2023-09-08T15:17:20,304 Created temporary directory: /tmp/pip-build-tracker-ebav455r 2023-09-08T15:17:20,305 Initialized build tracking at /tmp/pip-build-tracker-ebav455r 2023-09-08T15:17:20,305 Created build tracker: /tmp/pip-build-tracker-ebav455r 2023-09-08T15:17:20,306 Entered build tracker: /tmp/pip-build-tracker-ebav455r 2023-09-08T15:17:20,307 Created temporary directory: /tmp/pip-wheel-mfm5ivph 2023-09-08T15:17:20,310 Created temporary directory: /tmp/pip-ephem-wheel-cache-u1oz1dmm 2023-09-08T15:17:20,331 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T15:17:20,335 2 location(s) to search for versions of khmer: 2023-09-08T15:17:20,335 * https://pypi.org/simple/khmer/ 2023-09-08T15:17:20,335 * https://www.piwheels.org/simple/khmer/ 2023-09-08T15:17:20,336 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2023-09-08T15:17:20,337 Getting page https://pypi.org/simple/khmer/ 2023-09-08T15:17:20,338 Found index url https://pypi.org/simple/ 2023-09-08T15:17:20,478 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2023-09-08T15:17:20,486 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,486 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,487 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2023-09-08T15:17:20,488 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6.1 2023-09-08T15:17:20,488 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,489 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2023-09-08T15:17:20,490 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,490 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7.1 2023-09-08T15:17:20,491 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,492 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2023-09-08T15:17:20,492 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,493 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2023-09-08T15:17:20,494 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,494 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0.1 2023-09-08T15:17:20,495 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2023-09-08T15:17:20,496 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,496 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2023-09-08T15:17:20,497 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,497 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2023-09-08T15:17:20,498 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,498 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2023-09-08T15:17:20,499 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,499 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,500 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4.1 2023-09-08T15:17:20,501 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,501 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,502 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,502 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,503 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2023-09-08T15:17:20,504 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2023-09-08T15:17:20,504 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,505 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2023-09-08T15:17:20,506 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,506 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,507 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,507 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,507 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T15:17:20,508 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1.1 2023-09-08T15:17:20,509 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2023-09-08T15:17:20,509 Getting page https://www.piwheels.org/simple/khmer/ 2023-09-08T15:17:20,511 Found index url https://www.piwheels.org/simple/ 2023-09-08T15:17:20,771 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2023-09-08T15:17:20,773 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2023-09-08T15:17:20,773 Skipping link: not a file: https://pypi.org/simple/khmer/ 2023-09-08T15:17:20,793 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2023-09-08T15:17:20,811 Collecting khmer==1.0 2023-09-08T15:17:20,813 Created temporary directory: /tmp/pip-unpack-an1sp9f2 2023-09-08T15:17:21,059 Downloading khmer-1.0.tar.gz (43.5 MB) 2023-09-08T15:18:37,354 Added khmer==1.0 from https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz to build tracker '/tmp/pip-build-tracker-ebav455r' 2023-09-08T15:18:37,357 Running setup.py (path:/tmp/pip-wheel-mfm5ivph/khmer_196503a7fed248748380d31fe158bfc3/setup.py) egg_info for package khmer 2023-09-08T15:18:37,358 Created temporary directory: /tmp/pip-pip-egg-info-momkb44e 2023-09-08T15:18:37,359 Preparing metadata (setup.py): started 2023-09-08T15:18:37,360 Running command python setup.py egg_info 2023-09-08T15:18:38,326 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T15:18:38,326 !! 2023-09-08T15:18:38,327 ******************************************************************************** 2023-09-08T15:18:38,328 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T15:18:38,328 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T15:18:38,329 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T15:18:38,330 or your builds will no longer be supported. 2023-09-08T15:18:38,331 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T15:18:38,332 ******************************************************************************** 2023-09-08T15:18:38,332 !! 2023-09-08T15:18:38,333 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T15:18:38,521 running egg_info 2023-09-08T15:18:38,523 creating /tmp/pip-pip-egg-info-momkb44e/khmer.egg-info 2023-09-08T15:18:38,549 writing /tmp/pip-pip-egg-info-momkb44e/khmer.egg-info/PKG-INFO 2023-09-08T15:18:38,554 writing dependency_links to /tmp/pip-pip-egg-info-momkb44e/khmer.egg-info/dependency_links.txt 2023-09-08T15:18:38,556 writing requirements to /tmp/pip-pip-egg-info-momkb44e/khmer.egg-info/requires.txt 2023-09-08T15:18:38,557 writing top-level names to /tmp/pip-pip-egg-info-momkb44e/khmer.egg-info/top_level.txt 2023-09-08T15:18:38,558 writing manifest file '/tmp/pip-pip-egg-info-momkb44e/khmer.egg-info/SOURCES.txt' 2023-09-08T15:18:38,590 dependency lib/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,591 dependency lib/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,592 dependency lib/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,592 dependency lib/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,593 dependency lib/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,594 dependency lib/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,594 dependency lib/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,595 dependency lib/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,596 dependency lib/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,596 dependency lib/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,597 dependency lib/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,597 dependency lib/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,598 dependency lib/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,599 dependency lib/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,599 dependency lib/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,600 dependency lib/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,601 dependency lib/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,601 dependency lib/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:38,651 reading manifest file '/tmp/pip-pip-egg-info-momkb44e/khmer.egg-info/SOURCES.txt' 2023-09-08T15:18:38,652 reading manifest template 'MANIFEST.in' 2023-09-08T15:18:40,078 no previously-included directories found matching 'doc/doxygen' 2023-09-08T15:18:40,081 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T15:18:40,100 writing manifest file '/tmp/pip-pip-egg-info-momkb44e/khmer.egg-info/SOURCES.txt' 2023-09-08T15:18:40,214 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T15:18:40,218 Source in /tmp/pip-wheel-mfm5ivph/khmer_196503a7fed248748380d31fe158bfc3 has version 1.0, which satisfies requirement khmer==1.0 from https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz 2023-09-08T15:18:40,219 Removed khmer==1.0 from https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz from build tracker '/tmp/pip-build-tracker-ebav455r' 2023-09-08T15:18:40,223 Created temporary directory: /tmp/pip-unpack-5iz8zig1 2023-09-08T15:18:40,224 Created temporary directory: /tmp/pip-unpack-119jreyk 2023-09-08T15:18:40,238 Building wheels for collected packages: khmer 2023-09-08T15:18:40,242 Created temporary directory: /tmp/pip-wheel-cee2wqxn 2023-09-08T15:18:40,242 Building wheel for khmer (setup.py): started 2023-09-08T15:18:40,244 Destination directory: /tmp/pip-wheel-cee2wqxn 2023-09-08T15:18:40,244 Running command python setup.py bdist_wheel 2023-09-08T15:18:41,093 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T15:18:41,094 !! 2023-09-08T15:18:41,095 ******************************************************************************** 2023-09-08T15:18:41,095 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T15:18:41,096 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T15:18:41,097 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T15:18:41,097 or your builds will no longer be supported. 2023-09-08T15:18:41,098 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T15:18:41,098 ******************************************************************************** 2023-09-08T15:18:41,099 !! 2023-09-08T15:18:41,100 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T15:18:41,273 running bdist_wheel 2023-09-08T15:18:41,319 running build 2023-09-08T15:18:41,320 got version from file /tmp/pip-wheel-mfm5ivph/khmer_196503a7fed248748380d31fe158bfc3/khmer/_version.py {'version': '1.0', 'full': '4c1e91f063bf0da81f6e6ea41de038b966eb9ff2'} 2023-09-08T15:18:41,321 running build_py 2023-09-08T15:18:41,346 creating build 2023-09-08T15:18:41,347 creating build/lib.linux-armv7l-cpython-311 2023-09-08T15:18:41,348 creating build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,349 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,351 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,352 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,354 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,356 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,358 copying khmer/file.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,360 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,361 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:41,363 running egg_info 2023-09-08T15:18:41,396 creating khmer.egg-info 2023-09-08T15:18:41,420 writing khmer.egg-info/PKG-INFO 2023-09-08T15:18:41,424 writing dependency_links to khmer.egg-info/dependency_links.txt 2023-09-08T15:18:41,426 writing requirements to khmer.egg-info/requires.txt 2023-09-08T15:18:41,427 writing top-level names to khmer.egg-info/top_level.txt 2023-09-08T15:18:41,429 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:18:41,433 dependency lib/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,433 dependency lib/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,434 dependency lib/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,434 dependency lib/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,435 dependency lib/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,435 dependency lib/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,436 dependency lib/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,436 dependency lib/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,437 dependency lib/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,437 dependency lib/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,438 dependency lib/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,438 dependency lib/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,438 dependency lib/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,439 dependency lib/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,439 dependency lib/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,440 dependency lib/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,440 dependency lib/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,441 dependency lib/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2023-09-08T15:18:41,466 reading manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:18:41,467 reading manifest template 'MANIFEST.in' 2023-09-08T15:18:42,901 no previously-included directories found matching 'doc/doxygen' 2023-09-08T15:18:42,903 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T15:18:42,927 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T15:18:42,939 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T15:18:42,944 running build_ext 2023-09-08T15:18:42,945 bash -c "cd lib/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC" 2023-09-08T15:18:43,045 Checking for gcc... 2023-09-08T15:18:43,284 Building static library libz.a version 1.2.8 with gcc. 2023-09-08T15:18:43,407 Checking for off64_t... Yes. 2023-09-08T15:18:43,414 Checking for fseeko... Yes. 2023-09-08T15:18:43,617 Checking for strerror... Yes. 2023-09-08T15:18:43,625 cp: cannot stat 'zconf.h.in': No such file or directory 2023-09-08T15:18:43,746 Checking for unistd.h... Yes. 2023-09-08T15:18:43,852 Checking for stdarg.h... Yes. 2023-09-08T15:18:43,983 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). 2023-09-08T15:18:44,222 Checking for vsnprintf() in stdio.h... Yes. 2023-09-08T15:18:44,334 Checking for return value of vsnprintf()... Yes. 2023-09-08T15:18:44,421 Checking for attribute(visibility) support... Yes. 2023-09-08T15:18:44,453 ./configure: line 806: zlib.pc.in: No such file or directory 2023-09-08T15:18:44,488 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c 2023-09-08T15:18:44,852 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c 2023-09-08T15:18:45,297 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c 2023-09-08T15:18:47,293 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c 2023-09-08T15:18:48,133 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c 2023-09-08T15:18:48,586 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c 2023-09-08T15:18:50,472 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c 2023-09-08T15:18:50,992 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c 2023-09-08T15:18:52,397 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c 2023-09-08T15:18:52,569 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c 2023-09-08T15:18:52,708 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c 2023-09-08T15:18:52,839 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c 2023-09-08T15:18:52,994 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c 2023-09-08T15:18:53,464 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c 2023-09-08T15:18:54,037 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c 2023-09-08T15:18:54,620 bash -c "cd lib/bzip2 && make -f Makefile-libbz2_so all" 2023-09-08T15:18:54,635 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2023-09-08T15:18:55,523 In function ‘mainSimpleSort’, 2023-09-08T15:18:55,524 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2023-09-08T15:18:55,524 inlined from ‘mainSort’ at blocksort.c:897:19: 2023-09-08T15:18:55,525 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:18:55,525 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:18:55,526 | ^~~~~~~ 2023-09-08T15:18:55,527 blocksort.c:514:18: note: called from here 2023-09-08T15:18:55,527 514 | while ( mainGtU ( 2023-09-08T15:18:55,528 | ^~~~~~~~~ 2023-09-08T15:18:55,529 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:18:55,530 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:18:55,530 516 | ) ) { 2023-09-08T15:18:55,531 | ~ 2023-09-08T15:18:55,532 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:18:55,532 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:18:55,533 | ^~~~~~~ 2023-09-08T15:18:55,534 blocksort.c:528:18: note: called from here 2023-09-08T15:18:55,535 528 | while ( mainGtU ( 2023-09-08T15:18:55,535 | ^~~~~~~~~ 2023-09-08T15:18:55,536 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:18:55,537 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:18:55,537 530 | ) ) { 2023-09-08T15:18:55,538 | ~ 2023-09-08T15:18:55,539 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T15:18:55,539 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T15:18:55,540 | ^~~~~~~ 2023-09-08T15:18:55,540 blocksort.c:542:18: note: called from here 2023-09-08T15:18:55,541 542 | while ( mainGtU ( 2023-09-08T15:18:55,542 | ^~~~~~~~~ 2023-09-08T15:18:55,542 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T15:18:55,543 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:18:55,544 544 | ) ) { 2023-09-08T15:18:55,544 | ~ 2023-09-08T15:18:56,330 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2023-09-08T15:18:56,788 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2023-09-08T15:18:56,899 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2023-09-08T15:18:57,011 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2023-09-08T15:19:01,502 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2023-09-08T15:19:04,052 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2023-09-08T15:19:05,984 #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 2023-09-08T15:19:05,987 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2023-09-08T15:19:05,989 #rm -f libbz2.so.1.0 2023-09-08T15:19:05,991 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2023-09-08T15:19:06,505 building 'khmer._khmermodule' extension 2023-09-08T15:19:06,506 creating build/temp.linux-armv7l-cpython-311 2023-09-08T15:19:06,506 creating build/temp.linux-armv7l-cpython-311/khmer 2023-09-08T15:19:06,507 creating build/temp.linux-armv7l-cpython-311/lib 2023-09-08T15:19:06,508 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION=1.0 -UNO_UNIQUE_RC -Ilib -Ilib/zlib -Ilib/bzip2 -I/usr/include/python3.11 -c khmer/_khmermodule.cc -o build/temp.linux-armv7l-cpython-311/khmer/_khmermodule.o -O3 2023-09-08T15:19:09,401 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2023-09-08T15:19:09,402 khmer/_khmermodule.cc:85:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2023-09-08T15:19:09,402 85 | tobj.ob_size = 0; 2023-09-08T15:19:09,403 | ^~~~~~~ 2023-09-08T15:19:09,404 khmer/_khmermodule.cc:86:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:19:09,405 86 | tobj.ob_type = &PyType_Type; 2023-09-08T15:19:09,405 | ^~~~~~~ 2023-09-08T15:19:09,411 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:19:09,412 khmer/_khmermodule.cc:206:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:09,413 206 | "Config", sizeof(khmer_ConfigObject), 2023-09-08T15:19:09,413 | ^~~~~~~~ 2023-09-08T15:19:09,414 | | 2023-09-08T15:19:09,414 | const char* 2023-09-08T15:19:09,415 khmer/_khmermodule.cc:208:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:09,416 208 | khmer_config_dealloc, /*tp_dealloc*/ 2023-09-08T15:19:09,417 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,417 | | 2023-09-08T15:19:09,418 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:19:09,419 khmer/_khmermodule.cc:210:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:19:09,420 210 | khmer_config_getattr, /*tp_getattr*/ 2023-09-08T15:19:09,420 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,421 | | 2023-09-08T15:19:09,421 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:19:09,422 In file included from /usr/include/python3.11/Python.h:44, 2023-09-08T15:19:09,423 from khmer/_khmermodule.cc:13: 2023-09-08T15:19:09,423 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:19:09,424 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:19:09,425 | ~~~ 2023-09-08T15:19:09,426 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:19:09,426 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:19:09,427 | | 2023-09-08T15:19:09,428 | int 2023-09-08T15:19:09,428 424 | 0) 2023-09-08T15:19:09,429 | ~~ 2023-09-08T15:19:09,429 khmer/_khmermodule.cc:223:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:19:09,429 223 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:19:09,430 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,430 khmer/_khmermodule.cc:224:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:19:09,431 224 | "config object", /* tp_doc */ 2023-09-08T15:19:09,431 | ^~~~~~~~~~~~~~~ 2023-09-08T15:19:09,432 | | 2023-09-08T15:19:09,432 | const char* 2023-09-08T15:19:09,452 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2023-09-08T15:19:09,453 khmer/_khmermodule.cc:312:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:19:09,453 312 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2023-09-08T15:19:09,454 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,454 | PyLong_FromSize_t 2023-09-08T15:19:09,478 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2023-09-08T15:19:09,479 khmer/_khmermodule.cc:370:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:19:09,480 370 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2023-09-08T15:19:09,480 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,481 | PyLong_FromSize_t 2023-09-08T15:19:09,504 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2023-09-08T15:19:09,505 khmer/_khmermodule.cc:399:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:19:09,506 399 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2023-09-08T15:19:09,507 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,508 | PyLong_FromSize_t 2023-09-08T15:19:09,531 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2023-09-08T15:19:09,532 khmer/_khmermodule.cc:466:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:19:09,533 466 | return Py_FindMethod(khmer_config_methods, obj, name); 2023-09-08T15:19:09,534 | ^~~~~~~~~~~~~ 2023-09-08T15:19:09,534 | PyCMethod 2023-09-08T15:19:09,560 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2023-09-08T15:19:09,561 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:19:09,561 504 | PyString_FromString( \ 2023-09-08T15:19:09,562 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,563 khmer/_khmermodule.cc:513:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:19:09,563 513 | return KHMER_READ_STRING_GETTER( self, name ); 2023-09-08T15:19:09,564 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,589 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2023-09-08T15:19:09,590 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:19:09,591 504 | PyString_FromString( \ 2023-09-08T15:19:09,591 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,592 khmer/_khmermodule.cc:521:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:19:09,593 521 | return KHMER_READ_STRING_GETTER( self, sequence ); 2023-09-08T15:19:09,593 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,618 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2023-09-08T15:19:09,619 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:19:09,619 504 | PyString_FromString( \ 2023-09-08T15:19:09,620 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,620 khmer/_khmermodule.cc:529:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:19:09,621 529 | return KHMER_READ_STRING_GETTER( self, accuracy ); 2023-09-08T15:19:09,621 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,647 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2023-09-08T15:19:09,647 khmer/_khmermodule.cc:504:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:19:09,648 504 | PyString_FromString( \ 2023-09-08T15:19:09,648 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,649 khmer/_khmermodule.cc:537:12: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T15:19:09,649 537 | return KHMER_READ_STRING_GETTER( self, annotations ); 2023-09-08T15:19:09,650 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,696 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2023-09-08T15:19:09,696 khmer/_khmermodule.cc:874:24: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,697 874 | PyObject * value = PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ); 2023-09-08T15:19:09,697 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,698 | PyLong_FromLong 2023-09-08T15:19:09,702 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:19:09,703 khmer/_khmermodule.cc:987:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:09,703 987 | "KSubset", sizeof(khmer_KSubsetPartitionObject), 2023-09-08T15:19:09,704 | ^~~~~~~~~ 2023-09-08T15:19:09,705 | | 2023-09-08T15:19:09,706 | const char* 2023-09-08T15:19:09,706 khmer/_khmermodule.cc:989:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:09,707 989 | khmer_subset_dealloc, /*tp_dealloc*/ 2023-09-08T15:19:09,708 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,708 | | 2023-09-08T15:19:09,709 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:19:09,710 khmer/_khmermodule.cc:991:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:19:09,710 991 | khmer_subset_getattr, /*tp_getattr*/ 2023-09-08T15:19:09,711 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,712 | | 2023-09-08T15:19:09,712 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:19:09,713 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:19:09,713 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:19:09,714 | ~~~ 2023-09-08T15:19:09,715 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:19:09,716 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:19:09,717 | | 2023-09-08T15:19:09,718 | int 2023-09-08T15:19:09,718 424 | 0) 2023-09-08T15:19:09,719 | ~~ 2023-09-08T15:19:09,719 khmer/_khmermodule.cc:1004:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:19:09,720 1004 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:19:09,720 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,721 khmer/_khmermodule.cc:1005:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:19:09,722 1005 | "subset object", /* tp_doc */ 2023-09-08T15:19:09,722 | ^~~~~~~~~~~~~~~ 2023-09-08T15:19:09,723 | | 2023-09-08T15:19:09,723 | const char* 2023-09-08T15:19:09,739 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2023-09-08T15:19:09,739 khmer/_khmermodule.cc:1101:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,740 1101 | return PyInt_FromLong(1); 2023-09-08T15:19:09,741 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,741 | PyLong_FromLong 2023-09-08T15:19:09,761 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2023-09-08T15:19:09,762 khmer/_khmermodule.cc:1118:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,762 1118 | return PyInt_FromLong(0); 2023-09-08T15:19:09,763 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,764 | PyLong_FromLong 2023-09-08T15:19:09,787 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2023-09-08T15:19:09,787 khmer/_khmermodule.cc:1206:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,788 1206 | return PyInt_FromLong(n_consumed); 2023-09-08T15:19:09,789 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,790 | PyLong_FromLong 2023-09-08T15:19:09,810 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2023-09-08T15:19:09,810 khmer/_khmermodule.cc:1238:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,811 1238 | return PyInt_FromLong(n_consumed); 2023-09-08T15:19:09,812 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,813 | PyLong_FromLong 2023-09-08T15:19:09,832 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2023-09-08T15:19:09,833 khmer/_khmermodule.cc:1261:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,834 1261 | return PyInt_FromLong(N); 2023-09-08T15:19:09,835 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,835 | PyLong_FromLong 2023-09-08T15:19:09,855 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2023-09-08T15:19:09,856 khmer/_khmermodule.cc:1284:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,857 1284 | return PyInt_FromLong(N); 2023-09-08T15:19:09,857 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,858 | PyLong_FromLong 2023-09-08T15:19:09,878 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2023-09-08T15:19:09,878 khmer/_khmermodule.cc:1387:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:19:09,879 1387 | if (PyInt_Check(arg)) { 2023-09-08T15:19:09,880 | ^~~~~~~~~~~ 2023-09-08T15:19:09,881 | PySet_Check 2023-09-08T15:19:09,897 khmer/_khmermodule.cc:1388:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:19:09,898 1388 | long pos = PyInt_AsLong(arg); 2023-09-08T15:19:09,898 | ^~~~~~~~~~~~ 2023-09-08T15:19:09,899 | PyLong_AsLong 2023-09-08T15:19:09,920 khmer/_khmermodule.cc:1390:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:19:09,921 1390 | } else if (PyString_Check(arg)) { 2023-09-08T15:19:09,921 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,922 | PyMapping_Check 2023-09-08T15:19:09,946 khmer/_khmermodule.cc:1391:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:19:09,947 1391 | std::string s = PyString_AsString(arg); 2023-09-08T15:19:09,948 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:19:09,968 khmer/_khmermodule.cc:1395:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,969 1395 | return PyInt_FromLong(count); 2023-09-08T15:19:09,969 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,970 | PyLong_FromLong 2023-09-08T15:19:09,991 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2023-09-08T15:19:09,992 khmer/_khmermodule.cc:1411:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:09,992 1411 | return PyInt_FromLong(count); 2023-09-08T15:19:09,993 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:09,994 | PyLong_FromLong 2023-09-08T15:19:10,019 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2023-09-08T15:19:10,020 khmer/_khmermodule.cc:1435:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:19:10,021 1435 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:19:10,021 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,022 | PyBytes_FromStringAndSize 2023-09-08T15:19:10,048 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2023-09-08T15:19:10,048 khmer/_khmermodule.cc:1465:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:19:10,049 1465 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:19:10,050 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,051 | PyBytes_FromStringAndSize 2023-09-08T15:19:10,076 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2023-09-08T15:19:10,077 khmer/_khmermodule.cc:1606:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,077 1606 | return PyInt_FromLong(k); 2023-09-08T15:19:10,078 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,079 | PyLong_FromLong 2023-09-08T15:19:10,110 khmer/_khmermodule.cc: In function ‘PyObject* hash_find_all_tags_truncate_on_abundance(PyObject*, PyObject*)’: 2023-09-08T15:19:10,111 khmer/_khmermodule.cc:1718:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:19:10,112 1718 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T15:19:10,112 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,113 | PyLong_FromVoidPtr 2023-09-08T15:19:10,138 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2023-09-08T15:19:10,138 khmer/_khmermodule.cc:1824:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:19:10,139 1824 | return Py_FindMethod(khmer_counting_methods, obj, name); 2023-09-08T15:19:10,140 | ^~~~~~~~~~~~~ 2023-09-08T15:19:10,140 | PyCMethod 2023-09-08T15:19:10,141 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:19:10,142 khmer/_khmermodule.cc:1834:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:10,142 1834 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2023-09-08T15:19:10,143 | ^~~~~~~~~~~~~~~ 2023-09-08T15:19:10,143 | | 2023-09-08T15:19:10,144 | const char* 2023-09-08T15:19:10,144 khmer/_khmermodule.cc:1836:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:10,145 1836 | khmer_counting_dealloc, /*tp_dealloc*/ 2023-09-08T15:19:10,146 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,146 | | 2023-09-08T15:19:10,147 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:19:10,147 khmer/_khmermodule.cc:1838:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:19:10,148 1838 | khmer_counting_getattr, /*tp_getattr*/ 2023-09-08T15:19:10,149 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,149 | | 2023-09-08T15:19:10,150 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:19:10,151 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:19:10,151 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:19:10,152 | ~~~ 2023-09-08T15:19:10,152 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:19:10,153 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:19:10,154 | | 2023-09-08T15:19:10,154 | int 2023-09-08T15:19:10,155 424 | 0) 2023-09-08T15:19:10,155 | ~~ 2023-09-08T15:19:10,156 khmer/_khmermodule.cc:1851:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:19:10,157 1851 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:19:10,157 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,158 khmer/_khmermodule.cc:1852:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:19:10,159 1852 | "counting hash object", /* tp_doc */ 2023-09-08T15:19:10,159 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,160 | | 2023-09-08T15:19:10,160 | const char* 2023-09-08T15:19:10,161 khmer/_khmermodule.cc: In function ‘PyObject* _new_counting_hash(PyObject*, PyObject*)’: 2023-09-08T15:19:10,162 khmer/_khmermodule.cc:1903:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:19:10,163 1903 | if (PyInt_Check(size_o)) { 2023-09-08T15:19:10,163 | ^~~~~~~~~~~ 2023-09-08T15:19:10,164 | PySet_Check 2023-09-08T15:19:10,181 khmer/_khmermodule.cc:1904:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:19:10,182 1904 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:19:10,182 | ^~~~~~~~~~~~ 2023-09-08T15:19:10,183 | PyLong_AsLong 2023-09-08T15:19:10,184 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:19:10,185 khmer/_khmermodule.cc:1940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:10,185 1940 | "Hashbits", sizeof(khmer_KHashbitsObject), 2023-09-08T15:19:10,186 | ^~~~~~~~~~ 2023-09-08T15:19:10,186 | | 2023-09-08T15:19:10,187 | const char* 2023-09-08T15:19:10,187 khmer/_khmermodule.cc:1942:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:10,188 1942 | (destructor)khmer_hashbits_dealloc, /*tp_dealloc*/ 2023-09-08T15:19:10,188 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,189 | | 2023-09-08T15:19:10,190 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:19:10,190 khmer/_khmermodule.cc:1944:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:19:10,191 1944 | khmer_hashbits_getattr, /*tp_getattr*/ 2023-09-08T15:19:10,191 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,192 | | 2023-09-08T15:19:10,192 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:19:10,193 khmer/_khmermodule.cc:1957:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:19:10,193 1957 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /*tp_flags*/ 2023-09-08T15:19:10,194 khmer/_khmermodule.cc:1958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:19:10,195 1958 | "hashbits object", /* tp_doc */ 2023-09-08T15:19:10,195 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,196 | | 2023-09-08T15:19:10,197 | const char* 2023-09-08T15:19:10,217 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2023-09-08T15:19:10,217 khmer/_khmermodule.cc:2131:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:19:10,218 2131 | return PyInt_FromSize_t(hashbits->n_tags()); 2023-09-08T15:19:10,219 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,220 | PyLong_FromSize_t 2023-09-08T15:19:10,239 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2023-09-08T15:19:10,240 khmer/_khmermodule.cc:2153:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,241 2153 | return PyInt_FromLong(1); 2023-09-08T15:19:10,242 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,242 | PyLong_FromLong 2023-09-08T15:19:10,262 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2023-09-08T15:19:10,263 khmer/_khmermodule.cc:2176:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,263 2176 | return PyInt_FromLong(n_consumed); 2023-09-08T15:19:10,264 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,265 | PyLong_FromLong 2023-09-08T15:19:10,296 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2023-09-08T15:19:10,297 khmer/_khmermodule.cc:2283:40: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,298 2283 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2023-09-08T15:19:10,298 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,299 | PyLong_AsVoidPtr 2023-09-08T15:19:10,318 khmer/_khmermodule.cc:2293:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,319 2293 | return PyInt_FromLong(next_largest); 2023-09-08T15:19:10,319 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,320 | PyLong_FromLong 2023-09-08T15:19:10,336 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2023-09-08T15:19:10,337 khmer/_khmermodule.cc:2309:9: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:19:10,337 2309 | if (PyInt_Check(arg)) { 2023-09-08T15:19:10,338 | ^~~~~~~~~~~ 2023-09-08T15:19:10,338 | PySet_Check 2023-09-08T15:19:10,355 khmer/_khmermodule.cc:2310:20: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:19:10,356 2310 | long pos = PyInt_AsLong(arg); 2023-09-08T15:19:10,357 | ^~~~~~~~~~~~ 2023-09-08T15:19:10,357 | PyLong_AsLong 2023-09-08T15:19:10,378 khmer/_khmermodule.cc:2312:16: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T15:19:10,379 2312 | } else if (PyString_Check(arg)) { 2023-09-08T15:19:10,380 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,380 | PyMapping_Check 2023-09-08T15:19:10,405 khmer/_khmermodule.cc:2313:25: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T15:19:10,406 2313 | std::string s = PyString_AsString(arg); 2023-09-08T15:19:10,407 | ^~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,427 khmer/_khmermodule.cc:2320:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,428 2320 | return PyInt_FromLong(count); 2023-09-08T15:19:10,428 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,429 | PyLong_FromLong 2023-09-08T15:19:10,451 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2023-09-08T15:19:10,451 khmer/_khmermodule.cc:2362:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,452 2362 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2023-09-08T15:19:10,453 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,454 | PyLong_FromLong 2023-09-08T15:19:10,479 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2023-09-08T15:19:10,480 khmer/_khmermodule.cc:2383:27: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T15:19:10,481 2383 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T15:19:10,481 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,482 | PyBytes_FromStringAndSize 2023-09-08T15:19:10,522 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2023-09-08T15:19:10,523 khmer/_khmermodule.cc:2458:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:19:10,524 2458 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T15:19:10,524 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,525 | PyLong_FromVoidPtr 2023-09-08T15:19:10,549 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2023-09-08T15:19:10,549 khmer/_khmermodule.cc:2486:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T15:19:10,550 2486 | if (!PyCObject_Check(subset_obj)) { 2023-09-08T15:19:10,551 | ^~~~~~~~~~~~~~~ 2023-09-08T15:19:10,552 | PyODict_Check 2023-09-08T15:19:10,578 khmer/_khmermodule.cc:2492:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,578 2492 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:19:10,579 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,580 | PyLong_AsVoidPtr 2023-09-08T15:19:10,619 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2023-09-08T15:19:10,620 khmer/_khmermodule.cc:2756:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:19:10,621 2756 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T15:19:10,621 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,622 | PyLong_FromVoidPtr 2023-09-08T15:19:10,645 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2023-09-08T15:19:10,646 khmer/_khmermodule.cc:2769:10: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T15:19:10,646 2769 | if (!PyCObject_Check(ppi_obj)) { 2023-09-08T15:19:10,647 | ^~~~~~~~~~~~~~~ 2023-09-08T15:19:10,647 | PyODict_Check 2023-09-08T15:19:10,674 khmer/_khmermodule.cc:2775:35: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,675 2775 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2023-09-08T15:19:10,675 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,676 | PyLong_AsVoidPtr 2023-09-08T15:19:10,696 khmer/_khmermodule.cc:2781:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,696 2781 | return PyInt_FromLong(p); 2023-09-08T15:19:10,697 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,698 | PyLong_FromLong 2023-09-08T15:19:10,724 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2023-09-08T15:19:10,725 khmer/_khmermodule.cc:2896:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,726 2896 | return PyInt_FromLong(n_partitions); 2023-09-08T15:19:10,727 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,727 | PyLong_FromLong 2023-09-08T15:19:10,748 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2023-09-08T15:19:10,749 khmer/_khmermodule.cc:2927:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,749 2927 | return PyInt_FromLong(n_singletons); 2023-09-08T15:19:10,750 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,751 | PyLong_FromLong 2023-09-08T15:19:10,782 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2023-09-08T15:19:10,782 khmer/_khmermodule.cc:3026:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,783 3026 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:19:10,784 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,785 | PyLong_AsVoidPtr 2023-09-08T15:19:10,812 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2023-09-08T15:19:10,812 khmer/_khmermodule.cc:3043:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,813 3043 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:19:10,814 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,815 | PyLong_AsVoidPtr 2023-09-08T15:19:10,870 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:19:10,870 khmer/_khmermodule.cc:3154:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,871 3154 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:19:10,871 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,872 | PyLong_AsVoidPtr 2023-09-08T15:19:10,901 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:19:10,901 khmer/_khmermodule.cc:3185:12: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T15:19:10,902 3185 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T15:19:10,903 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,903 | PyLong_FromVoidPtr 2023-09-08T15:19:10,924 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2023-09-08T15:19:10,925 khmer/_khmermodule.cc:3214:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:10,926 3214 | return PyInt_FromLong(d); 2023-09-08T15:19:10,926 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:10,927 | PyLong_FromLong 2023-09-08T15:19:10,954 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2023-09-08T15:19:10,954 khmer/_khmermodule.cc:3230:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,955 3230 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T15:19:10,956 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,957 | PyLong_AsVoidPtr 2023-09-08T15:19:10,984 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2023-09-08T15:19:10,985 khmer/_khmermodule.cc:3256:37: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:10,986 3256 | subset1_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T15:19:10,986 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:10,987 | PyLong_AsVoidPtr 2023-09-08T15:19:11,014 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T15:19:11,015 khmer/_khmermodule.cc:3277:36: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T15:19:11,015 3277 | subset_p = (SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T15:19:11,016 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,017 | PyLong_AsVoidPtr 2023-09-08T15:19:11,038 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2023-09-08T15:19:11,038 khmer/_khmermodule.cc:3313:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:11,039 3313 | return PyInt_FromLong(p1); 2023-09-08T15:19:11,040 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:11,041 | PyLong_FromLong 2023-09-08T15:19:11,061 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2023-09-08T15:19:11,061 khmer/_khmermodule.cc:3330:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:11,062 3330 | return PyInt_FromLong(partition_id); 2023-09-08T15:19:11,063 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:11,063 | PyLong_FromLong 2023-09-08T15:19:11,089 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2023-09-08T15:19:11,089 khmer/_khmermodule.cc:3472:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T15:19:11,090 3472 | return PyInt_FromLong(k); 2023-09-08T15:19:11,090 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:11,091 | PyLong_FromLong 2023-09-08T15:19:11,129 In file included from /usr/include/python3.11/Python.h:38: 2023-09-08T15:19:11,129 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2023-09-08T15:19:11,130 khmer/_khmermodule.cc:3516:31: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:19:11,131 3516 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T15:19:11,131 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,132 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T15:19:11,132 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T15:19:11,132 | ^~~~ 2023-09-08T15:19:11,133 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T15:19:11,133 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T15:19:11,134 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:11,135 khmer/_khmermodule.cc:3516:9: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T15:19:11,135 3516 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T15:19:11,136 | ^~~~~~~~~~~~~~~ 2023-09-08T15:19:11,158 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2023-09-08T15:19:11,159 khmer/_khmermodule.cc:3623:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:19:11,160 3623 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2023-09-08T15:19:11,161 | ^~~~~~~~~~~~~ 2023-09-08T15:19:11,162 | PyCMethod 2023-09-08T15:19:11,177 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_new(PyTypeObject*, PyObject*, PyObject*)’: 2023-09-08T15:19:11,178 khmer/_khmermodule.cc:3648:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:19:11,179 3648 | if (PyInt_Check(size_o)) { 2023-09-08T15:19:11,179 | ^~~~~~~~~~~ 2023-09-08T15:19:11,180 | PySet_Check 2023-09-08T15:19:11,197 khmer/_khmermodule.cc:3649:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:19:11,198 3649 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:19:11,199 | ^~~~~~~~~~~~ 2023-09-08T15:19:11,199 | PyLong_AsLong 2023-09-08T15:19:11,258 khmer/_khmermodule.cc: In function ‘PyObject* khmer_subset_getattr(PyObject*, char*)’: 2023-09-08T15:19:11,259 khmer/_khmermodule.cc:3859:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:19:11,260 3859 | return Py_FindMethod(khmer_subset_methods, obj, name); 2023-09-08T15:19:11,261 | ^~~~~~~~~~~~~ 2023-09-08T15:19:11,261 | PyCMethod 2023-09-08T15:19:11,278 khmer/_khmermodule.cc: In function ‘PyObject* khmer_labelhash_new(PyTypeObject*, PyObject*, PyObject*)’: 2023-09-08T15:19:11,279 khmer/_khmermodule.cc:3915:17: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:19:11,279 3915 | if (PyInt_Check(size_o)) { 2023-09-08T15:19:11,280 | ^~~~~~~~~~~ 2023-09-08T15:19:11,280 | PySet_Check 2023-09-08T15:19:11,298 khmer/_khmermodule.cc:3916:48: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:19:11,298 3916 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:19:11,299 | ^~~~~~~~~~~~ 2023-09-08T15:19:11,300 | PyLong_AsLong 2023-09-08T15:19:11,345 khmer/_khmermodule.cc: In function ‘PyObject* labelhash_n_labels(PyObject*, PyObject*)’: 2023-09-08T15:19:11,345 khmer/_khmermodule.cc:4221:12: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T15:19:11,346 4221 | return PyInt_FromSize_t(labelhash->n_labels()); 2023-09-08T15:19:11,346 | ^~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,347 | PyLong_FromSize_t 2023-09-08T15:19:11,348 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:19:11,348 khmer/_khmermodule.cc:4240:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:11,349 4240 | "_LabelHash", /* tp_name */ 2023-09-08T15:19:11,349 | ^~~~~~~~~~~~ 2023-09-08T15:19:11,350 | | 2023-09-08T15:19:11,350 | const char* 2023-09-08T15:19:11,351 khmer/_khmermodule.cc:4243:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:11,352 4243 | (destructor)khmer_labelhash_dealloc, /* tp_dealloc */ 2023-09-08T15:19:11,352 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,353 | | 2023-09-08T15:19:11,354 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:19:11,355 khmer/_khmermodule.cc:4258:24: error: invalid conversion from ‘long unsigned int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:19:11,356 4258 | Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ 2023-09-08T15:19:11,356 khmer/_khmermodule.cc:4266:5: error: cannot convert ‘PyMethodDef*’ to ‘PyMemberDef*’ in initialization 2023-09-08T15:19:11,357 4266 | khmer_labelhash_methods, /* tp_methods */ 2023-09-08T15:19:11,358 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,359 | | 2023-09-08T15:19:11,359 | PyMethodDef* 2023-09-08T15:19:11,379 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2023-09-08T15:19:11,379 khmer/_khmermodule.cc:4349:12: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T15:19:11,380 4349 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2023-09-08T15:19:11,381 | ^~~~~~~~~~~~~ 2023-09-08T15:19:11,381 | PyCMethod 2023-09-08T15:19:11,382 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:19:11,383 khmer/_khmermodule.cc:4367:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:11,383 4367 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2023-09-08T15:19:11,384 | ^~~~~~~~~~~~~ 2023-09-08T15:19:11,385 | | 2023-09-08T15:19:11,386 | const char* 2023-09-08T15:19:11,387 khmer/_khmermodule.cc:4369:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T15:19:11,387 4369 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2023-09-08T15:19:11,388 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,389 | | 2023-09-08T15:19:11,390 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T15:19:11,390 khmer/_khmermodule.cc:4371:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T15:19:11,391 4371 | khmer_readaligner_getattr, /*tp_getattr*/ 2023-09-08T15:19:11,391 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,392 | | 2023-09-08T15:19:11,392 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T15:19:11,393 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T15:19:11,393 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T15:19:11,394 | ~~~ 2023-09-08T15:19:11,394 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T15:19:11,394 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T15:19:11,395 | | 2023-09-08T15:19:11,395 | int 2023-09-08T15:19:11,396 424 | 0) 2023-09-08T15:19:11,396 | ~~ 2023-09-08T15:19:11,397 khmer/_khmermodule.cc:4384:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T15:19:11,397 4384 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T15:19:11,398 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,398 khmer/_khmermodule.cc:4385:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T15:19:11,398 4385 | "ReadAligner object", /* tp_doc */ 2023-09-08T15:19:11,399 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,400 | | 2023-09-08T15:19:11,400 | const char* 2023-09-08T15:19:11,403 khmer/_khmermodule.cc: In function ‘PyObject* _new_hashbits(PyObject*, PyObject*)’: 2023-09-08T15:19:11,404 khmer/_khmermodule.cc:4445:13: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T15:19:11,405 4445 | if (PyInt_Check(size_o)) { 2023-09-08T15:19:11,406 | ^~~~~~~~~~~ 2023-09-08T15:19:11,406 | PySet_Check 2023-09-08T15:19:11,423 khmer/_khmermodule.cc:4446:44: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T15:19:11,424 4446 | sizes.push_back((HashIntoType) PyInt_AsLong(size_o)); 2023-09-08T15:19:11,425 | ^~~~~~~~~~~~ 2023-09-08T15:19:11,426 | PyLong_AsLong 2023-09-08T15:19:11,430 khmer/_khmermodule.cc: In function ‘void khmer_hashbits_dealloc(PyObject*)’: 2023-09-08T15:19:11,431 khmer/_khmermodule.cc:4536:11: error: ‘struct khmer_KHashbitsObject’ has no member named ‘ob_type’ 2023-09-08T15:19:11,432 4536 | self->ob_type->tp_free((PyObject*)obj); 2023-09-08T15:19:11,432 | ^~~~~~~ 2023-09-08T15:19:11,460 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2023-09-08T15:19:11,460 khmer/_khmermodule.cc:4611:12: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T15:19:11,461 4611 | return PyString_FromString(_revhash(val, ksize).c_str()); 2023-09-08T15:19:11,462 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:11,462 | PyLong_FromString 2023-09-08T15:19:11,463 khmer/_khmermodule.cc: At global scope: 2023-09-08T15:19:11,464 khmer/_khmermodule.cc:4687:1: error: conflicting declaration of C function ‘PyObject* init_khmer()’ 2023-09-08T15:19:11,465 4687 | init_khmer(void) 2023-09-08T15:19:11,466 | ^~~~~~~~~~ 2023-09-08T15:19:11,466 khmer/_khmermodule.cc:33:10: note: previous declaration ‘void init_khmer()’ 2023-09-08T15:19:11,467 33 | void init_khmer(); 2023-09-08T15:19:11,467 | ^~~~~~~~~~ 2023-09-08T15:19:11,468 khmer/_khmermodule.cc: In function ‘PyObject* init_khmer()’: 2023-09-08T15:19:11,469 khmer/_khmermodule.cc:4691:22: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:19:11,469 4691 | khmer_ConfigType.ob_type = &PyType_Type; 2023-09-08T15:19:11,470 | ^~~~~~~ 2023-09-08T15:19:11,470 khmer/_khmermodule.cc:4692:29: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T15:19:11,471 4692 | khmer_KCountingHashType.ob_type = &PyType_Type; 2023-09-08T15:19:11,472 | ^~~~~~~ 2023-09-08T15:19:11,473 khmer/_khmermodule.cc:4699:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:19:11,473 4699 | return; 2023-09-08T15:19:11,474 | ^~~~~~ 2023-09-08T15:19:11,474 khmer/_khmermodule.cc:4706:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:19:11,475 4706 | return; 2023-09-08T15:19:11,475 | ^~~~~~ 2023-09-08T15:19:11,490 khmer/_khmermodule.cc:4710:9: error: ‘Py_InitModule3’ was not declared in this scope 2023-09-08T15:19:11,490 4710 | m = Py_InitModule3( "_khmer", KhmerMethods, 2023-09-08T15:19:11,491 | ^~~~~~~~~~~~~~ 2023-09-08T15:19:11,492 khmer/_khmermodule.cc:4713:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:19:11,493 4713 | return; 2023-09-08T15:19:11,494 | ^~~~~~ 2023-09-08T15:19:11,495 khmer/_khmermodule.cc:4718:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:19:11,496 4718 | return; 2023-09-08T15:19:11,497 | ^~~~~~ 2023-09-08T15:19:11,498 khmer/_khmermodule.cc:4725:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:19:11,498 4725 | return; 2023-09-08T15:19:11,499 | ^~~~~~ 2023-09-08T15:19:11,500 khmer/_khmermodule.cc:4731:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:19:11,501 4731 | return; 2023-09-08T15:19:11,502 | ^~~~~~ 2023-09-08T15:19:11,502 khmer/_khmermodule.cc:4734:9: error: return-statement with no value, in function returning ‘PyObject*’ {aka ‘_object*’} [-fpermissive] 2023-09-08T15:19:11,503 4734 | return; 2023-09-08T15:19:11,504 | ^~~~~~ 2023-09-08T15:19:12,466 khmer/_khmermodule.cc:4744:23: warning: control reaches end of non-void function [-Wreturn-type] 2023-09-08T15:19:12,467 4744 | PyModule_AddObject(m, "_LabelHash", (PyObject *)&khmer_KLabelHashType); 2023-09-08T15:19:12,467 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T15:19:12,566 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T15:19:12,715 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T15:19:12,728 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T15:19:12,728 exec(compile('"'"''"'"''"'"' 2023-09-08T15:19:12,728 # This is -- a caller that pip uses to run setup.py 2023-09-08T15:19:12,728 # 2023-09-08T15:19:12,728 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T15:19:12,728 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T15:19:12,728 # - It provides a clear error message when setuptools is not installed. 2023-09-08T15:19:12,728 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T15:19:12,728 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T15:19:12,728 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T15:19:12,728 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T15:19:12,728 import os, sys, tokenize 2023-09-08T15:19:12,728 2023-09-08T15:19:12,728 try: 2023-09-08T15:19:12,728 import setuptools 2023-09-08T15:19:12,728 except ImportError as error: 2023-09-08T15:19:12,728 print( 2023-09-08T15:19:12,728 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T15:19:12,728 "the build environment.", 2023-09-08T15:19:12,728 file=sys.stderr, 2023-09-08T15:19:12,728 ) 2023-09-08T15:19:12,728 sys.exit(1) 2023-09-08T15:19:12,728 2023-09-08T15:19:12,728 __file__ = %r 2023-09-08T15:19:12,728 sys.argv[0] = __file__ 2023-09-08T15:19:12,728 2023-09-08T15:19:12,728 if os.path.exists(__file__): 2023-09-08T15:19:12,728 filename = __file__ 2023-09-08T15:19:12,728 with tokenize.open(__file__) as f: 2023-09-08T15:19:12,728 setup_py_code = f.read() 2023-09-08T15:19:12,728 else: 2023-09-08T15:19:12,728 filename = "" 2023-09-08T15:19:12,728 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T15:19:12,728 2023-09-08T15:19:12,728 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T15:19:12,728 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-mfm5ivph/khmer_196503a7fed248748380d31fe158bfc3/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-cee2wqxn[/] 2023-09-08T15:19:12,728 [bold magenta]cwd[/]: /tmp/pip-wheel-mfm5ivph/khmer_196503a7fed248748380d31fe158bfc3/ 2023-09-08T15:19:12,729 Building wheel for khmer (setup.py): finished with status 'error' 2023-09-08T15:19:12,731 ERROR: Failed building wheel for khmer 2023-09-08T15:19:12,732 Running setup.py clean for khmer 2023-09-08T15:19:12,733 Running command python setup.py clean 2023-09-08T15:19:13,595 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T15:19:13,596 !! 2023-09-08T15:19:13,597 ******************************************************************************** 2023-09-08T15:19:13,597 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T15:19:13,598 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T15:19:13,599 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T15:19:13,600 or your builds will no longer be supported. 2023-09-08T15:19:13,601 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T15:19:13,601 ******************************************************************************** 2023-09-08T15:19:13,602 !! 2023-09-08T15:19:13,603 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T15:19:13,979 running clean 2023-09-08T15:19:14,003 removing 'build/temp.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T15:19:14,006 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T15:19:14,010 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-08T15:19:14,011 'build/scripts-3.11' does not exist -- can't clean it 2023-09-08T15:19:14,012 removing 'build' 2023-09-08T15:19:14,124 Failed to build khmer 2023-09-08T15:19:14,125 ERROR: Failed to build one or more wheels 2023-09-08T15:19:14,127 Exception information: 2023-09-08T15:19:14,127 Traceback (most recent call last): 2023-09-08T15:19:14,127 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T15:19:14,127 status = run_func(*args) 2023-09-08T15:19:14,127 ^^^^^^^^^^^^^^^ 2023-09-08T15:19:14,127 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T15:19:14,127 return func(self, options, args) 2023-09-08T15:19:14,127 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T15:19:14,127 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T15:19:14,127 raise CommandError("Failed to build one or more wheels") 2023-09-08T15:19:14,127 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T15:19:14,132 Removed build tracker: '/tmp/pip-build-tracker-ebav455r'