2025-09-07T23:59:19,688 Created temporary directory: /tmp/pip-build-tracker-0crswaie 2025-09-07T23:59:19,688 Initialized build tracking at /tmp/pip-build-tracker-0crswaie 2025-09-07T23:59:19,689 Created build tracker: /tmp/pip-build-tracker-0crswaie 2025-09-07T23:59:19,689 Entered build tracker: /tmp/pip-build-tracker-0crswaie 2025-09-07T23:59:19,689 Created temporary directory: /tmp/pip-wheel-h5o1337j 2025-09-07T23:59:19,692 Created temporary directory: /tmp/pip-ephem-wheel-cache-ajzspl4x 2025-09-07T23:59:19,749 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:59:19,752 2 location(s) to search for versions of khmer: 2025-09-07T23:59:19,752 * https://pypi.org/simple/khmer/ 2025-09-07T23:59:19,752 * https://www.piwheels.org/simple/khmer/ 2025-09-07T23:59:19,752 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2025-09-07T23:59:19,752 Getting page https://pypi.org/simple/khmer/ 2025-09-07T23:59:19,753 Found index url https://pypi.org/simple/ 2025-09-07T23:59:19,824 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:59:19,829 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/) 2025-09-07T23:59:19,829 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/) 2025-09-07T23:59:19,830 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2025-09-07T23:59:19,830 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 2025-09-07T23:59:19,830 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/) 2025-09-07T23:59:19,830 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2025-09-07T23:59:19,830 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/) 2025-09-07T23:59:19,831 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 2025-09-07T23:59:19,831 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/) 2025-09-07T23:59:19,831 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2025-09-07T23:59:19,831 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/) 2025-09-07T23:59:19,831 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2025-09-07T23:59:19,831 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/) 2025-09-07T23:59:19,832 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 2025-09-07T23:59:19,832 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2025-09-07T23:59:19,832 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/) 2025-09-07T23:59:19,832 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2025-09-07T23:59:19,832 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/) 2025-09-07T23:59:19,833 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2025-09-07T23:59:19,833 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/) 2025-09-07T23:59:19,833 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2025-09-07T23:59:19,833 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/) 2025-09-07T23:59:19,833 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/) 2025-09-07T23:59:19,833 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 2025-09-07T23:59:19,834 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/) 2025-09-07T23:59:19,834 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/) 2025-09-07T23:59:19,834 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/) 2025-09-07T23:59:19,834 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/) 2025-09-07T23:59:19,834 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2025-09-07T23:59:19,834 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2025-09-07T23:59:19,834 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/) 2025-09-07T23:59:19,835 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2025-09-07T23:59:19,835 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/) 2025-09-07T23:59:19,835 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/) 2025-09-07T23:59:19,835 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/) 2025-09-07T23:59:19,835 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/) 2025-09-07T23:59:19,835 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/) 2025-09-07T23:59:19,835 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 2025-09-07T23:59:19,836 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:59:19,836 Getting page https://www.piwheels.org/simple/khmer/ 2025-09-07T23:59:19,837 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:59:19,929 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2025-09-07T23:59:19,930 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:59:19,930 Skipping link: not a file: https://pypi.org/simple/khmer/ 2025-09-07T23:59:19,953 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2025-09-07T23:59:19,954 Collecting khmer==1.1 2025-09-07T23:59:19,956 Created temporary directory: /tmp/pip-unpack-dg0hfw_3 2025-09-07T23:59:20,100 Downloading khmer-1.1.tar.gz (3.6 MB) 2025-09-07T23:59:20,983 Added khmer==1.1 from https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz to build tracker '/tmp/pip-build-tracker-0crswaie' 2025-09-07T23:59:20,984 Running setup.py (path:/tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/setup.py) egg_info for package khmer 2025-09-07T23:59:20,985 Created temporary directory: /tmp/pip-pip-egg-info-edliz5sn 2025-09-07T23:59:20,985 Preparing metadata (setup.py): started 2025-09-07T23:59:20,986 Running command python setup.py egg_info 2025-09-07T23:59:21,520 /tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/ez_setup.py:126: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T23:59:21,520 import pkg_resources 2025-09-07T23:59:22,087 /tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/versioneer.py:324: SyntaxWarning: invalid escape sequence '\s' 2025-09-07T23:59:22,088 mo = re.search(r'=\s*"(.*)"', line) 2025-09-07T23:59:22,199 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'include-dirs' in 'build_ext' (setup.cfg), please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:22,199 !! 2025-09-07T23:59:22,199 ******************************************************************************** 2025-09-07T23:59:22,199 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:59:22,199 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:22,200 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:59:22,200 or your builds will no longer be supported. 2025-09-07T23:59:22,200 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:59:22,200 ******************************************************************************** 2025-09-07T23:59:22,200 !! 2025-09-07T23:59:22,200 opt = self._enforce_underscore(opt, section) 2025-09-07T23:59:22,469 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'include-dirs' in 'build_ext' (setup.cfg), please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:22,470 !! 2025-09-07T23:59:22,470 ******************************************************************************** 2025-09-07T23:59:22,470 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:59:22,470 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:22,470 (Affected: khmer). 2025-09-07T23:59:22,470 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:59:22,470 or your builds will no longer be supported. 2025-09-07T23:59:22,471 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:59:22,471 ******************************************************************************** 2025-09-07T23:59:22,471 !! 2025-09-07T23:59:22,471 opt = self._enforce_underscore(opt, section) 2025-09-07T23:59:22,471 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:59:22,471 !! 2025-09-07T23:59:22,471 ******************************************************************************** 2025-09-07T23:59:22,471 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:59:22,472 License :: OSI Approved :: BSD License 2025-09-07T23:59:22,472 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:59:22,472 ******************************************************************************** 2025-09-07T23:59:22,472 !! 2025-09-07T23:59:22,472 self._finalize_license_expression() 2025-09-07T23:59:22,543 running egg_info 2025-09-07T23:59:22,616 creating /tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info 2025-09-07T23:59:22,616 writing /tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info/PKG-INFO 2025-09-07T23:59:22,619 writing dependency_links to /tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info/dependency_links.txt 2025-09-07T23:59:22,621 writing requirements to /tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info/requires.txt 2025-09-07T23:59:22,621 writing top-level names to /tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info/top_level.txt 2025-09-07T23:59:22,621 writing manifest file '/tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info/SOURCES.txt' 2025-09-07T23:59:22,702 dependency third-party/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,702 dependency third-party/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,702 dependency third-party/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,702 dependency third-party/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,703 dependency third-party/zlib/gzclose.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,703 dependency third-party/zlib/gzlib.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,703 dependency third-party/zlib/gzread.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,703 dependency third-party/zlib/gzwrite.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,704 dependency third-party/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,704 dependency third-party/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,704 dependency third-party/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,704 dependency third-party/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,705 dependency third-party/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,705 dependency third-party/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,705 dependency third-party/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,705 dependency third-party/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,706 dependency third-party/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,706 dependency third-party/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,706 dependency third-party/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,706 dependency third-party/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,707 dependency third-party/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,707 dependency third-party/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:22,861 reading manifest file '/tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info/SOURCES.txt' 2025-09-07T23:59:22,862 reading manifest template 'MANIFEST.in' 2025-09-07T23:59:23,069 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2025-09-07T23:59:23,070 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2025-09-07T23:59:23,077 warning: no previously-included files matching '*.orig' found anywhere in distribution 2025-09-07T23:59:23,079 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-07T23:59:23,079 adding license file 'LICENSE' 2025-09-07T23:59:23,092 writing manifest file '/tmp/pip-pip-egg-info-edliz5sn/khmer.egg-info/SOURCES.txt' 2025-09-07T23:59:23,216 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:59:23,221 Source in /tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb has version 1.1, which satisfies requirement khmer==1.1 from https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz 2025-09-07T23:59:23,221 Removed khmer==1.1 from https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz from build tracker '/tmp/pip-build-tracker-0crswaie' 2025-09-07T23:59:23,226 Created temporary directory: /tmp/pip-unpack-w5f8tsip 2025-09-07T23:59:23,226 Created temporary directory: /tmp/pip-unpack-dcg6kt53 2025-09-07T23:59:23,226 Building wheels for collected packages: khmer 2025-09-07T23:59:23,228 Created temporary directory: /tmp/pip-wheel-6zof2hmk 2025-09-07T23:59:23,228 DEPRECATION: Building 'khmer' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'khmer'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-07T23:59:23,229 Building wheel for khmer (setup.py): started 2025-09-07T23:59:23,230 Destination directory: /tmp/pip-wheel-6zof2hmk 2025-09-07T23:59:23,230 Running command python setup.py bdist_wheel 2025-09-07T23:59:23,757 /tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/ez_setup.py:126: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T23:59:23,757 import pkg_resources 2025-09-07T23:59:24,427 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'include-dirs' in 'build_ext' (setup.cfg), please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:24,427 !! 2025-09-07T23:59:24,427 ******************************************************************************** 2025-09-07T23:59:24,428 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:59:24,428 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:24,428 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:59:24,428 or your builds will no longer be supported. 2025-09-07T23:59:24,428 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:59:24,428 ******************************************************************************** 2025-09-07T23:59:24,428 !! 2025-09-07T23:59:24,429 opt = self._enforce_underscore(opt, section) 2025-09-07T23:59:24,699 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'include-dirs' in 'build_ext' (setup.cfg), please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:24,699 !! 2025-09-07T23:59:24,699 ******************************************************************************** 2025-09-07T23:59:24,699 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:59:24,699 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:24,700 (Affected: khmer). 2025-09-07T23:59:24,700 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:59:24,700 or your builds will no longer be supported. 2025-09-07T23:59:24,700 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:59:24,700 ******************************************************************************** 2025-09-07T23:59:24,700 !! 2025-09-07T23:59:24,700 opt = self._enforce_underscore(opt, section) 2025-09-07T23:59:24,700 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:59:24,701 !! 2025-09-07T23:59:24,701 ******************************************************************************** 2025-09-07T23:59:24,701 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:59:24,701 License :: OSI Approved :: BSD License 2025-09-07T23:59:24,701 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:59:24,701 ******************************************************************************** 2025-09-07T23:59:24,701 !! 2025-09-07T23:59:24,701 self._finalize_license_expression() 2025-09-07T23:59:24,702 running bdist_wheel 2025-09-07T23:59:24,920 running build 2025-09-07T23:59:24,920 got version from file /tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/khmer/_version.py {'version': '1.1', 'full': '1fe98c92b5a9b3f46a5f4f05cd35d3229ce2ff0a'} 2025-09-07T23:59:24,920 running build_py 2025-09-07T23:59:24,996 creating build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:24,996 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:24,997 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:24,998 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:24,998 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:24,999 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:24,999 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:25,000 copying khmer/file.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:25,000 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:25,001 creating build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,001 copying tests/test_threaded_sequence_processor.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,002 copying tests/test_subset_graph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,003 copying tests/test_scripts.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,003 copying tests/test_script_arguments.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,004 copying tests/test_sandbox_scripts.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,004 copying tests/test_read_parsers.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,005 copying tests/test_lump.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,005 copying tests/test_labelhash.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,006 copying tests/test_khmer_config.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,006 copying tests/test_hashbits_obj.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,007 copying tests/test_hashbits.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,008 copying tests/test_graph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,008 copying tests/test_functions.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,009 copying tests/test_filter.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,009 copying tests/test_counting_single.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,010 copying tests/test_counting_hash.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,010 copying tests/test_c_wrapper.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,011 copying tests/test_align.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,011 copying tests/khmer_tst_utils.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,012 copying tests/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,012 running egg_info 2025-09-07T23:59:25,086 creating khmer.egg-info 2025-09-07T23:59:25,086 writing khmer.egg-info/PKG-INFO 2025-09-07T23:59:25,089 writing dependency_links to khmer.egg-info/dependency_links.txt 2025-09-07T23:59:25,090 writing requirements to khmer.egg-info/requires.txt 2025-09-07T23:59:25,091 writing top-level names to khmer.egg-info/top_level.txt 2025-09-07T23:59:25,091 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:59:25,095 dependency third-party/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,095 dependency third-party/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,096 dependency third-party/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,096 dependency third-party/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,096 dependency third-party/zlib/gzclose.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,096 dependency third-party/zlib/gzlib.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,097 dependency third-party/zlib/gzread.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,097 dependency third-party/zlib/gzwrite.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,097 dependency third-party/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,098 dependency third-party/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,098 dependency third-party/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,098 dependency third-party/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,099 dependency third-party/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,099 dependency third-party/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,099 dependency third-party/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,099 dependency third-party/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,100 dependency third-party/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,100 dependency third-party/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,100 dependency third-party/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,100 dependency third-party/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,101 dependency third-party/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,101 dependency third-party/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:59:25,177 reading manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:59:25,178 reading manifest template 'MANIFEST.in' 2025-09-07T23:59:25,386 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2025-09-07T23:59:25,386 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2025-09-07T23:59:25,394 warning: no previously-included files matching '*.orig' found anywhere in distribution 2025-09-07T23:59:25,395 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-07T23:59:25,396 adding license file 'LICENSE' 2025-09-07T23:59:25,408 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:59:25,420 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:59:25,421 copying tests/.gitignore -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-07T23:59:25,422 creating build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,422 copying tests/test-data/100-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,423 copying tests/test-data/100-reads.fq.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,423 copying tests/test-data/all-A.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,424 copying tests/test-data/badversion-k12.ht -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,424 copying tests/test-data/badversion-k12.kh -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,425 copying tests/test-data/badversion-k32.stoptags -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,425 copying tests/test-data/badversion-k32.tagset -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,426 copying tests/test-data/biglump-random-20-a.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,426 copying tests/test-data/combine_parts_1.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,427 copying tests/test-data/empty-file -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,427 copying tests/test-data/fakelump.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,428 copying tests/test-data/fakelump.fa.stoptags.txt -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,428 copying tests/test-data/filter-test-A.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,429 copying tests/test-data/filter-test-B.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,429 copying tests/test-data/goodversion-k12.ht -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,430 copying tests/test-data/goodversion-k12.ht.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,430 copying tests/test-data/goodversion-k32.stoptags -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,431 copying tests/test-data/goodversion-k32.tagset -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,431 copying tests/test-data/overlap.curve -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,432 copying tests/test-data/overlap.out -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,432 copying tests/test-data/paired-mixed.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,433 copying tests/test-data/paired-mixed.fa.pe -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,433 copying tests/test-data/paired-mixed.fa.se -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,434 copying tests/test-data/paired-mixed.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,434 copying tests/test-data/paired-mixed.fq.pe -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,435 copying tests/test-data/paired-mixed.fq.se -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,435 copying tests/test-data/paired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,436 copying tests/test-data/paired.fa.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,436 copying tests/test-data/paired.fa.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,437 copying tests/test-data/paired.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,437 copying tests/test-data/paired.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,438 copying tests/test-data/paired.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,438 copying tests/test-data/random-20-X2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,439 copying tests/test-data/random-20-a.even.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,439 copying tests/test-data/random-20-a.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,440 copying tests/test-data/random-20-a.fa.part -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,441 copying tests/test-data/random-20-a.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,441 copying tests/test-data/random-20-a.odd.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,442 copying tests/test-data/random-20-b.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,442 copying tests/test-data/random-31-c.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,443 copying tests/test-data/real-partition-small.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,443 copying tests/test-data/real-partition-tiny.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,444 copying tests/test-data/simple_1.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,444 copying tests/test-data/simple_2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,445 copying tests/test-data/simple_3.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,445 copying tests/test-data/single-read.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,446 copying tests/test-data/test-abund-read-2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,447 copying tests/test-data/test-abund-read-2.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,448 copying tests/test-data/test-abund-read-3.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,448 copying tests/test-data/test-abund-read-impaired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,449 copying tests/test-data/test-abund-read-paired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,449 copying tests/test-data/test-abund-read.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,450 copying tests/test-data/test-colors.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,450 copying tests/test-data/test-empty.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,451 copying tests/test-data/test-empty.fa.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,451 copying tests/test-data/test-error-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,452 copying tests/test-data/test-est.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,452 copying tests/test-data/test-fastq-n-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,453 copying tests/test-data/test-fastq-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,454 copying tests/test-data/test-graph.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,454 copying tests/test-data/test-graph2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,455 copying tests/test-data/test-graph3.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,455 copying tests/test-data/test-graph4.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,455 copying tests/test-data/test-graph5.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,456 copying tests/test-data/test-graph6.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,457 copying tests/test-data/test-labels.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,457 copying tests/test-data/test-output-partitions.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,458 copying tests/test-data/test-overlap1.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,463 copying tests/test-data/test-overlap2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,469 copying tests/test-data/test-reads.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,479 copying tests/test-data/test-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,482 copying tests/test-data/test-short.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,482 copying tests/test-data/test-sweep-contigs.fp -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,483 copying tests/test-data/test-sweep-reads.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,483 copying tests/test-data/test-sweep-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,484 copying tests/test-data/test-transcript.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-07T23:59:25,485 running build_ext 2025-09-07T23:59:25,485 bash -c "cd third-party/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC" 2025-09-07T23:59:25,606 Checking for gcc... 2025-09-07T23:59:25,873 Building static library libz.a version 1.2.8 with gcc. 2025-09-07T23:59:25,974 Checking for off64_t... Yes. 2025-09-07T23:59:25,982 Checking for fseeko... Yes. 2025-09-07T23:59:26,206 Checking for strerror... Yes. 2025-09-07T23:59:26,349 Checking for unistd.h... Yes. 2025-09-07T23:59:26,468 Checking for stdarg.h... Yes. 2025-09-07T23:59:26,610 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). 2025-09-07T23:59:26,831 Checking for vsnprintf() in stdio.h... Yes. 2025-09-07T23:59:26,950 Checking for return value of vsnprintf()... Yes. 2025-09-07T23:59:27,048 Checking for attribute(visibility) support... Yes. 2025-09-07T23:59:27,115 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c 2025-09-07T23:59:27,502 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c 2025-09-07T23:59:27,991 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c 2025-09-07T23:59:30,087 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c 2025-09-07T23:59:30,988 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c 2025-09-07T23:59:31,492 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c 2025-09-07T23:59:33,505 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c 2025-09-07T23:59:34,090 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c 2025-09-07T23:59:35,615 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c 2025-09-07T23:59:35,804 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c 2025-09-07T23:59:35,954 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c 2025-09-07T23:59:36,094 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c 2025-09-07T23:59:36,148 In file included from /usr/include/features.h:415, 2025-09-07T23:59:36,149 from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2025-09-07T23:59:36,149 from /usr/include/stdio.h:28, 2025-09-07T23:59:36,149 from gzguts.h:21, 2025-09-07T23:59:36,149 from gzclose.c:6: 2025-09-07T23:59:36,149 /usr/include/features-time64.h:26:5: error: #error "_TIME_BITS=64 is allowed only with _FILE_OFFSET_BITS=64" 2025-09-07T23:59:36,149 26 | # error "_TIME_BITS=64 is allowed only with _FILE_OFFSET_BITS=64" 2025-09-07T23:59:36,149 | ^~~~~ 2025-09-07T23:59:36,230 make: *** [Makefile:159: gzclose.lo] Error 1 2025-09-07T23:59:36,231 error: command '/usr/bin/bash' failed with exit code 2 2025-09-07T23:59:36,357 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:59:36,368 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:59:36,368 exec(compile('"'"''"'"''"'"' 2025-09-07T23:59:36,368 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:59:36,368 # 2025-09-07T23:59:36,368 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:59:36,368 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:59:36,368 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:59:36,368 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:59:36,368 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:59:36,368 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:59:36,368 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:59:36,368 import os, sys, tokenize, traceback 2025-09-07T23:59:36,368 2025-09-07T23:59:36,368 try: 2025-09-07T23:59:36,368 import setuptools 2025-09-07T23:59:36,368 except ImportError: 2025-09-07T23:59:36,368 print( 2025-09-07T23:59:36,368 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:59:36,368 "the build environment with exception:", 2025-09-07T23:59:36,368 file=sys.stderr, 2025-09-07T23:59:36,368 ) 2025-09-07T23:59:36,368 traceback.print_exc() 2025-09-07T23:59:36,368 sys.exit(1) 2025-09-07T23:59:36,368 2025-09-07T23:59:36,368 __file__ = %r 2025-09-07T23:59:36,368 sys.argv[0] = __file__ 2025-09-07T23:59:36,368 2025-09-07T23:59:36,368 if os.path.exists(__file__): 2025-09-07T23:59:36,368 filename = __file__ 2025-09-07T23:59:36,368 with tokenize.open(__file__) as f: 2025-09-07T23:59:36,368 setup_py_code = f.read() 2025-09-07T23:59:36,368 else: 2025-09-07T23:59:36,368 filename = "" 2025-09-07T23:59:36,368 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:59:36,368 2025-09-07T23:59:36,368 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:59:36,368 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-6zof2hmk[/] 2025-09-07T23:59:36,368 [bold magenta]cwd[/]: /tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/ 2025-09-07T23:59:36,369 Building wheel for khmer (setup.py): finished with status 'error' 2025-09-07T23:59:36,369 ERROR: Failed building wheel for khmer 2025-09-07T23:59:36,370 Running setup.py clean for khmer 2025-09-07T23:59:36,371 Running command python setup.py clean 2025-09-07T23:59:36,909 /tmp/pip-wheel-h5o1337j/khmer_e16c2e252e204c17984ba5958d832fcb/ez_setup.py:126: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81. 2025-09-07T23:59:36,909 import pkg_resources 2025-09-07T23:59:37,576 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'include-dirs' in 'build_ext' (setup.cfg), please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:37,576 !! 2025-09-07T23:59:37,577 ******************************************************************************** 2025-09-07T23:59:37,577 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:59:37,577 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:37,577 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:59:37,577 or your builds will no longer be supported. 2025-09-07T23:59:37,577 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:59:37,577 ******************************************************************************** 2025-09-07T23:59:37,578 !! 2025-09-07T23:59:37,578 opt = self._enforce_underscore(opt, section) 2025-09-07T23:59:37,855 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'include-dirs' in 'build_ext' (setup.cfg), please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:37,855 !! 2025-09-07T23:59:37,855 ******************************************************************************** 2025-09-07T23:59:37,855 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:59:37,855 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:59:37,855 (Affected: khmer). 2025-09-07T23:59:37,855 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:59:37,855 or your builds will no longer be supported. 2025-09-07T23:59:37,856 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:59:37,856 ******************************************************************************** 2025-09-07T23:59:37,856 !! 2025-09-07T23:59:37,856 opt = self._enforce_underscore(opt, section) 2025-09-07T23:59:37,856 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:59:37,856 !! 2025-09-07T23:59:37,856 ******************************************************************************** 2025-09-07T23:59:37,856 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:59:37,857 License :: OSI Approved :: BSD License 2025-09-07T23:59:37,857 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:59:37,857 ******************************************************************************** 2025-09-07T23:59:37,857 !! 2025-09-07T23:59:37,857 self._finalize_license_expression() 2025-09-07T23:59:37,933 running clean 2025-09-07T23:59:38,007 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:59:38,013 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:59:38,013 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:59:38,013 removing 'build' 2025-09-07T23:59:38,136 Failed to build khmer 2025-09-07T23:59:38,137 ERROR: Failed to build one or more wheels 2025-09-07T23:59:38,138 Exception information: 2025-09-07T23:59:38,138 Traceback (most recent call last): 2025-09-07T23:59:38,138 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:59:38,138 status = _inner_run() 2025-09-07T23:59:38,138 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:59:38,138 return self.run(options, args) 2025-09-07T23:59:38,138 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:59:38,138 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:59:38,138 return func(self, options, args) 2025-09-07T23:59:38,138 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:59:38,138 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:59:38,138 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:59:38,142 Removed build tracker: '/tmp/pip-build-tracker-0crswaie'