2021-07-09T22:25:02,754 Created temporary directory: /tmp/pip-ephem-wheel-cache-0f4s_re2 2021-07-09T22:25:02,759 Created temporary directory: /tmp/pip-req-tracker-pc_b39nf 2021-07-09T22:25:02,760 Initialized build tracking at /tmp/pip-req-tracker-pc_b39nf 2021-07-09T22:25:02,760 Created build tracker: /tmp/pip-req-tracker-pc_b39nf 2021-07-09T22:25:02,760 Entered build tracker: /tmp/pip-req-tracker-pc_b39nf 2021-07-09T22:25:02,761 Created temporary directory: /tmp/pip-wheel-dou8b6jh 2021-07-09T22:25:02,794 1 location(s) to search for versions of khmer: 2021-07-09T22:25:02,794 * https://pypi.org/simple/khmer/ 2021-07-09T22:25:02,794 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2021-07-09T22:25:02,795 Getting page https://pypi.org/simple/khmer/ 2021-07-09T22:25:02,796 Found index url https://pypi.org/simple 2021-07-09T22:25:02,901 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/) 2021-07-09T22:25:02,902 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/) 2021-07-09T22:25:02,902 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 2021-07-09T22:25:02,902 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 2021-07-09T22:25:02,918 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/) 2021-07-09T22:25:02,919 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 2021-07-09T22:25:02,919 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/) 2021-07-09T22:25:02,919 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 2021-07-09T22:25:02,920 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/) 2021-07-09T22:25:02,920 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 2021-07-09T22:25:02,921 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/) 2021-07-09T22:25:02,921 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 2021-07-09T22:25:02,922 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/) 2021-07-09T22:25:02,922 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 2021-07-09T22:25:02,922 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 2021-07-09T22:25:02,923 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/) 2021-07-09T22:25:02,923 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 2021-07-09T22:25:02,923 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/) 2021-07-09T22:25:02,924 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 2021-07-09T22:25:02,924 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/) 2021-07-09T22:25:02,924 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 2021-07-09T22:25:02,925 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/) 2021-07-09T22:25:02,925 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/) 2021-07-09T22:25:02,926 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 2021-07-09T22:25:02,926 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/) 2021-07-09T22:25:02,927 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/) 2021-07-09T22:25:02,927 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/) 2021-07-09T22:25:02,927 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/) 2021-07-09T22:25:02,928 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 2021-07-09T22:25:02,928 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 2021-07-09T22:25:02,928 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/) 2021-07-09T22:25:02,929 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 2021-07-09T22:25:02,929 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/) 2021-07-09T22:25:02,930 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/) 2021-07-09T22:25:02,930 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/) 2021-07-09T22:25:02,931 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/) 2021-07-09T22:25:02,931 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/) 2021-07-09T22:25:02,931 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 2021-07-09T22:25:02,932 Skipping link: not a file: https://pypi.org/simple/khmer/ 2021-07-09T22:25:02,935 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2021-07-09T22:25:02,952 Collecting khmer==1.1 2021-07-09T22:25:02,953 Created temporary directory: /tmp/pip-unpack-rarn_5_r 2021-07-09T22:25:04,351 Downloading khmer-1.1.tar.gz (3.6 MB) 2021-07-09T22:25:06,085 Added khmer==1.1 from https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz#sha256=05f5cf4a8f634c3c2f77a2e65fcc5dfa7887d4cf12c519af141a13ae84c9dd1d to build tracker '/tmp/pip-req-tracker-pc_b39nf' 2021-07-09T22:25:06,086 Running setup.py (path:/tmp/pip-wheel-dou8b6jh/khmer_0e645919b6ef483c9a48ab457c731fc2/setup.py) egg_info for package khmer 2021-07-09T22:25:06,087 Created temporary directory: /tmp/pip-pip-egg-info-axy0njox 2021-07-09T22:25:06,087 Running command python setup.py egg_info 2021-07-09T22:25:07,046 /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 2021-07-09T22:25:07,047 warnings.warn( 2021-07-09T22:25:07,083 running egg_info 2021-07-09T22:25:07,085 creating /tmp/pip-pip-egg-info-axy0njox/khmer.egg-info 2021-07-09T22:25:07,086 writing /tmp/pip-pip-egg-info-axy0njox/khmer.egg-info/PKG-INFO 2021-07-09T22:25:07,089 writing dependency_links to /tmp/pip-pip-egg-info-axy0njox/khmer.egg-info/dependency_links.txt 2021-07-09T22:25:07,091 writing requirements to /tmp/pip-pip-egg-info-axy0njox/khmer.egg-info/requires.txt 2021-07-09T22:25:07,092 writing top-level names to /tmp/pip-pip-egg-info-axy0njox/khmer.egg-info/top_level.txt 2021-07-09T22:25:07,094 writing manifest file '/tmp/pip-pip-egg-info-axy0njox/khmer.egg-info/SOURCES.txt' 2021-07-09T22:25:07,246 reading manifest file '/tmp/pip-pip-egg-info-axy0njox/khmer.egg-info/SOURCES.txt' 2021-07-09T22:25:07,247 reading manifest template 'MANIFEST.in' 2021-07-09T22:25:09,144 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2021-07-09T22:25:09,145 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2021-07-09T22:25:09,174 warning: no previously-included files matching '*.orig' found anywhere in distribution 2021-07-09T22:25:09,176 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-09T22:25:09,176 adding license file 'LICENSE' 2021-07-09T22:25:09,192 writing manifest file '/tmp/pip-pip-egg-info-axy0njox/khmer.egg-info/SOURCES.txt' 2021-07-09T22:25:09,269 Source in /tmp/pip-wheel-dou8b6jh/khmer_0e645919b6ef483c9a48ab457c731fc2 has version 1.1, which satisfies requirement khmer==1.1 from https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz#sha256=05f5cf4a8f634c3c2f77a2e65fcc5dfa7887d4cf12c519af141a13ae84c9dd1d 2021-07-09T22:25:09,270 Removed khmer==1.1 from https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz#sha256=05f5cf4a8f634c3c2f77a2e65fcc5dfa7887d4cf12c519af141a13ae84c9dd1d from build tracker '/tmp/pip-req-tracker-pc_b39nf' 2021-07-09T22:25:09,275 Created temporary directory: /tmp/pip-unpack-8ki_1qqz 2021-07-09T22:25:09,275 Building wheels for collected packages: khmer 2021-07-09T22:25:09,280 Created temporary directory: /tmp/pip-wheel-eoy2aph9 2021-07-09T22:25:09,280 Building wheel for khmer (setup.py): started 2021-07-09T22:25:09,280 Destination directory: /tmp/pip-wheel-eoy2aph9 2021-07-09T22:25:09,281 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-dou8b6jh/khmer_0e645919b6ef483c9a48ab457c731fc2/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-dou8b6jh/khmer_0e645919b6ef483c9a48ab457c731fc2/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-eoy2aph9 2021-07-09T22:25:10,454 /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 2021-07-09T22:25:10,454 warnings.warn( 2021-07-09T22:25:10,502 running bdist_wheel 2021-07-09T22:25:10,505 running build 2021-07-09T22:25:10,506 got version from file /tmp/pip-wheel-dou8b6jh/khmer_0e645919b6ef483c9a48ab457c731fc2/khmer/_version.py {'version': '1.1', 'full': '1fe98c92b5a9b3f46a5f4f05cd35d3229ce2ff0a'} 2021-07-09T22:25:10,507 running build_py 2021-07-09T22:25:10,647 creating build 2021-07-09T22:25:10,647 creating build/lib.linux-armv7l-3.9 2021-07-09T22:25:10,648 creating build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,649 copying khmer/load_pe.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,651 copying khmer/__init__.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,653 copying khmer/thread_utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,655 copying khmer/file.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,658 copying khmer/khmer_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,660 copying khmer/threading_args.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,662 copying khmer/utils.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,664 copying khmer/_version.py -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:10,667 creating build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,668 copying tests/khmer_tst_utils.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,670 copying tests/test_threaded_sequence_processor.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,672 copying tests/__init__.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,674 copying tests/test_read_parsers.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,676 copying tests/test_hashbits_obj.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,679 copying tests/test_functions.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,681 copying tests/test_labelhash.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,684 copying tests/test_c_wrapper.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,686 copying tests/test_script_arguments.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,688 copying tests/test_align.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,691 copying tests/test_sandbox_scripts.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,693 copying tests/test_counting_single.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,696 copying tests/test_counting_hash.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,699 copying tests/test_filter.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,701 copying tests/test_khmer_config.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,703 copying tests/test_hashbits.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,707 copying tests/test_subset_graph.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,710 copying tests/test_lump.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,713 copying tests/test_scripts.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,717 copying tests/test_graph.py -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:10,719 running egg_info 2021-07-09T22:25:10,731 creating khmer.egg-info 2021-07-09T22:25:10,731 writing khmer.egg-info/PKG-INFO 2021-07-09T22:25:10,734 writing dependency_links to khmer.egg-info/dependency_links.txt 2021-07-09T22:25:10,737 writing requirements to khmer.egg-info/requires.txt 2021-07-09T22:25:10,738 writing top-level names to khmer.egg-info/top_level.txt 2021-07-09T22:25:10,739 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T22:25:10,749 reading manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T22:25:10,751 reading manifest template 'MANIFEST.in' 2021-07-09T22:25:12,514 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2021-07-09T22:25:12,515 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2021-07-09T22:25:12,541 warning: no previously-included files matching '*.orig' found anywhere in distribution 2021-07-09T22:25:12,543 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2021-07-09T22:25:12,543 adding license file 'LICENSE' 2021-07-09T22:25:12,558 writing manifest file 'khmer.egg-info/SOURCES.txt' 2021-07-09T22:25:12,576 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-3.9/khmer 2021-07-09T22:25:12,583 copying tests/.gitignore -> build/lib.linux-armv7l-3.9/khmer/tests 2021-07-09T22:25:12,586 creating build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,587 copying tests/test-data/100-reads.fq.bz2 -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,590 copying tests/test-data/100-reads.fq.gz -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,593 copying tests/test-data/all-A.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,595 copying tests/test-data/badversion-k12.ht -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,597 copying tests/test-data/badversion-k12.kh -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,600 copying tests/test-data/badversion-k32.stoptags -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,602 copying tests/test-data/badversion-k32.tagset -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,604 copying tests/test-data/biglump-random-20-a.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,607 copying tests/test-data/combine_parts_1.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,609 copying tests/test-data/empty-file -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,611 copying tests/test-data/fakelump.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,614 copying tests/test-data/fakelump.fa.stoptags.txt -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,617 copying tests/test-data/filter-test-A.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,619 copying tests/test-data/filter-test-B.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,622 copying tests/test-data/goodversion-k12.ht -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,624 copying tests/test-data/goodversion-k12.ht.gz -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,626 copying tests/test-data/goodversion-k32.stoptags -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,628 copying tests/test-data/goodversion-k32.tagset -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,630 copying tests/test-data/overlap.curve -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,633 copying tests/test-data/overlap.out -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,635 copying tests/test-data/paired-mixed.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,637 copying tests/test-data/paired-mixed.fa.pe -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,640 copying tests/test-data/paired-mixed.fa.se -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,642 copying tests/test-data/paired-mixed.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,644 copying tests/test-data/paired-mixed.fq.pe -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,646 copying tests/test-data/paired-mixed.fq.se -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,649 copying tests/test-data/paired.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,651 copying tests/test-data/paired.fa.1 -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,653 copying tests/test-data/paired.fa.2 -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,655 copying tests/test-data/paired.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,657 copying tests/test-data/paired.fq.1 -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,660 copying tests/test-data/paired.fq.2 -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,662 copying tests/test-data/random-20-X2.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,666 copying tests/test-data/random-20-a.even.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,668 copying tests/test-data/random-20-a.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,671 copying tests/test-data/random-20-a.fa.part -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,674 copying tests/test-data/random-20-a.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,677 copying tests/test-data/random-20-a.odd.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,680 copying tests/test-data/random-20-b.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,683 copying tests/test-data/random-31-c.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,692 copying tests/test-data/real-partition-small.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,695 copying tests/test-data/real-partition-tiny.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,697 copying tests/test-data/simple_1.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,700 copying tests/test-data/simple_2.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,702 copying tests/test-data/simple_3.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,704 copying tests/test-data/single-read.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,706 copying tests/test-data/test-abund-read-2.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,710 copying tests/test-data/test-abund-read-2.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,714 copying tests/test-data/test-abund-read-3.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,716 copying tests/test-data/test-abund-read-impaired.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,718 copying tests/test-data/test-abund-read-paired.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,721 copying tests/test-data/test-abund-read.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,723 copying tests/test-data/test-colors.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,725 copying tests/test-data/test-empty.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,727 copying tests/test-data/test-empty.fa.bz2 -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,729 copying tests/test-data/test-error-reads.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,732 copying tests/test-data/test-est.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,734 copying tests/test-data/test-fastq-n-reads.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,737 copying tests/test-data/test-fastq-reads.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,741 copying tests/test-data/test-graph.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,743 copying tests/test-data/test-graph2.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,745 copying tests/test-data/test-graph3.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,747 copying tests/test-data/test-graph4.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,749 copying tests/test-data/test-graph5.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,751 copying tests/test-data/test-graph6.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,754 copying tests/test-data/test-labels.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,757 copying tests/test-data/test-output-partitions.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,759 copying tests/test-data/test-overlap1.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,791 copying tests/test-data/test-overlap2.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,829 copying tests/test-data/test-reads.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,884 copying tests/test-data/test-reads.fq.bz2 -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,899 copying tests/test-data/test-short.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,901 copying tests/test-data/test-sweep-contigs.fp -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,903 copying tests/test-data/test-sweep-reads.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,905 copying tests/test-data/test-sweep-reads.fq -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,907 copying tests/test-data/test-transcript.fa -> build/lib.linux-armv7l-3.9/khmer/tests/test-data 2021-07-09T22:25:12,912 running build_ext 2021-07-09T22:25:12,912 bash -c cd third-party/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC 2021-07-09T22:25:13,080 Checking for gcc... 2021-07-09T22:25:13,378 Building static library libz.a version 1.2.8 with gcc. 2021-07-09T22:25:13,507 Checking for off64_t... Yes. 2021-07-09T22:25:13,515 Checking for fseeko... Yes. 2021-07-09T22:25:13,746 Checking for strerror... Yes. 2021-07-09T22:25:13,930 Checking for unistd.h... Yes. 2021-07-09T22:25:14,074 Checking for stdarg.h... Yes. 2021-07-09T22:25:14,244 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). 2021-07-09T22:25:14,483 Checking for vsnprintf() in stdio.h... Yes. 2021-07-09T22:25:14,624 Checking for return value of vsnprintf()... Yes. 2021-07-09T22:25:14,740 Checking for attribute(visibility) support... Yes. 2021-07-09T22:25:14,845 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c 2021-07-09T22:25:15,178 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c 2021-07-09T22:25:15,583 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c 2021-07-09T22:25:17,339 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c 2021-07-09T22:25:18,107 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c 2021-07-09T22:25:18,551 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c 2021-07-09T22:25:20,249 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c 2021-07-09T22:25:20,746 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c 2021-07-09T22:25:21,986 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c 2021-07-09T22:25:22,186 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c 2021-07-09T22:25:22,355 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c 2021-07-09T22:25:22,511 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c 2021-07-09T22:25:22,699 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c 2021-07-09T22:25:23,138 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c 2021-07-09T22:25:23,668 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c 2021-07-09T22:25:24,194 bash -c cd third-party/bzip2 && make -f Makefile-libbz2_so all 2021-07-09T22:25:24,219 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2021-07-09T22:25:24,961 blocksort.c: In function ‘mainSort’: 2021-07-09T22:25:24,962 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T22:25:24,962 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T22:25:24,962 | ^~~~~~~ 2021-07-09T22:25:24,962 blocksort.c:514:18: note: called from here 2021-07-09T22:25:24,962 514 | while ( mainGtU ( 2021-07-09T22:25:24,962 | ^~~~~~~~~ 2021-07-09T22:25:24,962 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T22:25:24,962 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:24,963 516 | ) ) { 2021-07-09T22:25:24,963 | ~ 2021-07-09T22:25:24,963 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T22:25:24,963 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T22:25:24,963 | ^~~~~~~ 2021-07-09T22:25:24,963 blocksort.c:528:18: note: called from here 2021-07-09T22:25:24,963 528 | while ( mainGtU ( 2021-07-09T22:25:24,964 | ^~~~~~~~~ 2021-07-09T22:25:24,964 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T22:25:24,964 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:24,964 530 | ) ) { 2021-07-09T22:25:24,964 | ~ 2021-07-09T22:25:24,964 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2021-07-09T22:25:24,964 347 | Bool mainGtU ( UInt32 i1, 2021-07-09T22:25:24,965 | ^~~~~~~ 2021-07-09T22:25:24,965 blocksort.c:542:18: note: called from here 2021-07-09T22:25:24,965 542 | while ( mainGtU ( 2021-07-09T22:25:24,965 | ^~~~~~~~~ 2021-07-09T22:25:24,965 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2021-07-09T22:25:24,965 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:24,965 544 | ) ) { 2021-07-09T22:25:24,965 | ~ 2021-07-09T22:25:25,646 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2021-07-09T22:25:26,051 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2021-07-09T22:25:26,179 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2021-07-09T22:25:26,308 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2021-07-09T22:25:30,153 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2021-07-09T22:25:32,387 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2021-07-09T22:25:34,020 #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 2021-07-09T22:25:34,022 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2021-07-09T22:25:34,025 #rm -f libbz2.so.1.0 2021-07-09T22:25:34,028 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2021-07-09T22:25:34,037 building 'khmer._khmermodule' extension 2021-07-09T22:25:34,038 creating build/temp.linux-armv7l-3.9 2021-07-09T22:25:34,039 creating build/temp.linux-armv7l-3.9/khmer 2021-07-09T22:25:34,040 creating build/temp.linux-armv7l-3.9/lib 2021-07-09T22:25:34,041 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=1.1 -UNO_UNIQUE_RC -Ilib -Ithird-party/zlib -Ithird-party/bzip2 -I/usr/include/python3.9 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-3.9/khmer/_khmermodule.o -O3 2021-07-09T22:25:36,309 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2021-07-09T22:25:36,309 khmer/_khmermodule.cc:79:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2021-07-09T22:25:36,310 79 | tobj.ob_size = 0; 2021-07-09T22:25:36,310 | ^~~~~~~ 2021-07-09T22:25:36,310 khmer/_khmermodule.cc:80:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T22:25:36,310 80 | tobj.ob_type = &PyType_Type; 2021-07-09T22:25:36,310 | ^~~~~~~ 2021-07-09T22:25:36,314 khmer/_khmermodule.cc: At global scope: 2021-07-09T22:25:36,315 khmer/_khmermodule.cc:200:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,315 200 | "Config", sizeof(khmer_ConfigObject), 2021-07-09T22:25:36,315 | ^~~~~~~~ 2021-07-09T22:25:36,315 | | 2021-07-09T22:25:36,315 | const char* 2021-07-09T22:25:36,316 khmer/_khmermodule.cc:202:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,316 202 | khmer_config_dealloc, /*tp_dealloc*/ 2021-07-09T22:25:36,316 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,316 | | 2021-07-09T22:25:36,316 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T22:25:36,316 khmer/_khmermodule.cc:204:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T22:25:36,317 204 | khmer_config_getattr, /*tp_getattr*/ 2021-07-09T22:25:36,317 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,317 | | 2021-07-09T22:25:36,317 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T22:25:36,317 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T22:25:36,318 from /usr/include/python3.9/Python.h:85, 2021-07-09T22:25:36,318 from khmer/_khmermodule.cc:13: 2021-07-09T22:25:36,318 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T22:25:36,318 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T22:25:36,318 | ~~~ 2021-07-09T22:25:36,318 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T22:25:36,318 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,318 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T22:25:36,318 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T22:25:36,319 | | 2021-07-09T22:25:36,319 | long unsigned int 2021-07-09T22:25:36,319 353 | 0) 2021-07-09T22:25:36,319 | ~~ 2021-07-09T22:25:36,319 khmer/_khmermodule.cc:217:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T22:25:36,319 217 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T22:25:36,319 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,319 khmer/_khmermodule.cc:218:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T22:25:36,320 218 | "config object", /* tp_doc */ 2021-07-09T22:25:36,320 | ^~~~~~~~~~~~~~~ 2021-07-09T22:25:36,320 | | 2021-07-09T22:25:36,320 | const char* 2021-07-09T22:25:36,325 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2021-07-09T22:25:36,326 khmer/_khmermodule.cc:306:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T22:25:36,326 306 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2021-07-09T22:25:36,326 | ^~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,326 | PyLong_FromSize_t 2021-07-09T22:25:36,335 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2021-07-09T22:25:36,335 khmer/_khmermodule.cc:364:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T22:25:36,336 364 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2021-07-09T22:25:36,336 | ^~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,336 | PyLong_FromSize_t 2021-07-09T22:25:36,344 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2021-07-09T22:25:36,345 khmer/_khmermodule.cc:393:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T22:25:36,345 393 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2021-07-09T22:25:36,345 | ^~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,345 | PyLong_FromSize_t 2021-07-09T22:25:36,355 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2021-07-09T22:25:36,355 khmer/_khmermodule.cc:460:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T22:25:36,355 460 | return Py_FindMethod(khmer_config_methods, obj, name); 2021-07-09T22:25:36,355 | ^~~~~~~~~~~~~ 2021-07-09T22:25:36,356 | PyCMethod 2021-07-09T22:25:36,365 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2021-07-09T22:25:36,365 khmer/_khmermodule.cc:498:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T22:25:36,366 498 | PyString_FromString( \ 2021-07-09T22:25:36,366 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,366 khmer/_khmermodule.cc:507:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T22:25:36,366 507 | return KHMER_READ_STRING_GETTER( self, name ); 2021-07-09T22:25:36,366 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,375 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2021-07-09T22:25:36,375 khmer/_khmermodule.cc:498:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T22:25:36,375 498 | PyString_FromString( \ 2021-07-09T22:25:36,376 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,376 khmer/_khmermodule.cc:515:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T22:25:36,376 515 | return KHMER_READ_STRING_GETTER( self, sequence ); 2021-07-09T22:25:36,376 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,384 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2021-07-09T22:25:36,385 khmer/_khmermodule.cc:498:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T22:25:36,385 498 | PyString_FromString( \ 2021-07-09T22:25:36,385 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,385 khmer/_khmermodule.cc:523:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T22:25:36,385 523 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2021-07-09T22:25:36,386 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,394 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2021-07-09T22:25:36,394 khmer/_khmermodule.cc:498:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T22:25:36,394 498 | PyString_FromString( \ 2021-07-09T22:25:36,395 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,395 khmer/_khmermodule.cc:531:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2021-07-09T22:25:36,395 531 | return KHMER_READ_STRING_GETTER( self, annotations ); 2021-07-09T22:25:36,395 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,419 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2021-07-09T22:25:36,419 khmer/_khmermodule.cc:871:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,419 871 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2021-07-09T22:25:36,419 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,420 | PyLong_FromLong 2021-07-09T22:25:36,422 khmer/_khmermodule.cc: At global scope: 2021-07-09T22:25:36,422 khmer/_khmermodule.cc:983:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,422 983 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2021-07-09T22:25:36,422 | ^~~~~~~~~ 2021-07-09T22:25:36,422 | | 2021-07-09T22:25:36,422 | const char* 2021-07-09T22:25:36,423 khmer/_khmermodule.cc:985:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,423 985 | khmer_subset_dealloc, /*tp_dealloc*/ 2021-07-09T22:25:36,423 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,423 | | 2021-07-09T22:25:36,423 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T22:25:36,423 khmer/_khmermodule.cc:987:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T22:25:36,424 987 | khmer_subset_getattr, /*tp_getattr*/ 2021-07-09T22:25:36,424 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,424 | | 2021-07-09T22:25:36,424 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T22:25:36,424 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T22:25:36,424 from /usr/include/python3.9/Python.h:85, 2021-07-09T22:25:36,424 from khmer/_khmermodule.cc:13: 2021-07-09T22:25:36,425 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T22:25:36,425 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T22:25:36,425 | ~~~ 2021-07-09T22:25:36,425 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T22:25:36,425 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,426 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T22:25:36,426 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T22:25:36,426 | | 2021-07-09T22:25:36,426 | long unsigned int 2021-07-09T22:25:36,426 353 | 0) 2021-07-09T22:25:36,426 | ~~ 2021-07-09T22:25:36,426 khmer/_khmermodule.cc:1000:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T22:25:36,426 1000 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T22:25:36,426 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,427 khmer/_khmermodule.cc:1001:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T22:25:36,427 1001 | "subset object", /* tp_doc */ 2021-07-09T22:25:36,427 | ^~~~~~~~~~~~~~~ 2021-07-09T22:25:36,427 | | 2021-07-09T22:25:36,427 | const char* 2021-07-09T22:25:36,432 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2021-07-09T22:25:36,433 khmer/_khmermodule.cc:1099:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,433 1099 | return PyInt_FromLong(1); 2021-07-09T22:25:36,433 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,433 | PyLong_FromLong 2021-07-09T22:25:36,441 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2021-07-09T22:25:36,441 khmer/_khmermodule.cc:1116:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,441 1116 | return PyInt_FromLong(0); 2021-07-09T22:25:36,442 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,442 | PyLong_FromLong 2021-07-09T22:25:36,452 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2021-07-09T22:25:36,452 khmer/_khmermodule.cc:1214:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,452 1214 | return PyInt_FromLong(n_consumed); 2021-07-09T22:25:36,452 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,453 | PyLong_FromLong 2021-07-09T22:25:36,461 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2021-07-09T22:25:36,461 khmer/_khmermodule.cc:1246:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,461 1246 | return PyInt_FromLong(n_consumed); 2021-07-09T22:25:36,461 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,461 | PyLong_FromLong 2021-07-09T22:25:36,469 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2021-07-09T22:25:36,470 khmer/_khmermodule.cc:1269:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,470 1269 | return PyInt_FromLong(N); 2021-07-09T22:25:36,470 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,470 | PyLong_FromLong 2021-07-09T22:25:36,478 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2021-07-09T22:25:36,478 khmer/_khmermodule.cc:1292:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,478 1292 | return PyInt_FromLong(N); 2021-07-09T22:25:36,478 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,479 | PyLong_FromLong 2021-07-09T22:25:36,486 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2021-07-09T22:25:36,486 khmer/_khmermodule.cc:1358:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T22:25:36,487 1358 | if (PyInt_Check(arg)) { 2021-07-09T22:25:36,487 | ^~~~~~~~~~~ 2021-07-09T22:25:36,487 | PySet_Check 2021-07-09T22:25:36,493 khmer/_khmermodule.cc:1359:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T22:25:36,494 1359 | long pos = PyInt_AsLong(arg); 2021-07-09T22:25:36,494 | ^~~~~~~~~~~~ 2021-07-09T22:25:36,494 | PyLong_AsLong 2021-07-09T22:25:36,501 khmer/_khmermodule.cc:1361:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T22:25:36,502 1361 | } else if (PyString_Check(arg)) { 2021-07-09T22:25:36,502 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,502 | PyMapping_Check 2021-07-09T22:25:36,512 khmer/_khmermodule.cc:1362:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T22:25:36,512 1362 | std::string s = PyString_AsString(arg); 2021-07-09T22:25:36,513 | ^~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,520 khmer/_khmermodule.cc:1366:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,520 1366 | return PyInt_FromLong(count); 2021-07-09T22:25:36,520 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,521 | PyLong_FromLong 2021-07-09T22:25:36,531 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2021-07-09T22:25:36,531 khmer/_khmermodule.cc:1390:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T22:25:36,531 1390 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T22:25:36,531 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,532 | PyBytes_FromStringAndSize 2021-07-09T22:25:36,542 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2021-07-09T22:25:36,542 khmer/_khmermodule.cc:1417:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T22:25:36,542 1417 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T22:25:36,542 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,543 | PyBytes_FromStringAndSize 2021-07-09T22:25:36,556 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2021-07-09T22:25:36,556 khmer/_khmermodule.cc:1577:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,556 1577 | return PyInt_FromLong(k); 2021-07-09T22:25:36,556 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,557 | PyLong_FromLong 2021-07-09T22:25:36,572 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2021-07-09T22:25:36,572 khmer/_khmermodule.cc:1691:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T22:25:36,572 1691 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T22:25:36,572 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,573 | PyLong_FromVoidPtr 2021-07-09T22:25:36,584 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2021-07-09T22:25:36,585 khmer/_khmermodule.cc:1794:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T22:25:36,585 1794 | return Py_FindMethod(khmer_counting_methods, obj, name); 2021-07-09T22:25:36,585 | ^~~~~~~~~~~~~ 2021-07-09T22:25:36,585 | PyCMethod 2021-07-09T22:25:36,585 khmer/_khmermodule.cc: At global scope: 2021-07-09T22:25:36,585 khmer/_khmermodule.cc:1804:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,586 1804 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2021-07-09T22:25:36,586 | ^~~~~~~~~~~~~~~ 2021-07-09T22:25:36,586 | | 2021-07-09T22:25:36,586 | const char* 2021-07-09T22:25:36,586 khmer/_khmermodule.cc:1806:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,586 1806 | khmer_counting_dealloc, /*tp_dealloc*/ 2021-07-09T22:25:36,586 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,587 | | 2021-07-09T22:25:36,587 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T22:25:36,587 khmer/_khmermodule.cc:1808:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T22:25:36,587 1808 | khmer_counting_getattr, /*tp_getattr*/ 2021-07-09T22:25:36,587 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,588 | | 2021-07-09T22:25:36,588 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T22:25:36,588 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T22:25:36,588 from /usr/include/python3.9/Python.h:85, 2021-07-09T22:25:36,588 from khmer/_khmermodule.cc:13: 2021-07-09T22:25:36,588 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T22:25:36,588 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T22:25:36,588 | ~~~ 2021-07-09T22:25:36,589 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T22:25:36,589 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,589 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T22:25:36,589 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T22:25:36,589 | | 2021-07-09T22:25:36,589 | long unsigned int 2021-07-09T22:25:36,589 353 | 0) 2021-07-09T22:25:36,589 | ~~ 2021-07-09T22:25:36,590 khmer/_khmermodule.cc:1821:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T22:25:36,590 1821 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T22:25:36,590 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,590 khmer/_khmermodule.cc:1822:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T22:25:36,590 1822 | "counting hash object", /* tp_doc */ 2021-07-09T22:25:36,590 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,591 | | 2021-07-09T22:25:36,591 | const char* 2021-07-09T22:25:36,593 khmer/_khmermodule.cc: In function ‘PyObject* _new_counting_hash(PyObject*, PyObject*)’: 2021-07-09T22:25:36,594 khmer/_khmermodule.cc:1873:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T22:25:36,594 1873 | if (PyInt_Check(size_o)) { 2021-07-09T22:25:36,594 | ^~~~~~~~~~~ 2021-07-09T22:25:36,594 | PySet_Check 2021-07-09T22:25:36,600 khmer/_khmermodule.cc:1874:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T22:25:36,601 1874 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T22:25:36,601 | ^~~~~~~~~~~~ 2021-07-09T22:25:36,601 | PyLong_AsLong 2021-07-09T22:25:36,602 khmer/_khmermodule.cc: At global scope: 2021-07-09T22:25:36,603 khmer/_khmermodule.cc:1912:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,603 1912 | "Hashbits", sizeof(khmer_KHashbitsObject), 2021-07-09T22:25:36,603 | ^~~~~~~~~~ 2021-07-09T22:25:36,603 | | 2021-07-09T22:25:36,603 | const char* 2021-07-09T22:25:36,603 khmer/_khmermodule.cc:1914:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:36,603 1914 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2021-07-09T22:25:36,604 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,604 | | 2021-07-09T22:25:36,604 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T22:25:36,604 khmer/_khmermodule.cc:1916:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T22:25:36,604 1916 | khmer_hashbits_getattr, /*tp_getattr*/ 2021-07-09T22:25:36,604 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,604 | | 2021-07-09T22:25:36,605 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T22:25:36,605 khmer/_khmermodule.cc:1929:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T22:25:36,605 1929 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2021-07-09T22:25:36,605 khmer/_khmermodule.cc:1930:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T22:25:36,605 1930 | "hashbits object", /* tp_doc */ 2021-07-09T22:25:36,605 | ^~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,606 | | 2021-07-09T22:25:36,606 | const char* 2021-07-09T22:25:36,617 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2021-07-09T22:25:36,618 khmer/_khmermodule.cc:2116:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T22:25:36,618 2116 | return PyInt_FromSize_t(hashbits->n_tags()); 2021-07-09T22:25:36,618 | ^~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,618 | PyLong_FromSize_t 2021-07-09T22:25:36,626 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2021-07-09T22:25:36,626 khmer/_khmermodule.cc:2138:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,626 2138 | return PyInt_FromLong(1); 2021-07-09T22:25:36,627 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,627 | PyLong_FromLong 2021-07-09T22:25:36,634 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2021-07-09T22:25:36,635 khmer/_khmermodule.cc:2161:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,635 2161 | return PyInt_FromLong(n_consumed); 2021-07-09T22:25:36,635 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,635 | PyLong_FromLong 2021-07-09T22:25:36,650 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2021-07-09T22:25:36,650 khmer/_khmermodule.cc:2275:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T22:25:36,651 2275 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2021-07-09T22:25:36,651 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,651 | PyLong_AsVoidPtr 2021-07-09T22:25:36,658 khmer/_khmermodule.cc:2285:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,658 2285 | return PyInt_FromLong(next_largest); 2021-07-09T22:25:36,658 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,659 | PyLong_FromLong 2021-07-09T22:25:36,664 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2021-07-09T22:25:36,665 khmer/_khmermodule.cc:2301:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T22:25:36,665 2301 | if (PyInt_Check(arg)) { 2021-07-09T22:25:36,665 | ^~~~~~~~~~~ 2021-07-09T22:25:36,665 | PySet_Check 2021-07-09T22:25:36,672 khmer/_khmermodule.cc:2302:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T22:25:36,672 2302 | long pos = PyInt_AsLong(arg); 2021-07-09T22:25:36,672 | ^~~~~~~~~~~~ 2021-07-09T22:25:36,672 | PyLong_AsLong 2021-07-09T22:25:36,680 khmer/_khmermodule.cc:2304:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2021-07-09T22:25:36,680 2304 | } else if (PyString_Check(arg)) { 2021-07-09T22:25:36,680 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,681 | PyMapping_Check 2021-07-09T22:25:36,691 khmer/_khmermodule.cc:2305:25: error: ‘PyString_AsString’ was not declared in this scope 2021-07-09T22:25:36,691 2305 | std::string s = PyString_AsString(arg); 2021-07-09T22:25:36,691 | ^~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,699 khmer/_khmermodule.cc:2312:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,699 2312 | return PyInt_FromLong(count); 2021-07-09T22:25:36,699 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,699 | PyLong_FromLong 2021-07-09T22:25:36,708 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2021-07-09T22:25:36,708 khmer/_khmermodule.cc:2354:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,708 2354 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2021-07-09T22:25:36,708 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,709 | PyLong_FromLong 2021-07-09T22:25:36,719 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2021-07-09T22:25:36,719 khmer/_khmermodule.cc:2375:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2021-07-09T22:25:36,719 2375 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2021-07-09T22:25:36,719 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,720 | PyBytes_FromStringAndSize 2021-07-09T22:25:36,748 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2021-07-09T22:25:36,749 khmer/_khmermodule.cc:2450:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T22:25:36,749 2450 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T22:25:36,749 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,749 | PyLong_FromVoidPtr 2021-07-09T22:25:36,758 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2021-07-09T22:25:36,759 khmer/_khmermodule.cc:2478:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T22:25:36,759 2478 | if (!PyCObject_Check(subset_obj)) { 2021-07-09T22:25:36,759 | ^~~~~~~~~~~~~~~ 2021-07-09T22:25:36,759 | PyODict_Check 2021-07-09T22:25:36,770 khmer/_khmermodule.cc:2484:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T22:25:36,770 2484 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T22:25:36,771 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,771 | PyLong_AsVoidPtr 2021-07-09T22:25:36,792 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2021-07-09T22:25:36,793 khmer/_khmermodule.cc:2776:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T22:25:36,793 2776 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2021-07-09T22:25:36,793 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,793 | PyLong_FromVoidPtr 2021-07-09T22:25:36,801 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2021-07-09T22:25:36,802 khmer/_khmermodule.cc:2789:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2021-07-09T22:25:36,802 2789 | if (!PyCObject_Check(ppi_obj)) { 2021-07-09T22:25:36,802 | ^~~~~~~~~~~~~~~ 2021-07-09T22:25:36,802 | PyODict_Check 2021-07-09T22:25:36,813 khmer/_khmermodule.cc:2795:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T22:25:36,814 2795 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2021-07-09T22:25:36,814 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,814 | PyLong_AsVoidPtr 2021-07-09T22:25:36,821 khmer/_khmermodule.cc:2801:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,822 2801 | return PyInt_FromLong(p); 2021-07-09T22:25:36,822 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,822 | PyLong_FromLong 2021-07-09T22:25:36,835 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2021-07-09T22:25:36,835 khmer/_khmermodule.cc:2920:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,835 2920 | return PyInt_FromLong(n_partitions); 2021-07-09T22:25:36,835 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,835 | PyLong_FromLong 2021-07-09T22:25:36,844 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2021-07-09T22:25:36,844 khmer/_khmermodule.cc:2951:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,844 2951 | return PyInt_FromLong(n_singletons); 2021-07-09T22:25:36,844 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,844 | PyLong_FromLong 2021-07-09T22:25:36,858 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2021-07-09T22:25:36,859 khmer/_khmermodule.cc:3051:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T22:25:36,859 3051 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T22:25:36,859 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,859 | PyLong_AsVoidPtr 2021-07-09T22:25:36,871 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2021-07-09T22:25:36,871 khmer/_khmermodule.cc:3069:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T22:25:36,871 3069 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T22:25:36,872 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,872 | PyLong_AsVoidPtr 2021-07-09T22:25:36,907 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T22:25:36,907 khmer/_khmermodule.cc:3191:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T22:25:36,908 3191 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T22:25:36,908 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,908 | PyLong_AsVoidPtr 2021-07-09T22:25:36,921 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T22:25:36,921 khmer/_khmermodule.cc:3235:16: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2021-07-09T22:25:36,921 3235 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2021-07-09T22:25:36,921 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,922 | PyLong_FromVoidPtr 2021-07-09T22:25:36,930 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2021-07-09T22:25:36,930 khmer/_khmermodule.cc:3265:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,930 3265 | return PyInt_FromLong(d); 2021-07-09T22:25:36,931 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,931 | PyLong_FromLong 2021-07-09T22:25:36,942 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2021-07-09T22:25:36,942 khmer/_khmermodule.cc:3277:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2021-07-09T22:25:36,942 3277 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2021-07-09T22:25:36,942 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,943 | PyLong_AsVoidPtr 2021-07-09T22:25:36,951 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2021-07-09T22:25:36,951 khmer/_khmermodule.cc:3313:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,951 3313 | return PyInt_FromLong(p1); 2021-07-09T22:25:36,952 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,952 | PyLong_FromLong 2021-07-09T22:25:36,960 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2021-07-09T22:25:36,960 khmer/_khmermodule.cc:3330:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,960 3330 | return PyInt_FromLong(partition_id); 2021-07-09T22:25:36,960 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,960 | PyLong_FromLong 2021-07-09T22:25:36,972 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2021-07-09T22:25:36,973 khmer/_khmermodule.cc:3472:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2021-07-09T22:25:36,973 3472 | return PyInt_FromLong(k); 2021-07-09T22:25:36,973 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:36,973 | PyLong_FromLong 2021-07-09T22:25:36,994 In file included from /usr/include/python3.9/listobject.h:45, 2021-07-09T22:25:36,994 from /usr/include/python3.9/Python.h:106, 2021-07-09T22:25:36,995 from khmer/_khmermodule.cc:13: 2021-07-09T22:25:36,995 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2021-07-09T22:25:36,995 khmer/_khmermodule.cc:3516:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T22:25:36,995 3516 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2021-07-09T22:25:36,995 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:36,995 /usr/include/python3.9/cpython/listobject.h:37:68: note: in definition of macro ‘PyList_SET_ITEM’ 2021-07-09T22:25:36,996 37 | #define PyList_SET_ITEM(op, i, v) (_PyList_CAST(op)->ob_item[i] = (v)) 2021-07-09T22:25:36,996 | ^ 2021-07-09T22:25:37,008 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2021-07-09T22:25:37,008 khmer/_khmermodule.cc:3621:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T22:25:37,008 3621 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2021-07-09T22:25:37,008 | ^~~~~~~~~~~~~ 2021-07-09T22:25:37,008 | PyCMethod 2021-07-09T22:25:37,015 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_new(PyTypeObject*, PyObject*, PyObject*)’: 2021-07-09T22:25:37,015 khmer/_khmermodule.cc:3646:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T22:25:37,015 3646 | if (PyInt_Check(size_o)) { 2021-07-09T22:25:37,015 | ^~~~~~~~~~~ 2021-07-09T22:25:37,016 | PySet_Check 2021-07-09T22:25:37,022 khmer/_khmermodule.cc:3647:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T22:25:37,022 3647 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T22:25:37,022 | ^~~~~~~~~~~~ 2021-07-09T22:25:37,023 | PyLong_AsLong 2021-07-09T22:25:37,062 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2021-07-09T22:25:37,062 khmer/_khmermodule.cc:3860:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T22:25:37,063 3860 | return Py_FindMethod(khmer_subset_methods, obj, name); 2021-07-09T22:25:37,063 | ^~~~~~~~~~~~~ 2021-07-09T22:25:37,063 | PyCMethod 2021-07-09T22:25:37,070 khmer/_khmermodule.cc: In function ‘PyObject* khmer_labelhash_new(PyTypeObject*, PyObject*, PyObject*)’: 2021-07-09T22:25:37,070 khmer/_khmermodule.cc:3916:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T22:25:37,070 3916 | if (PyInt_Check(size_o)) { 2021-07-09T22:25:37,070 | ^~~~~~~~~~~ 2021-07-09T22:25:37,070 | PySet_Check 2021-07-09T22:25:37,077 khmer/_khmermodule.cc:3917:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T22:25:37,077 3917 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T22:25:37,077 | ^~~~~~~~~~~~ 2021-07-09T22:25:37,077 | PyLong_AsLong 2021-07-09T22:25:37,106 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2021-07-09T22:25:37,106 khmer/_khmermodule.cc:4231:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2021-07-09T22:25:37,106 4231 | return PyInt_FromSize_t(labelhash->n_labels()); 2021-07-09T22:25:37,106 | ^~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,106 | PyLong_FromSize_t 2021-07-09T22:25:37,107 khmer/_khmermodule.cc: At global scope: 2021-07-09T22:25:37,107 khmer/_khmermodule.cc:4250:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:37,107 4250 | "_LabelHash", /* tp_name */ 2021-07-09T22:25:37,107 | ^~~~~~~~~~~~ 2021-07-09T22:25:37,107 | | 2021-07-09T22:25:37,108 | const char* 2021-07-09T22:25:37,108 khmer/_khmermodule.cc:4253:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:37,108 4253 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2021-07-09T22:25:37,108 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,108 | | 2021-07-09T22:25:37,108 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T22:25:37,108 khmer/_khmermodule.cc:4268:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T22:25:37,109 4268 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2021-07-09T22:25:37,109 khmer/_khmermodule.cc:4276:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2021-07-09T22:25:37,109 4276 | khmer_labelhash_methods, /* tp_methods */ 2021-07-09T22:25:37,109 | ^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,109 | | 2021-07-09T22:25:37,109 | PyMethodDef* 2021-07-09T22:25:37,122 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2021-07-09T22:25:37,122 khmer/_khmermodule.cc:4359:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2021-07-09T22:25:37,123 4359 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2021-07-09T22:25:37,123 | ^~~~~~~~~~~~~ 2021-07-09T22:25:37,123 | PyCMethod 2021-07-09T22:25:37,123 khmer/_khmermodule.cc: At global scope: 2021-07-09T22:25:37,123 khmer/_khmermodule.cc:4377:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:37,123 4377 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2021-07-09T22:25:37,123 | ^~~~~~~~~~~~~ 2021-07-09T22:25:37,124 | | 2021-07-09T22:25:37,124 | const char* 2021-07-09T22:25:37,124 khmer/_khmermodule.cc:4379:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2021-07-09T22:25:37,124 4379 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2021-07-09T22:25:37,124 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,124 | | 2021-07-09T22:25:37,124 | void (*)(PyObject*) {aka void (*)(_object*)} 2021-07-09T22:25:37,125 khmer/_khmermodule.cc:4381:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2021-07-09T22:25:37,125 4381 | khmer_readaligner_getattr, /*tp_getattr*/ 2021-07-09T22:25:37,125 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,125 | | 2021-07-09T22:25:37,125 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2021-07-09T22:25:37,125 In file included from /usr/include/python3.9/pytime.h:6, 2021-07-09T22:25:37,125 from /usr/include/python3.9/Python.h:85, 2021-07-09T22:25:37,126 from khmer/_khmermodule.cc:13: 2021-07-09T22:25:37,126 /usr/include/python3.9/object.h:352:46: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2021-07-09T22:25:37,126 350 | #define Py_TPFLAGS_DEFAULT ( \ 2021-07-09T22:25:37,126 | ~~~ 2021-07-09T22:25:37,126 351 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2021-07-09T22:25:37,127 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,127 352 | Py_TPFLAGS_HAVE_VERSION_TAG | \ 2021-07-09T22:25:37,127 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2021-07-09T22:25:37,127 | | 2021-07-09T22:25:37,127 | long unsigned int 2021-07-09T22:25:37,127 353 | 0) 2021-07-09T22:25:37,127 | ~~ 2021-07-09T22:25:37,127 khmer/_khmermodule.cc:4394:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2021-07-09T22:25:37,128 4394 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2021-07-09T22:25:37,128 | ^~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,128 khmer/_khmermodule.cc:4395:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2021-07-09T22:25:37,128 4395 | "ReadAligner object", /* tp_doc */ 2021-07-09T22:25:37,128 | ^~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,128 | | 2021-07-09T22:25:37,128 | const char* 2021-07-09T22:25:37,132 khmer/_khmermodule.cc: In function ‘PyObject* _new_hashbits(PyObject*, PyObject*)’: 2021-07-09T22:25:37,132 khmer/_khmermodule.cc:4455:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2021-07-09T22:25:37,132 4455 | if (PyInt_Check(size_o)) { 2021-07-09T22:25:37,132 | ^~~~~~~~~~~ 2021-07-09T22:25:37,133 | PySet_Check 2021-07-09T22:25:37,139 khmer/_khmermodule.cc:4456:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2021-07-09T22:25:37,139 4456 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2021-07-09T22:25:37,139 | ^~~~~~~~~~~~ 2021-07-09T22:25:37,140 | PyLong_AsLong 2021-07-09T22:25:37,145 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2021-07-09T22:25:37,145 khmer/_khmermodule.cc:4537:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2021-07-09T22:25:37,145 4537 | self->ob_type->tp_free((PyObject*)obj); 2021-07-09T22:25:37,146 | ^~~~~~~ 2021-07-09T22:25:37,156 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2021-07-09T22:25:37,157 khmer/_khmermodule.cc:4612:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2021-07-09T22:25:37,157 4612 | return PyString_FromString(_revhash(val, ksize).c_str()); 2021-07-09T22:25:37,157 | ^~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:37,157 | PyLong_FromString 2021-07-09T22:25:37,158 khmer/_khmermodule.cc: At global scope: 2021-07-09T22:25:37,158 khmer/_khmermodule.cc:4688:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2021-07-09T22:25:37,158 4688 | init_khmer(void) 2021-07-09T22:25:37,158 | ^~~~~~~~~~ 2021-07-09T22:25:37,158 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2021-07-09T22:25:37,159 33 | void init_khmer(); 2021-07-09T22:25:37,159 | ^~~~~~~~~~ 2021-07-09T22:25:37,159 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2021-07-09T22:25:37,159 khmer/_khmermodule.cc:4692:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T22:25:37,159 4692 | khmer_ConfigType.ob_type = &PyType_Type; 2021-07-09T22:25:37,160 | ^~~~~~~ 2021-07-09T22:25:37,160 khmer/_khmermodule.cc:4693:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2021-07-09T22:25:37,160 4693 | khmer_KCountingHashType.ob_type = &PyType_Type; 2021-07-09T22:25:37,160 | ^~~~~~~ 2021-07-09T22:25:37,160 khmer/_khmermodule.cc:4700:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T22:25:37,160 4700 | return; 2021-07-09T22:25:37,161 | ^~~~~~ 2021-07-09T22:25:37,161 khmer/_khmermodule.cc:4707:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T22:25:37,161 4707 | return; 2021-07-09T22:25:37,161 | ^~~~~~ 2021-07-09T22:25:37,169 khmer/_khmermodule.cc:4711:9: error: ‘Py_InitModule3’ was not declared in this scope 2021-07-09T22:25:37,170 4711 | m = Py_InitModule3( "_khmer", KhmerMethods, 2021-07-09T22:25:37,170 | ^~~~~~~~~~~~~~ 2021-07-09T22:25:37,170 khmer/_khmermodule.cc:4714:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T22:25:37,170 4714 | return; 2021-07-09T22:25:37,170 | ^~~~~~ 2021-07-09T22:25:37,170 khmer/_khmermodule.cc:4719:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T22:25:37,171 4719 | return; 2021-07-09T22:25:37,171 | ^~~~~~ 2021-07-09T22:25:37,171 khmer/_khmermodule.cc:4726:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T22:25:37,171 4726 | return; 2021-07-09T22:25:37,171 | ^~~~~~ 2021-07-09T22:25:37,171 khmer/_khmermodule.cc:4732:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T22:25:37,172 4732 | return; 2021-07-09T22:25:37,172 | ^~~~~~ 2021-07-09T22:25:37,172 khmer/_khmermodule.cc:4735:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2021-07-09T22:25:37,172 4735 | return; 2021-07-09T22:25:37,172 | ^~~~~~ 2021-07-09T22:25:37,932 khmer/_khmermodule.cc:4745:23: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-09T22:25:37,933 4745 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2021-07-09T22:25:37,933 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-09T22:25:38,025 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-09T22:25:38,108 Building wheel for khmer (setup.py): finished with status 'error' 2021-07-09T22:25:38,109 ERROR: Failed building wheel for khmer 2021-07-09T22:25:38,110 Running setup.py clean for khmer 2021-07-09T22:25:38,110 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-dou8b6jh/khmer_0e645919b6ef483c9a48ab457c731fc2/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-dou8b6jh/khmer_0e645919b6ef483c9a48ab457c731fc2/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 2021-07-09T22:25:39,009 /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 2021-07-09T22:25:39,010 warnings.warn( 2021-07-09T22:25:39,041 running clean 2021-07-09T22:25:39,042 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-09T22:25:39,045 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-09T22:25:39,085 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-09T22:25:39,085 'build/scripts-3.9' does not exist -- can't clean it 2021-07-09T22:25:39,085 removing 'build' 2021-07-09T22:25:39,154 Failed to build khmer 2021-07-09T22:25:39,155 ERROR: Failed to build one or more wheels 2021-07-09T22:25:39,156 Exception information: 2021-07-09T22:25:39,156 Traceback (most recent call last): 2021-07-09T22:25:39,156 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-09T22:25:39,156 status = self.run(options, args) 2021-07-09T22:25:39,156 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-09T22:25:39,156 return func(self, options, args) 2021-07-09T22:25:39,156 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-09T22:25:39,156 raise CommandError( 2021-07-09T22:25:39,156 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-09T22:25:39,158 Removed build tracker: '/tmp/pip-req-tracker-pc_b39nf'