) { 2021-07-09T19:35:49,687 | ^~~~~~~~~~~~~~~ 2021-07-09T19:35:49,687 | PyODict_Check 2021-07-09T19:35:49,698 khmer/_khmermodule.cc:3008:33: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,699 3008 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2021-07-09T19:35:49,699 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,699 | PyLong_AsVoidPtr 2021-07-09T19:35:49,707 khmer/_khmermodule.cc:3014:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,707 3014 | return PyInt_FromLong(p); 2021-07-09T19:35:49,707 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,707 | PyLong_FromLong 2021-07-09T19:35:49,721 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2021-07-09T19:35:49,721 khmer/_khmermodule.cc:3130:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,721 3130 | return PyInt_FromLong(n_partitions); 2021-07-09T19:35:49,722 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,722 | PyLong_FromLong 2021-07-09T19:35:49,731 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2021-07-09T19:35:49,731 khmer/_khmermodule.cc:3161:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,732 3161 | return PyInt_FromLong(n_singletons); 2021-07-09T19:35:49,732 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,732 | PyLong_FromLong 2021-07-09T19:35:49,748 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2021-07-09T19:35:49,748 khmer/_khmermodule.cc:3260:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,748 3260 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:35:49,748 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,749 | PyLong_AsVoidPtr 2021-07-09T19:35:49,760 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2021-07-09T19:35:49,760 khmer/_khmermodule.cc:3278:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,760 3278 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:35:49,761 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,761 | PyLong_AsVoidPtr 2021-07-09T19:35:49,796 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T19:35:49,796 khmer/_khmermodule.cc:3389:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,796 3389 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:35:49,796 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,797 | PyLong_AsVoidPtr 2021-07-09T19:35:49,809 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T19:35:49,809 khmer/_khmermodule.cc:3420:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T19:35:49,809 3420 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T19:35:49,810 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,810 | PyLong_FromVoidPtr 2021-07-09T19:35:49,818 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2021-07-09T19:35:49,818 khmer/_khmermodule.cc:3449:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,818 3449 | return PyInt_FromLong(d); 2021-07-09T19:35:49,818 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,819 | PyLong_FromLong 2021-07-09T19:35:49,830 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2021-07-09T19:35:49,830 khmer/_khmermodule.cc:3465:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,830 3465 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T19:35:49,830 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,831 | PyLong_AsVoidPtr 2021-07-09T19:35:49,842 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2021-07-09T19:35:49,843 khmer/_khmermodule.cc:3491:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,843 3491 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T19:35:49,843 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,843 | PyLong_AsVoidPtr 2021-07-09T19:35:49,855 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T19:35:49,855 khmer/_khmermodule.cc:3512:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T19:35:49,855 3512 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T19:35:49,855 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,856 | PyLong_AsVoidPtr 2021-07-09T19:35:49,864 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2021-07-09T19:35:49,864 khmer/_khmermodule.cc:3548:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,865 3548 | return PyInt_FromLong(p1); 2021-07-09T19:35:49,865 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,865 | PyLong_FromLong 2021-07-09T19:35:49,873 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2021-07-09T19:35:49,873 khmer/_khmermodule.cc:3565:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,873 3565 | return PyInt_FromLong(partition_id); 2021-07-09T19:35:49,873 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,873 | PyLong_FromLong 2021-07-09T19:35:49,888 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_density_explosion(PyObject*, PyObject*)’: 2021-07-09T19:35:49,888 khmer/_khmermodule.cc:3689:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T19:35:49,888 3689 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T19:35:49,889 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,889 | PyBytes_FromStringAndSize 2021-07-09T19:35:49,897 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2021-07-09T19:35:49,898 khmer/_khmermodule.cc:3738:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T19:35:49,898 3738 | return PyInt_FromLong(k); 2021-07-09T19:35:49,898 | ^~~~~~~~~~~~~~ 2021-07-09T19:35:49,898 | PyLong_FromLong 2021-07-09T19:35:49,919 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T19:35:49,920 from /usr/include/python3.9/Python.h:106, 2021-07-09T19:35:49,920 from khmer/_khmermodule.cc:12: 2021-07-09T19:35:49,920 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2021-07-09T19:35:49,920 khmer/_khmermodule.cc:3782:27: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:35:49,920 3782 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2021-07-09T19:35:49,920 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,920 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T19:35:49,921 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T19:35:49,921 | ^ 2021-07-09T19:35:49,933 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2021-07-09T19:35:49,933 khmer/_khmermodule.cc:3893:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:35:49,934 3893 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2021-07-09T19:35:49,934 | ^~~~~~~~~~~~~ 2021-07-09T19:35:49,934 | PyCMethod 2021-07-09T19:35:49,948 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2021-07-09T19:35:49,948 khmer/_khmermodule.cc:3967:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T19:35:49,948 3967 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2021-07-09T19:35:49,949 | ^~~~~~~~~~~~~ 2021-07-09T19:35:49,949 | PyCMethod 2021-07-09T19:35:49,949 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:35:49,949 khmer/_khmermodule.cc:3985:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,949 3985 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2021-07-09T19:35:49,949 | ^~~~~~~~~~~~~ 2021-07-09T19:35:49,950 | | 2021-07-09T19:35:49,950 | const char* 2021-07-09T19:35:49,950 khmer/_khmermodule.cc:3987:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T19:35:49,950 3987 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2021-07-09T19:35:49,950 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,950 | | 2021-07-09T19:35:49,950 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T19:35:49,951 khmer/_khmermodule.cc:3989:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T19:35:49,951 3989 | khmer_readaligner_getattr, /*tp_getattr*/ 2021-07-09T19:35:49,951 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,951 | | 2021-07-09T19:35:49,951 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T19:35:49,951 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:35:49,951 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:35:49,952 from khmer/_khmermodule.cc:12: 2021-07-09T19:35:49,952 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T19:35:49,952 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T19:35:49,952 | ~~~ 2021-07-09T19:35:49,952 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T19:35:49,952 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,952 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T19:35:49,952 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T19:35:49,953 | | 2021-07-09T19:35:49,953 | long unsigned int 2021-07-09T19:35:49,953 353 | 0) 2021-07-09T19:35:49,953 | ~~ 2021-07-09T19:35:49,953 khmer/_khmermodule.cc:4002:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T19:35:49,953 4002 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T19:35:49,953 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,954 khmer/_khmermodule.cc:4003:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T19:35:49,954 4003 | "ReadAligner object", /* tp_doc */ 2021-07-09T19:35:49,954 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,954 | | 2021-07-09T19:35:49,954 | const char* 2021-07-09T19:35:49,968 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2021-07-09T19:35:49,969 khmer/_khmermodule.cc:4195:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T19:35:49,969 4195 | return PyString_FromString(khmer::_revhash(val, ksize).c_str()); 2021-07-09T19:35:49,969 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:49,969 | PyLong_FromString 2021-07-09T19:35:49,970 khmer/_khmermodule.cc: At global scope: 2021-07-09T19:35:49,970 khmer/_khmermodule.cc:4251:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2021-07-09T19:35:49,970 4251 | init_khmer(void) 2021-07-09T19:35:49,970 | ^~~~~~~~~~ 2021-07-09T19:35:49,970 khmer/_khmermodule.cc:30:8: note: previous declaration ‘void init_khmer()’ 2021-07-09T19:35:49,971 30 | void init_khmer(); 2021-07-09T19:35:49,971 | ^~~~~~~~~~ 2021-07-09T19:35:49,971 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2021-07-09T19:35:49,971 khmer/_khmermodule.cc:4256:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T19:35:49,971 4256 | khmer_ConfigType.ob_type = &PyType_Type; 2021-07-09T19:35:49,972 | ^~~~~~~ 2021-07-09T19:35:49,972 khmer/_khmermodule.cc:4257:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T19:35:49,972 4257 | khmer_KTableType.ob_type = &PyType_Type; 2021-07-09T19:35:49,972 | ^~~~~~~ 2021-07-09T19:35:49,972 khmer/_khmermodule.cc:4258:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T19:35:49,972 4258 | khmer_KCountingHashType.ob_type = &PyType_Type; 2021-07-09T19:35:49,972 | ^~~~~~~ 2021-07-09T19:35:49,980 khmer/_khmermodule.cc:4261:9: error: ‘Py_InitModule’ was not declared in this scope 2021-07-09T19:35:49,980 4261 | m = Py_InitModule( "_khmer", KhmerMethods ); 2021-07-09T19:35:49,980 | ^~~~~~~~~~~~~ 2021-07-09T19:35:49,980 khmer/_khmermodule.cc:4263:2: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T19:35:49,980 4263 | return; 2021-07-09T19:35:49,980 | ^~~~~~ 2021-07-09T19:35:49,981 khmer/_khmermodule.cc:4268:2: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T19:35:49,981 4268 | return; 2021-07-09T19:35:49,981 | ^~~~~~ 2021-07-09T19:35:49,981 khmer/_khmermodule.cc:4275:2: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T19:35:49,981 4275 | return; 2021-07-09T19:35:49,981 | ^~~~~~ 2021-07-09T19:35:49,981 khmer/_khmermodule.cc:4281:2: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T19:35:49,982 4281 | return; 2021-07-09T19:35:49,982 | ^~~~~~ 2021-07-09T19:35:49,982 khmer/_khmermodule.cc:4284:2: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T19:35:49,982 4284 | return; 2021-07-09T19:35:49,982 | ^~~~~~ 2021-07-09T19:35:50,610 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T19:35:50,610 from /usr/include/python3.9/Python.h:85, 2021-07-09T19:35:50,611 from khmer/_khmermodule.cc:12: 2021-07-09T19:35:50,611 /usr/include/python3.9/object.h:411:33: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-09T19:35:50,611 411 | #define Py_INCREF(op) _Py_INCREF(_PyObject_CAST(op)) 2021-07-09T19:35:50,611 | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2021-07-09T19:35:50,611 khmer/_khmermodule.cc:4286:5: note: in expansion of macro ‘Py_INCREF’ 2021-07-09T19:35:50,611 4286 | Py_INCREF(&ReadParser_Type); 2021-07-09T19:35:50,611 | ^~~~~~~~~ 2021-07-09T19:35:50,636 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T19:35:50,711 Building wheel for khmer (setup.py): finished with status 'error' 2021-07-09T19:35:50,711 ERROR: Failed building wheel for khmer 2021-07-09T19:35:50,712 Running setup.py clean for khmer 2021-07-09T19:35:50,712 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-yr_eqtjv/khmer_08f5253071f44e19ae81112e5536223f/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-yr_eqtjv/khmer_08f5253071f44e19ae81112e5536223f/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 2021-07-09T19:35:53,040 running clean 2021-07-09T19:35:53,041 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T19:35:53,043 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T19:35:53,047 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T19:35:53,048 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T19:35:53,048 removing 'build' 2021-07-09T19:35:53,107 Failed to build khmer 2021-07-09T19:35:53,108 ERROR: Failed to build one or more wheels 2021-07-09T19:35:53,109 Exception information: 2021-07-09T19:35:53,109 Traceback (most recent call last): 2021-07-09T19:35:53,109 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T19:35:53,109 status = self.run(options, args) 2021-07-09T19:35:53,109 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T19:35:53,109 return func(self, options, args) 2021-07-09T19:35:53,109 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T19:35:53,109 raise CommandError( 2021-07-09T19:35:53,109 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T19:35:53,112 Removed build tracker: '/tmp/pip-req-tracker-k_fkf633'