2021-07-09T21:59:11,751 Created temporary directory: /tmp/pip-ephem-wheel-cache-fj6vymsr 2021-07-09T21:59:11,754 Created temporary directory: /tmp/pip-req-tracker-le42eis8 2021-07-09T21:59:11,754 Initialized build tracking at /tmp/pip-req-tracker-le42eis8 2021-07-09T21:59:11,755 Created build tracker: /tmp/pip-req-tracker-le42eis8 2021-07-09T21:59:11,755 Entered build tracker: /tmp/pip-req-tracker-le42eis8 2021-07-09T21:59:11,755 Created temporary directory: /tmp/pip-wheel-nftul14k 2021-07-09T21:59:11,789 1 location(s) to search for versions of khmer: 2021-07-09T21:59:11,789 * https://pypi.org/simple/khmer/ 2021-07-09T21:59:11,789 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2021-07-09T21:59:11,790 Getting page https://pypi.org/simple/khmer/ 2021-07-09T21:59:11,791 Found index url https://pypi.org/simple 2021-07-09T21:59:11,896 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg#sha256=ebc63236f68de37edb1895fbe6507c0db3fcbc2b1fd54ea2952c28bcf26e23e6 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,896 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg#sha256=6dfaaca9076162129b1c3b2b7015ce267590784e20646082cf46e6f964564478 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,896 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz#sha256=b3aecbfb7465e5e6d7963513e40fa77bb63d3918fc47deba82102f13a69517ff (from https://pypi.org/simple/khmer/), version: 0.6 2021-07-09T21:59:11,897 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz#sha256=f552d041d1ac69077844e1a0303b5db9c123e28397b1bf9011ecdce010159f07 (from https://pypi.org/simple/khmer/), version: 0.6.1 2021-07-09T21:59:11,913 Skipping link: none of the wheel's tags (cp27-none-macosx_10_8_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl#sha256=0535143a6c2399efcddcc35dae42b2ad6042309debcd4c39c1a27faeb6273473 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,913 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz#sha256=5a8a45cbd59fe5de27cb1372d2817a4ab22460fa9591ad04780a8a4026cce2f9 (from https://pypi.org/simple/khmer/), version: 0.7 2021-07-09T21:59:11,914 Skipping link: none of the wheel's tags (cp27-none-macosx_10_8_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl#sha256=a23be5a2a74f0967b9669579c3253978a7516d59c96485113b009ec07cf31d42 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,914 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz#sha256=08f7b20fc7f4405bbe27145d47e710e61d50639f79ab4763f685780f24935ddd (from https://pypi.org/simple/khmer/), version: 0.7.1 2021-07-09T21:59:11,914 Skipping link: none of the wheel's tags (cp27-none-macosx_10_9_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl#sha256=e43f87d4f2a34197c74fe0b6eb52d31e9ed3d569652544de8d12d7f1a887f0b0 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,915 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz#sha256=3fc678c7c7987a2e203ee053270e9565d1fc845ff472851e52c93efa19887c46 (from https://pypi.org/simple/khmer/), version: 0.8 2021-07-09T21:59:11,915 Skipping link: none of the wheel's tags (cp27-none-macosx_10_9_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl#sha256=b2323e7f1252e51dffabf75001588c47d9d5516fb852bc7a07ec76248a645467 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,915 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz#sha256=05de0be6826aa4dda0a58eb6657b5928c769b6d1b433f8e7d78310fbdc8026ff (from https://pypi.org/simple/khmer/), version: 1.0 2021-07-09T21:59:11,916 Skipping link: none of the wheel's tags (cp27-none-macosx_10_9_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl#sha256=2618d646a155290fde19ad81846f94d7b2fccb5d87f602aef53cbb978caf0a3e (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,916 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz#sha256=9ab86b43de964265f94cb535ea9de41bc3868710561c5daa29e540e8237c27a0 (from https://pypi.org/simple/khmer/), version: 1.0.1 2021-07-09T21:59:11,917 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz#sha256=05f5cf4a8f634c3c2f77a2e65fcc5dfa7887d4cf12c519af141a13ae84c9dd1d (from https://pypi.org/simple/khmer/), version: 1.1 2021-07-09T21:59:11,917 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl#sha256=83a8adf4ec51f327ac6eb2836b3f7c778593bab1d4bad55e5fe1ae5b6f8f7a62 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,917 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz#sha256=8734414fdd2adf7e96b291243061d2066cf52a5dce7e3091db088ffa03db772f (from https://pypi.org/simple/khmer/), version: 1.2 2021-07-09T21:59:11,918 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl#sha256=4c8bed026fac3c74ecae93b6e22f4e7dada585f4006984bce7dec527fdc8b574 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,918 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz#sha256=6a878df7a9e10f3c40c730d7deb860f3150662526c469a87dbfb2451a03cf20f (from https://pypi.org/simple/khmer/), version: 1.3 2021-07-09T21:59:11,919 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl#sha256=2cc862a13ce1a9acf58633de51f5491fe8415992566a0bb2186bff15d608c61e (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,919 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz#sha256=f51c7db2a8eb29a51b8bc7342b524324663116a61dc7f24692cb04863b2dda41 (from https://pypi.org/simple/khmer/), version: 1.4 2021-07-09T21:59:11,919 Skipping link: none of the wheel's tags (cp27-none-macosx_10_10_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl#sha256=15522aa0f1c0ea082dfcc00f5525c48f4b1e1bd4fe91688688b7c05d8fc5a7d1 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,920 Skipping link: none of the wheel's tags (cp27-none-macosx_10_6_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl#sha256=ba5ea34ce63a0834cc9b1b3f4ac0b6ea8aabbfbe675cd60761bf9247793a4327 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,920 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz#sha256=1d42851ce5d4088b807509413af2a54c88f06091e2b03bd408b26a8056936650 (from https://pypi.org/simple/khmer/), version: 1.4.1 2021-07-09T21:59:11,920 Skipping link: none of the wheel's tags (cp27-none-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl#sha256=9443cb21d5b2c81acc39b4030ec1d3d34b7dc693ad9eea439c2f09309d666692 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,921 Skipping link: none of the wheel's tags (cp33-cp33m-macosx_10_6_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl#sha256=c8b768ed0f6dd9fd83a2ba04dc7b1d240512adba18512552a35989d54e369bf4 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,921 Skipping link: none of the wheel's tags (cp34-cp34m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl#sha256=4eade77bd6d1dc3d366594fd73d0db2ffc4e8a770654dfea9f2b224991e95aea (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,922 Skipping link: none of the wheel's tags (cp35-cp35m-macosx_10_6_intel) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl#sha256=d5ccb50aac89563ba5fb2ac93e1b9ab426e083fd6e03abf1a423caeaeb85b844 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,922 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz#sha256=6a8c6809b50adaf2d7d7307eefcca173f4b536329562530400fb1c88a12e6071 (from https://pypi.org/simple/khmer/), version: 2.0 2021-07-09T21:59:11,922 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz#sha256=baef38d2d577cb666002a70ac8eca5d247593758ac1357bb17c066bea251e77a (from https://pypi.org/simple/khmer/), version: 2.1rc3 2021-07-09T21:59:11,923 Skipping link: none of the wheel's tags (cp36-cp36m-macosx_10_12_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl#sha256=bb2f957f6776a8553033015a20dcd41a6a20bc447c1756541d2318bd907b5d47 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,923 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz#sha256=43c741b44911fa8c79f549433f996e7fc90a58c6db06b5602adc8d8d1df5f3d6 (from https://pypi.org/simple/khmer/), version: 2.1 2021-07-09T21:59:11,924 Skipping link: none of the wheel's tags (cp27-cp27m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl#sha256=4a62de0eaafc3dbf4ea01006504a3e98853f4a0b8b37e72c9e93082181f0f2c5 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,924 Skipping link: none of the wheel's tags (cp27-cp27mu-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl#sha256=10d448f3131303c5c4745aecad7473f6e35ac5737d6fa2a7b731aedeea874e77 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,925 Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl#sha256=deef940b791731d1af110cc1973c4ee5f437701181fc16537b468f857a62a2fa (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,925 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl#sha256=06a1e981744c3aea2e74fdc668914afb13e36bce96f12777852fa9b9b14d9658 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,926 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl#sha256=6b5548c457aa506bc43962c36d4fa2ffcd5a0762b862d18e915041e3adba8737 (from https://pypi.org/simple/khmer/) 2021-07-09T21:59:11,926 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz#sha256=a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24 (from https://pypi.org/simple/khmer/), version: 2.1.1 2021-07-09T21:59:11,926 Skipping link: not a file: https://pypi.org/simple/khmer/ 2021-07-09T21:59:11,929 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2021-07-09T21:59:11,946 Collecting khmer==1.0.1 2021-07-09T21:59:11,948 Created temporary directory: /tmp/pip-unpack-s5_kzjnc 2021-07-09T21:59:14,983 Downloading khmer-1.0.1.tar.gz (19.0 MB) 2021-07-09T21:59:19,629 Added khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz#sha256=9ab86b43de964265f94cb535ea9de41bc3868710561c5daa29e540e8237c27a0 to build tracker '/tmp/pip-req-tracker-le42eis8' 2021-07-09T21:59:19,630 Running setup.py (path:/tmp/pip-wheel-nftul14k/khmer_93aec4e399be460e9caf672d72e90142/setup.py) egg_info for package khmer 2021-07-09T21:59:19,630 Created temporary directory: /tmp/pip-pip-egg-info-i405a4k6 2021-07-09T21:59:19,631 Running command python setup.py egg_info 2021-07-09T21:59:20,574 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead 2021-07-09T21:59:20,575 warnings.warn( 2021-07-09T21:59:20,613 running egg_info 2021-07-09T21:59:20,615 creating /tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info 2021-07-09T21:59:20,616 writing /tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info/PKG-INFO 2021-07-09T21:59:20,619 writing dependency_links to /tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info/dependency_links.txt 2021-07-09T21:59:20,621 writing requirements to /tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info/requires.txt 2021-07-09T21:59:20,622 writing top-level names to /tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info/top_level.txt 2021-07-09T21:59:20,624 writing manifest file '/tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info/SOURCES.txt' 2021-07-09T21:59:20,783 reading manifest file '/tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info/SOURCES.txt' 2021-07-09T21:59:20,785 reading manifest template 'MANIFEST.in' 2021-07-09T21:59:23,085 warning: no previously-included files found matching 'lib/zlib/Makefile' 2021-07-09T21:59:23,086 warning: no previously-included files found matching 'lib/zlib/zconf.h' 2021-07-09T21:59:23,110 no previously-included directories found matching 'doc/doxygen' 2021-07-09T21:59:23,120 warning: no previously-included files matching '*.orig' found anywhere in distribution 2021-07-09T21:59:23,121 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-09T21:59:23,122 adding license file 'LICENSE' 2021-07-09T21:59:23,138 writing manifest file '/tmp/pip-pip-egg-info-i405a4k6/khmer.egg-info/SOURCES.txt' 2021-07-09T21:59:23,217 Source in /tmp/pip-wheel-nftul14k/khmer_93aec4e399be460e9caf672d72e90142 has version 1.0.1, which satisfies requirement khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz#sha256=9ab86b43de964265f94cb535ea9de41bc3868710561c5daa29e540e8237c27a0 2021-07-09T21:59:23,218 Removed khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz#sha256=9ab86b43de964265f94cb535ea9de41bc3868710561c5daa29e540e8237c27a0 from build tracker '/tmp/pip-req-tracker-le42eis8' 2021-07-09T21:59:23,223 Created temporary directory: /tmp/pip-unpack-z6sx9chu 2021-07-09T21:59:23,223 Building wheels for collected packages: khmer 2021-07-09T21:59:23,227 Created temporary directory: /tmp/pip-wheel-yp5t7lbv 2021-07-09T21:59:23,228 Building wheel for khmer (setup.py): started 2021-07-09T21:59:23,228 Destination directory: /tmp/pip-wheel-yp5t7lbv 2021-07-09T21:59:23,228 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-nftul14k/khmer_93aec4e399be460e9caf672d72e90142/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-nftul14k/khmer_93aec4e399be460e9caf672d72e90142/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-yp5t7lbv 2021-07-09T21:59:24,155 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead 2021-07-09T21:59:24,156 warnings.warn( 2021-07-09T21:59:24,207 running bdist_wheel 2021-07-09T21:59:24,210 running build 2021-07-09T21:59:24,211 got version from file /tmp/pip-wheel-nftul14k/khmer_93aec4e399be460e9caf672d72e90142/khmer/_version.py {'version': '1.0.1', 'full': '53a97858f0b445a323419829a0c5baef5f242e4e'} 2021-07-09T21:59:24,211 running build_py 2021-07-09T21:59:24,351 creating build 2021-07-09T21:59:24,352 creating build/lib.linux-armv7l-3.9 2021-07-09T21:59:24,352 creating build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,353 copying khmer/_version.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,355 copying khmer/khmer_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,357 copying khmer/thread_utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,359 copying khmer/file.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,361 copying khmer/utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,363 copying khmer/__init__.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,365 copying khmer/load_pe.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,366 copying khmer/threading_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:24,367 running egg_info 2021-07-09T21:59:24,379 creating khmer.egg-info 2021-07-09T21:59:24,379 writing khmer.egg-info/PKG-INFO 2021-07-09T21:59:24,382 writing dependency_links to khmer.egg-info/dependency_links.txt 2021-07-09T21:59:24,385 writing requirements to khmer.egg-info/requires.txt 2021-07-09T21:59:24,386 writing top-level names to khmer.egg-info/top_level.txt 2021-07-09T21:59:24,387 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T21:59:24,395 reading manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T21:59:24,396 reading manifest template 'MANIFEST.in' 2021-07-09T21:59:26,521 warning: no previously-included files found matching 'lib/zlib/Makefile' 2021-07-09T21:59:26,522 warning: no previously-included files found matching 'lib/zlib/zconf.h' 2021-07-09T21:59:26,543 no previously-included directories found matching 'doc/doxygen' 2021-07-09T21:59:26,552 warning: no previously-included files matching '*.orig' found anywhere in distribution 2021-07-09T21:59:26,554 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-09T21:59:26,555 adding license file 'LICENSE' 2021-07-09T21:59:26,574 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T21:59:26,586 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T21:59:26,592 running build_ext 2021-07-09T21:59:26,593 bash -c cd lib/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC 2021-07-09T21:59:26,793 Checking for gcc... 2021-07-09T21:59:27,103 Building static library libz.a version 1.2.8 with gcc. 2021-07-09T21:59:27,232 Checking for off64_t... Yes. 2021-07-09T21:59:27,239 Checking for fseeko... Yes. 2021-07-09T21:59:27,485 Checking for strerror... Yes. 2021-07-09T21:59:27,681 Checking for unistd.h... Yes. 2021-07-09T21:59:27,821 Checking for stdarg.h... Yes. 2021-07-09T21:59:27,984 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). 2021-07-09T21:59:28,213 Checking for vsnprintf() in stdio.h... Yes. 2021-07-09T21:59:28,346 Checking for return value of vsnprintf()... Yes. 2021-07-09T21:59:28,464 Checking for attribute(visibility) support... Yes. 2021-07-09T21:59:28,571 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c 2021-07-09T21:59:28,907 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c 2021-07-09T21:59:29,314 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c 2021-07-09T21:59:31,070 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c 2021-07-09T21:59:31,851 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c 2021-07-09T21:59:32,300 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c 2021-07-09T21:59:34,012 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c 2021-07-09T21:59:34,517 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c 2021-07-09T21:59:35,768 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c 2021-07-09T21:59:35,969 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c 2021-07-09T21:59:36,130 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c 2021-07-09T21:59:36,286 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c 2021-07-09T21:59:36,468 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c 2021-07-09T21:59:36,908 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c 2021-07-09T21:59:37,433 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c 2021-07-09T21:59:37,962 bash -c cd lib/bzip2 && make -f Makefile-libbz2_so all 2021-07-09T21:59:37,985 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2021-07-09T21:59:38,734 blocksort.c: In function ‘mainSort’: 2021-07-09T21:59:38,734 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T21:59:38,735 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T21:59:38,735 | ^~~~~~~ 2021-07-09T21:59:38,735 blocksort.c:514:18: note: called from here 2021-07-09T21:59:38,735 514 | while ( mainGtU ( 2021-07-09T21:59:38,735 | ^~~~~~~~~ 2021-07-09T21:59:38,735 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T21:59:38,735 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:38,736 516 | ) ) { 2021-07-09T21:59:38,736 | ~ 2021-07-09T21:59:38,736 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T21:59:38,736 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T21:59:38,736 | ^~~~~~~ 2021-07-09T21:59:38,736 blocksort.c:528:18: note: called from here 2021-07-09T21:59:38,736 528 | while ( mainGtU ( 2021-07-09T21:59:38,737 | ^~~~~~~~~ 2021-07-09T21:59:38,737 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T21:59:38,737 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:38,737 530 | ) ) { 2021-07-09T21:59:38,737 | ~ 2021-07-09T21:59:38,737 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T21:59:38,737 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T21:59:38,737 | ^~~~~~~ 2021-07-09T21:59:38,737 blocksort.c:542:18: note: called from here 2021-07-09T21:59:38,738 542 | while ( mainGtU ( 2021-07-09T21:59:38,738 | ^~~~~~~~~ 2021-07-09T21:59:38,738 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T21:59:38,738 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:38,738 544 | ) ) { 2021-07-09T21:59:38,738 | ~ 2021-07-09T21:59:39,427 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2021-07-09T21:59:39,833 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2021-07-09T21:59:39,959 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2021-07-09T21:59:40,084 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2021-07-09T21:59:43,943 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2021-07-09T21:59:46,191 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2021-07-09T21:59:47,876 #gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o 2021-07-09T21:59:47,878 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2021-07-09T21:59:47,881 #rm -f libbz2.so.1.0 2021-07-09T21:59:47,884 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2021-07-09T21:59:47,893 building 'khmer._khmermodule' extension 2021-07-09T21:59:47,895 creating build/temp.linux-armv7l-3.9 2021-07-09T21:59:47,895 creating build/temp.linux-armv7l-3.9/khmer 2021-07-09T21:59:47,896 creating build/temp.linux-armv7l-3.9/lib 2021-07-09T21:59:47,897 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=1.0.1 -UNO_UNIQUE_RC -Ilib -Ilib/zlib -Ilib/bzip2 -I/usr/include/python3.9 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-3.9/khmer/_khmermodule.o -O3 2021-07-09T21:59:50,212 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2021-07-09T21:59:50,212 khmer/_khmermodule.cc:85:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2021-07-09T21:59:50,212 85 | tobj.ob_size = 0; 2021-07-09T21:59:50,212 | ^~~~~~~ 2021-07-09T21:59:50,213 khmer/_khmermodule.cc:86:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T21:59:50,213 86 | tobj.ob_type = &PyType_Type; 2021-07-09T21:59:50,213 | ^~~~~~~ 2021-07-09T21:59:50,217 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:59:50,217 khmer/_khmermodule.cc:206:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,217 206 | "Config", sizeof(khmer_ConfigObject), 2021-07-09T21:59:50,218 | ^~~~~~~~ 2021-07-09T21:59:50,218 | | 2021-07-09T21:59:50,218 | const char* 2021-07-09T21:59:50,218 khmer/_khmermodule.cc:208:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,218 208 | khmer_config_dealloc, /*tp_dealloc*/ 2021-07-09T21:59:50,219 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,219 | | 2021-07-09T21:59:50,219 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:59:50,219 khmer/_khmermodule.cc:210:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:59:50,219 210 | khmer_config_getattr, /*tp_getattr*/ 2021-07-09T21:59:50,219 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,219 | | 2021-07-09T21:59:50,220 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:59:50,220 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:59:50,220 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:59:50,220 from khmer/_khmermodule.cc:13: 2021-07-09T21:59:50,220 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:59:50,220 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:59:50,221 | ~~~ 2021-07-09T21:59:50,221 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:59:50,221 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,221 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:59:50,221 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:59:50,221 | | 2021-07-09T21:59:50,221 | long unsigned int 2021-07-09T21:59:50,221 353 | 0) 2021-07-09T21:59:50,221 | ~~ 2021-07-09T21:59:50,222 khmer/_khmermodule.cc:223:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:59:50,222 223 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:59:50,222 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,222 khmer/_khmermodule.cc:224:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:59:50,222 224 | "config object", /* tp_doc */ 2021-07-09T21:59:50,222 | ^~~~~~~~~~~~~~~ 2021-07-09T21:59:50,222 | | 2021-07-09T21:59:50,222 | const char* 2021-07-09T21:59:50,228 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2021-07-09T21:59:50,228 khmer/_khmermodule.cc:312:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:59:50,229 312 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2021-07-09T21:59:50,229 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,229 | PyLong_FromSize_t 2021-07-09T21:59:50,238 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2021-07-09T21:59:50,238 khmer/_khmermodule.cc:370:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:59:50,238 370 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2021-07-09T21:59:50,239 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,239 | PyLong_FromSize_t 2021-07-09T21:59:50,247 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2021-07-09T21:59:50,248 khmer/_khmermodule.cc:399:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:59:50,248 399 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2021-07-09T21:59:50,248 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,248 | PyLong_FromSize_t 2021-07-09T21:59:50,258 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2021-07-09T21:59:50,258 khmer/_khmermodule.cc:466:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:59:50,258 466 | return Py_FindMethod(khmer_config_methods, obj, name); 2021-07-09T21:59:50,258 | ^~~~~~~~~~~~~ 2021-07-09T21:59:50,258 | PyCMethod 2021-07-09T21:59:50,268 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2021-07-09T21:59:50,268 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:59:50,268 504 | PyString_FromString( \ 2021-07-09T21:59:50,269 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,269 khmer/_khmermodule.cc:513:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:59:50,269 513 | return KHMER_READ_STRING_GETTER( self, name ); 2021-07-09T21:59:50,269 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,277 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2021-07-09T21:59:50,278 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:59:50,278 504 | PyString_FromString( \ 2021-07-09T21:59:50,278 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,278 khmer/_khmermodule.cc:521:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:59:50,279 521 | return KHMER_READ_STRING_GETTER( self, sequence ); 2021-07-09T21:59:50,279 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,287 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2021-07-09T21:59:50,287 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:59:50,288 504 | PyString_FromString( \ 2021-07-09T21:59:50,288 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,288 khmer/_khmermodule.cc:529:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:59:50,288 529 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2021-07-09T21:59:50,288 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,297 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2021-07-09T21:59:50,297 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:59:50,297 504 | PyString_FromString( \ 2021-07-09T21:59:50,297 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,297 khmer/_khmermodule.cc:537:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T21:59:50,298 537 | return KHMER_READ_STRING_GETTER( self, annotations ); 2021-07-09T21:59:50,298 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,322 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2021-07-09T21:59:50,322 khmer/_khmermodule.cc:874:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,322 874 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2021-07-09T21:59:50,322 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,322 | PyLong_FromLong 2021-07-09T21:59:50,324 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:59:50,325 khmer/_khmermodule.cc:987:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,325 987 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2021-07-09T21:59:50,325 | ^~~~~~~~~ 2021-07-09T21:59:50,325 | | 2021-07-09T21:59:50,325 | const char* 2021-07-09T21:59:50,325 khmer/_khmermodule.cc:989:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,326 989 | khmer_subset_dealloc, /*tp_dealloc*/ 2021-07-09T21:59:50,326 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,326 | | 2021-07-09T21:59:50,326 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:59:50,326 khmer/_khmermodule.cc:991:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:59:50,326 991 | khmer_subset_getattr, /*tp_getattr*/ 2021-07-09T21:59:50,326 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,327 | | 2021-07-09T21:59:50,327 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:59:50,327 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:59:50,327 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:59:50,327 from khmer/_khmermodule.cc:13: 2021-07-09T21:59:50,327 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:59:50,327 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:59:50,328 | ~~~ 2021-07-09T21:59:50,328 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:59:50,328 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,328 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:59:50,328 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:59:50,329 | | 2021-07-09T21:59:50,329 | long unsigned int 2021-07-09T21:59:50,329 353 | 0) 2021-07-09T21:59:50,329 | ~~ 2021-07-09T21:59:50,329 khmer/_khmermodule.cc:1004:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:59:50,329 1004 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:59:50,329 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,329 khmer/_khmermodule.cc:1005:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:59:50,329 1005 | "subset object", /* tp_doc */ 2021-07-09T21:59:50,330 | ^~~~~~~~~~~~~~~ 2021-07-09T21:59:50,330 | | 2021-07-09T21:59:50,330 | const char* 2021-07-09T21:59:50,335 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2021-07-09T21:59:50,336 khmer/_khmermodule.cc:1101:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,336 1101 | return PyInt_FromLong(1); 2021-07-09T21:59:50,336 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,336 | PyLong_FromLong 2021-07-09T21:59:50,344 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2021-07-09T21:59:50,344 khmer/_khmermodule.cc:1118:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,344 1118 | return PyInt_FromLong(0); 2021-07-09T21:59:50,344 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,345 | PyLong_FromLong 2021-07-09T21:59:50,354 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2021-07-09T21:59:50,354 khmer/_khmermodule.cc:1206:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,355 1206 | return PyInt_FromLong(n_consumed); 2021-07-09T21:59:50,355 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,355 | PyLong_FromLong 2021-07-09T21:59:50,363 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2021-07-09T21:59:50,363 khmer/_khmermodule.cc:1238:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,363 1238 | return PyInt_FromLong(n_consumed); 2021-07-09T21:59:50,363 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,364 | PyLong_FromLong 2021-07-09T21:59:50,372 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2021-07-09T21:59:50,372 khmer/_khmermodule.cc:1261:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,372 1261 | return PyInt_FromLong(N); 2021-07-09T21:59:50,372 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,372 | PyLong_FromLong 2021-07-09T21:59:50,380 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2021-07-09T21:59:50,380 khmer/_khmermodule.cc:1284:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,381 1284 | return PyInt_FromLong(N); 2021-07-09T21:59:50,381 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,381 | PyLong_FromLong 2021-07-09T21:59:50,389 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2021-07-09T21:59:50,390 khmer/_khmermodule.cc:1387:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:59:50,390 1387 | if (PyInt_Check(arg)) { 2021-07-09T21:59:50,390 | ^~~~~~~~~~~ 2021-07-09T21:59:50,390 | PySet_Check 2021-07-09T21:59:50,397 khmer/_khmermodule.cc:1388:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:59:50,397 1388 | long pos = PyInt_AsLong(arg); 2021-07-09T21:59:50,397 | ^~~~~~~~~~~~ 2021-07-09T21:59:50,397 | PyLong_AsLong 2021-07-09T21:59:50,405 khmer/_khmermodule.cc:1390:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T21:59:50,405 1390 | } else if (PyString_Check(arg)) { 2021-07-09T21:59:50,405 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,405 | PyMapping_Check 2021-07-09T21:59:50,415 khmer/_khmermodule.cc:1391:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T21:59:50,416 1391 | std::string s = PyString_AsString(arg); 2021-07-09T21:59:50,416 | ^~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,423 khmer/_khmermodule.cc:1395:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,424 1395 | return PyInt_FromLong(count); 2021-07-09T21:59:50,424 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,424 | PyLong_FromLong 2021-07-09T21:59:50,432 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2021-07-09T21:59:50,432 khmer/_khmermodule.cc:1411:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,432 1411 | return PyInt_FromLong(count); 2021-07-09T21:59:50,432 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,433 | PyLong_FromLong 2021-07-09T21:59:50,443 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2021-07-09T21:59:50,443 khmer/_khmermodule.cc:1435:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T21:59:50,443 1435 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T21:59:50,443 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,443 | PyBytes_FromStringAndSize 2021-07-09T21:59:50,454 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2021-07-09T21:59:50,454 khmer/_khmermodule.cc:1465:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T21:59:50,454 1465 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T21:59:50,454 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,455 | PyBytes_FromStringAndSize 2021-07-09T21:59:50,466 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2021-07-09T21:59:50,467 khmer/_khmermodule.cc:1606:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,467 1606 | return PyInt_FromLong(k); 2021-07-09T21:59:50,467 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,467 | PyLong_FromLong 2021-07-09T21:59:50,482 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2021-07-09T21:59:50,482 khmer/_khmermodule.cc:1718:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:59:50,483 1718 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T21:59:50,483 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,483 | PyLong_FromVoidPtr 2021-07-09T21:59:50,495 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2021-07-09T21:59:50,495 khmer/_khmermodule.cc:1824:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:59:50,495 1824 | return Py_FindMethod(khmer_counting_methods, obj, name); 2021-07-09T21:59:50,495 | ^~~~~~~~~~~~~ 2021-07-09T21:59:50,496 | PyCMethod 2021-07-09T21:59:50,496 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:59:50,496 khmer/_khmermodule.cc:1834:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,496 1834 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2021-07-09T21:59:50,496 | ^~~~~~~~~~~~~~~ 2021-07-09T21:59:50,496 | | 2021-07-09T21:59:50,497 | const char* 2021-07-09T21:59:50,497 khmer/_khmermodule.cc:1836:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,497 1836 | khmer_counting_dealloc, /*tp_dealloc*/ 2021-07-09T21:59:50,497 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,497 | | 2021-07-09T21:59:50,497 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:59:50,497 khmer/_khmermodule.cc:1838:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:59:50,498 1838 | khmer_counting_getattr, /*tp_getattr*/ 2021-07-09T21:59:50,498 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,498 | | 2021-07-09T21:59:50,498 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:59:50,498 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:59:50,499 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:59:50,499 from khmer/_khmermodule.cc:13: 2021-07-09T21:59:50,499 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:59:50,499 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:59:50,499 | ~~~ 2021-07-09T21:59:50,499 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:59:50,499 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,499 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:59:50,500 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:59:50,500 | | 2021-07-09T21:59:50,500 | long unsigned int 2021-07-09T21:59:50,500 353 | 0) 2021-07-09T21:59:50,500 | ~~ 2021-07-09T21:59:50,500 khmer/_khmermodule.cc:1851:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:59:50,500 1851 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:59:50,500 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,501 khmer/_khmermodule.cc:1852:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:59:50,501 1852 | "counting hash object", /* tp_doc */ 2021-07-09T21:59:50,501 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,501 | | 2021-07-09T21:59:50,501 | const char* 2021-07-09T21:59:50,504 khmer/_khmermodule.cc: In function ‘PyObject* _new_counting_hash(PyObject*, PyObject*)’: 2021-07-09T21:59:50,504 khmer/_khmermodule.cc:1903:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:59:50,505 1903 | if (PyInt_Check(size_o)) { 2021-07-09T21:59:50,505 | ^~~~~~~~~~~ 2021-07-09T21:59:50,505 | PySet_Check 2021-07-09T21:59:50,511 khmer/_khmermodule.cc:1904:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:59:50,511 1904 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:59:50,511 | ^~~~~~~~~~~~ 2021-07-09T21:59:50,512 | PyLong_AsLong 2021-07-09T21:59:50,513 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:59:50,513 khmer/_khmermodule.cc:1940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,513 1940 | "Hashbits", sizeof(khmer_KHashbitsObject), 2021-07-09T21:59:50,513 | ^~~~~~~~~~ 2021-07-09T21:59:50,514 | | 2021-07-09T21:59:50,514 | const char* 2021-07-09T21:59:50,514 khmer/_khmermodule.cc:1942:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:50,514 1942 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2021-07-09T21:59:50,514 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,514 | | 2021-07-09T21:59:50,515 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:59:50,515 khmer/_khmermodule.cc:1944:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:59:50,515 1944 | khmer_hashbits_getattr, /*tp_getattr*/ 2021-07-09T21:59:50,515 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,515 | | 2021-07-09T21:59:50,515 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:59:50,515 khmer/_khmermodule.cc:1957:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:59:50,516 1957 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2021-07-09T21:59:50,516 khmer/_khmermodule.cc:1958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:59:50,516 1958 | "hashbits object", /* tp_doc */ 2021-07-09T21:59:50,516 | ^~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,516 | | 2021-07-09T21:59:50,516 | const char* 2021-07-09T21:59:50,528 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2021-07-09T21:59:50,528 khmer/_khmermodule.cc:2131:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:59:50,528 2131 | return PyInt_FromSize_t(hashbits->n_tags()); 2021-07-09T21:59:50,528 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,529 | PyLong_FromSize_t 2021-07-09T21:59:50,536 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2021-07-09T21:59:50,536 khmer/_khmermodule.cc:2153:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,537 2153 | return PyInt_FromLong(1); 2021-07-09T21:59:50,537 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,537 | PyLong_FromLong 2021-07-09T21:59:50,545 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2021-07-09T21:59:50,545 khmer/_khmermodule.cc:2176:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,545 2176 | return PyInt_FromLong(n_consumed); 2021-07-09T21:59:50,545 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,546 | PyLong_FromLong 2021-07-09T21:59:50,560 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2021-07-09T21:59:50,560 khmer/_khmermodule.cc:2283:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,561 2283 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2021-07-09T21:59:50,561 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,561 | PyLong_AsVoidPtr 2021-07-09T21:59:50,568 khmer/_khmermodule.cc:2293:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,568 2293 | return PyInt_FromLong(next_largest); 2021-07-09T21:59:50,569 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,569 | PyLong_FromLong 2021-07-09T21:59:50,575 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2021-07-09T21:59:50,575 khmer/_khmermodule.cc:2309:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:59:50,575 2309 | if (PyInt_Check(arg)) { 2021-07-09T21:59:50,575 | ^~~~~~~~~~~ 2021-07-09T21:59:50,576 | PySet_Check 2021-07-09T21:59:50,582 khmer/_khmermodule.cc:2310:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:59:50,582 2310 | long pos = PyInt_AsLong(arg); 2021-07-09T21:59:50,583 | ^~~~~~~~~~~~ 2021-07-09T21:59:50,583 | PyLong_AsLong 2021-07-09T21:59:50,590 khmer/_khmermodule.cc:2312:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T21:59:50,590 2312 | } else if (PyString_Check(arg)) { 2021-07-09T21:59:50,591 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,591 | PyMapping_Check 2021-07-09T21:59:50,601 khmer/_khmermodule.cc:2313:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T21:59:50,601 2313 | std::string s = PyString_AsString(arg); 2021-07-09T21:59:50,601 | ^~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,609 khmer/_khmermodule.cc:2320:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,609 2320 | return PyInt_FromLong(count); 2021-07-09T21:59:50,609 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,609 | PyLong_FromLong 2021-07-09T21:59:50,618 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2021-07-09T21:59:50,618 khmer/_khmermodule.cc:2362:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,618 2362 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2021-07-09T21:59:50,619 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,619 | PyLong_FromLong 2021-07-09T21:59:50,629 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2021-07-09T21:59:50,629 khmer/_khmermodule.cc:2383:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T21:59:50,630 2383 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T21:59:50,630 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,630 | PyBytes_FromStringAndSize 2021-07-09T21:59:50,659 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2021-07-09T21:59:50,659 khmer/_khmermodule.cc:2458:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:59:50,659 2458 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T21:59:50,659 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,660 | PyLong_FromVoidPtr 2021-07-09T21:59:50,669 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2021-07-09T21:59:50,669 khmer/_khmermodule.cc:2486:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T21:59:50,669 2486 | if (!PyCObject_Check(subset_obj)) { 2021-07-09T21:59:50,670 | ^~~~~~~~~~~~~~~ 2021-07-09T21:59:50,670 | PyODict_Check 2021-07-09T21:59:50,681 khmer/_khmermodule.cc:2492:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,681 2492 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:59:50,681 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,681 | PyLong_AsVoidPtr 2021-07-09T21:59:50,701 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2021-07-09T21:59:50,701 khmer/_khmermodule.cc:2756:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:59:50,702 2756 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T21:59:50,702 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,702 | PyLong_FromVoidPtr 2021-07-09T21:59:50,710 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2021-07-09T21:59:50,711 khmer/_khmermodule.cc:2769:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T21:59:50,711 2769 | if (!PyCObject_Check(ppi_obj)) { 2021-07-09T21:59:50,711 | ^~~~~~~~~~~~~~~ 2021-07-09T21:59:50,711 | PyODict_Check 2021-07-09T21:59:50,722 khmer/_khmermodule.cc:2775:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,723 2775 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2021-07-09T21:59:50,723 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,723 | PyLong_AsVoidPtr 2021-07-09T21:59:50,730 khmer/_khmermodule.cc:2781:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,730 2781 | return PyInt_FromLong(p); 2021-07-09T21:59:50,731 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,731 | PyLong_FromLong 2021-07-09T21:59:50,743 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2021-07-09T21:59:50,743 khmer/_khmermodule.cc:2896:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,744 2896 | return PyInt_FromLong(n_partitions); 2021-07-09T21:59:50,744 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,744 | PyLong_FromLong 2021-07-09T21:59:50,752 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2021-07-09T21:59:50,752 khmer/_khmermodule.cc:2927:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,753 2927 | return PyInt_FromLong(n_singletons); 2021-07-09T21:59:50,753 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,753 | PyLong_FromLong 2021-07-09T21:59:50,767 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2021-07-09T21:59:50,767 khmer/_khmermodule.cc:3026:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,768 3026 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:59:50,768 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,768 | PyLong_AsVoidPtr 2021-07-09T21:59:50,779 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2021-07-09T21:59:50,780 khmer/_khmermodule.cc:3043:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,780 3043 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:59:50,780 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,780 | PyLong_AsVoidPtr 2021-07-09T21:59:50,815 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T21:59:50,816 khmer/_khmermodule.cc:3154:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,816 3154 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:59:50,816 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,816 | PyLong_AsVoidPtr 2021-07-09T21:59:50,828 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T21:59:50,829 khmer/_khmermodule.cc:3185:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T21:59:50,829 3185 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T21:59:50,829 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,829 | PyLong_FromVoidPtr 2021-07-09T21:59:50,837 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2021-07-09T21:59:50,838 khmer/_khmermodule.cc:3214:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,838 3214 | return PyInt_FromLong(d); 2021-07-09T21:59:50,838 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,838 | PyLong_FromLong 2021-07-09T21:59:50,850 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2021-07-09T21:59:50,850 khmer/_khmermodule.cc:3230:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,850 3230 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T21:59:50,850 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,850 | PyLong_AsVoidPtr 2021-07-09T21:59:50,862 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2021-07-09T21:59:50,862 khmer/_khmermodule.cc:3256:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,862 3256 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2021-07-09T21:59:50,863 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,863 | PyLong_AsVoidPtr 2021-07-09T21:59:50,875 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T21:59:50,875 khmer/_khmermodule.cc:3277:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T21:59:50,875 3277 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T21:59:50,875 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,875 | PyLong_AsVoidPtr 2021-07-09T21:59:50,884 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2021-07-09T21:59:50,884 khmer/_khmermodule.cc:3313:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,884 3313 | return PyInt_FromLong(p1); 2021-07-09T21:59:50,884 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,885 | PyLong_FromLong 2021-07-09T21:59:50,892 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2021-07-09T21:59:50,893 khmer/_khmermodule.cc:3330:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,893 3330 | return PyInt_FromLong(partition_id); 2021-07-09T21:59:50,893 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,893 | PyLong_FromLong 2021-07-09T21:59:50,905 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2021-07-09T21:59:50,906 khmer/_khmermodule.cc:3472:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T21:59:50,906 3472 | return PyInt_FromLong(k); 2021-07-09T21:59:50,906 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:50,906 | PyLong_FromLong 2021-07-09T21:59:50,927 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T21:59:50,928 from /usr/include/python3.9/Python.h:106, 2021-07-09T21:59:50,928 from khmer/_khmermodule.cc:13: 2021-07-09T21:59:50,928 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2021-07-09T21:59:50,928 khmer/_khmermodule.cc:3516:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:59:50,928 3516 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2021-07-09T21:59:50,928 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:50,928 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T21:59:50,929 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T21:59:50,929 | ^ 2021-07-09T21:59:50,941 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2021-07-09T21:59:50,941 khmer/_khmermodule.cc:3623:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:59:50,941 3623 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2021-07-09T21:59:50,942 | ^~~~~~~~~~~~~ 2021-07-09T21:59:50,942 | PyCMethod 2021-07-09T21:59:50,948 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_new(PyTypeObject*, PyObject*, PyObject*)’: 2021-07-09T21:59:50,948 khmer/_khmermodule.cc:3648:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:59:50,949 3648 | if (PyInt_Check(size_o)) { 2021-07-09T21:59:50,949 | ^~~~~~~~~~~ 2021-07-09T21:59:50,949 | PySet_Check 2021-07-09T21:59:50,955 khmer/_khmermodule.cc:3649:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:59:50,956 3649 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:59:50,956 | ^~~~~~~~~~~~ 2021-07-09T21:59:50,956 | PyLong_AsLong 2021-07-09T21:59:50,996 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2021-07-09T21:59:50,996 khmer/_khmermodule.cc:3859:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:59:50,996 3859 | return Py_FindMethod(khmer_subset_methods, obj, name); 2021-07-09T21:59:50,996 | ^~~~~~~~~~~~~ 2021-07-09T21:59:50,996 | PyCMethod 2021-07-09T21:59:51,003 khmer/_khmermodule.cc: In function ‘PyObject* khmer_labelhash_new(PyTypeObject*, PyObject*, PyObject*)’: 2021-07-09T21:59:51,003 khmer/_khmermodule.cc:3915:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:59:51,004 3915 | if (PyInt_Check(size_o)) { 2021-07-09T21:59:51,004 | ^~~~~~~~~~~ 2021-07-09T21:59:51,004 | PySet_Check 2021-07-09T21:59:51,010 khmer/_khmermodule.cc:3916:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:59:51,011 3916 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:59:51,011 | ^~~~~~~~~~~~ 2021-07-09T21:59:51,011 | PyLong_AsLong 2021-07-09T21:59:51,039 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2021-07-09T21:59:51,039 khmer/_khmermodule.cc:4221:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T21:59:51,039 4221 | return PyInt_FromSize_t(labelhash->n_labels()); 2021-07-09T21:59:51,039 | ^~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,040 | PyLong_FromSize_t 2021-07-09T21:59:51,040 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:59:51,040 khmer/_khmermodule.cc:4240:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:51,040 4240 | "_LabelHash", /* tp_name */ 2021-07-09T21:59:51,040 | ^~~~~~~~~~~~ 2021-07-09T21:59:51,041 | | 2021-07-09T21:59:51,041 | const char* 2021-07-09T21:59:51,041 khmer/_khmermodule.cc:4243:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:51,041 4243 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2021-07-09T21:59:51,041 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,041 | | 2021-07-09T21:59:51,042 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:59:51,042 khmer/_khmermodule.cc:4258:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:59:51,042 4258 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2021-07-09T21:59:51,042 khmer/_khmermodule.cc:4266:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2021-07-09T21:59:51,042 4266 | khmer_labelhash_methods, /* tp_methods */ 2021-07-09T21:59:51,042 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,042 | | 2021-07-09T21:59:51,043 | PyMethodDef* 2021-07-09T21:59:51,055 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2021-07-09T21:59:51,056 khmer/_khmermodule.cc:4349:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T21:59:51,056 4349 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2021-07-09T21:59:51,056 | ^~~~~~~~~~~~~ 2021-07-09T21:59:51,056 | PyCMethod 2021-07-09T21:59:51,056 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:59:51,056 khmer/_khmermodule.cc:4367:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:51,057 4367 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2021-07-09T21:59:51,057 | ^~~~~~~~~~~~~ 2021-07-09T21:59:51,057 | | 2021-07-09T21:59:51,057 | const char* 2021-07-09T21:59:51,057 khmer/_khmermodule.cc:4369:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T21:59:51,057 4369 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2021-07-09T21:59:51,057 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,058 | | 2021-07-09T21:59:51,058 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T21:59:51,058 khmer/_khmermodule.cc:4371:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T21:59:51,058 4371 | khmer_readaligner_getattr, /*tp_getattr*/ 2021-07-09T21:59:51,058 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,058 | | 2021-07-09T21:59:51,059 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T21:59:51,059 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T21:59:51,059 from /usr/include/python3.9/Python.h:85, 2021-07-09T21:59:51,059 from khmer/_khmermodule.cc:13: 2021-07-09T21:59:51,059 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T21:59:51,059 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T21:59:51,060 | ~~~ 2021-07-09T21:59:51,060 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T21:59:51,060 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,060 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T21:59:51,060 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T21:59:51,060 | | 2021-07-09T21:59:51,060 | long unsigned int 2021-07-09T21:59:51,060 353 | 0) 2021-07-09T21:59:51,061 | ~~ 2021-07-09T21:59:51,061 khmer/_khmermodule.cc:4384:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T21:59:51,061 4384 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T21:59:51,061 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,061 khmer/_khmermodule.cc:4385:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T21:59:51,061 4385 | "ReadAligner object", /* tp_doc */ 2021-07-09T21:59:51,061 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,061 | | 2021-07-09T21:59:51,062 | const char* 2021-07-09T21:59:51,065 khmer/_khmermodule.cc: In function ‘PyObject* _new_hashbits(PyObject*, PyObject*)’: 2021-07-09T21:59:51,065 khmer/_khmermodule.cc:4445:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T21:59:51,066 4445 | if (PyInt_Check(size_o)) { 2021-07-09T21:59:51,066 | ^~~~~~~~~~~ 2021-07-09T21:59:51,066 | PySet_Check 2021-07-09T21:59:51,072 khmer/_khmermodule.cc:4446:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T21:59:51,073 4446 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T21:59:51,073 | ^~~~~~~~~~~~ 2021-07-09T21:59:51,073 | PyLong_AsLong 2021-07-09T21:59:51,078 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2021-07-09T21:59:51,079 khmer/_khmermodule.cc:4536:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2021-07-09T21:59:51,079 4536 | self->ob_type->tp_free((PyObject*)obj); 2021-07-09T21:59:51,079 | ^~~~~~~ 2021-07-09T21:59:51,090 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2021-07-09T21:59:51,090 khmer/_khmermodule.cc:4611:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T21:59:51,090 4611 | return PyString_FromString(_revhash(val, ksize).c_str()); 2021-07-09T21:59:51,091 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,091 | PyLong_FromString 2021-07-09T21:59:51,091 khmer/_khmermodule.cc: At global scope: 2021-07-09T21:59:51,092 khmer/_khmermodule.cc:4687:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2021-07-09T21:59:51,092 4687 | init_khmer(void) 2021-07-09T21:59:51,092 | ^~~~~~~~~~ 2021-07-09T21:59:51,092 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2021-07-09T21:59:51,092 33 | void init_khmer(); 2021-07-09T21:59:51,092 | ^~~~~~~~~~ 2021-07-09T21:59:51,092 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2021-07-09T21:59:51,093 khmer/_khmermodule.cc:4691:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T21:59:51,093 4691 | khmer_ConfigType.ob_type = &PyType_Type; 2021-07-09T21:59:51,093 | ^~~~~~~ 2021-07-09T21:59:51,093 khmer/_khmermodule.cc:4692:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T21:59:51,093 4692 | khmer_KCountingHashType.ob_type = &PyType_Type; 2021-07-09T21:59:51,094 | ^~~~~~~ 2021-07-09T21:59:51,094 khmer/_khmermodule.cc:4699:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:59:51,094 4699 | return; 2021-07-09T21:59:51,094 | ^~~~~~ 2021-07-09T21:59:51,094 khmer/_khmermodule.cc:4706:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:59:51,094 4706 | return; 2021-07-09T21:59:51,094 | ^~~~~~ 2021-07-09T21:59:51,103 khmer/_khmermodule.cc:4710:9: error: ‘Py_InitModule3’ was not declared in this scope 2021-07-09T21:59:51,103 4710 | m = Py_InitModule3( "_khmer", KhmerMethods, 2021-07-09T21:59:51,103 | ^~~~~~~~~~~~~~ 2021-07-09T21:59:51,104 khmer/_khmermodule.cc:4713:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:59:51,104 4713 | return; 2021-07-09T21:59:51,104 | ^~~~~~ 2021-07-09T21:59:51,104 khmer/_khmermodule.cc:4718:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:59:51,104 4718 | return; 2021-07-09T21:59:51,104 | ^~~~~~ 2021-07-09T21:59:51,104 khmer/_khmermodule.cc:4725:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:59:51,105 4725 | return; 2021-07-09T21:59:51,105 | ^~~~~~ 2021-07-09T21:59:51,105 khmer/_khmermodule.cc:4731:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:59:51,105 4731 | return; 2021-07-09T21:59:51,105 | ^~~~~~ 2021-07-09T21:59:51,105 khmer/_khmermodule.cc:4734:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T21:59:51,105 4734 | return; 2021-07-09T21:59:51,106 | ^~~~~~ 2021-07-09T21:59:51,866 khmer/_khmermodule.cc:4744:23: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-09T21:59:51,866 4744 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2021-07-09T21:59:51,867 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T21:59:51,958 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T21:59:52,045 Building wheel for khmer (setup.py): finished with status 'error' 2021-07-09T21:59:52,046 ERROR: Failed building wheel for khmer 2021-07-09T21:59:52,046 Running setup.py clean for khmer 2021-07-09T21:59:52,047 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-nftul14k/khmer_93aec4e399be460e9caf672d72e90142/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-nftul14k/khmer_93aec4e399be460e9caf672d72e90142/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2021-07-09T21:59:52,958 /usr/local/lib/python3.9/dist-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead 2021-07-09T21:59:52,958 warnings.warn( 2021-07-09T21:59:52,989 running clean 2021-07-09T21:59:52,990 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T21:59:52,993 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T21:59:52,997 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T21:59:52,997 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T21:59:52,998 removing 'build' 2021-07-09T21:59:53,068 Failed to build khmer 2021-07-09T21:59:53,068 ERROR: Failed to build one or more wheels 2021-07-09T21:59:53,069 Exception information: 2021-07-09T21:59:53,069 Traceback (most recent call last): 2021-07-09T21:59:53,069 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T21:59:53,069 status = self.run(options, args) 2021-07-09T21:59:53,069 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T21:59:53,069 return func(self, options, args) 2021-07-09T21:59:53,069 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T21:59:53,069 raise CommandError( 2021-07-09T21:59:53,069 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T21:59:53,071 Removed build tracker: '/tmp/pip-req-tracker-le42eis8'