2025-09-07T23:51:12,830 Created temporary directory: /tmp/pip-build-tracker-xdphtxi7 2025-09-07T23:51:12,831 Initialized build tracking at /tmp/pip-build-tracker-xdphtxi7 2025-09-07T23:51:12,831 Created build tracker: /tmp/pip-build-tracker-xdphtxi7 2025-09-07T23:51:12,831 Entered build tracker: /tmp/pip-build-tracker-xdphtxi7 2025-09-07T23:51:12,831 Created temporary directory: /tmp/pip-wheel-cwezruyd 2025-09-07T23:51:12,835 Created temporary directory: /tmp/pip-ephem-wheel-cache-dix22ozu 2025-09-07T23:51:12,890 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:51:12,892 2 location(s) to search for versions of khmer: 2025-09-07T23:51:12,892 * https://pypi.org/simple/khmer/ 2025-09-07T23:51:12,892 * https://www.piwheels.org/simple/khmer/ 2025-09-07T23:51:12,893 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2025-09-07T23:51:12,893 Getting page https://pypi.org/simple/khmer/ 2025-09-07T23:51:12,894 Found index url https://pypi.org/simple/ 2025-09-07T23:51:12,965 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:51:12,970 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/) 2025-09-07T23:51:12,970 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/) 2025-09-07T23:51:12,970 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2025-09-07T23:51:12,971 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 2025-09-07T23:51:12,971 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/) 2025-09-07T23:51:12,971 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2025-09-07T23:51:12,971 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/) 2025-09-07T23:51:12,971 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 2025-09-07T23:51:12,972 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/) 2025-09-07T23:51:12,972 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2025-09-07T23:51:12,972 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/) 2025-09-07T23:51:12,972 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2025-09-07T23:51:12,972 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/) 2025-09-07T23:51:12,972 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 2025-09-07T23:51:12,973 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2025-09-07T23:51:12,973 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/) 2025-09-07T23:51:12,973 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2025-09-07T23:51:12,973 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/) 2025-09-07T23:51:12,973 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2025-09-07T23:51:12,974 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/) 2025-09-07T23:51:12,974 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2025-09-07T23:51:12,974 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/) 2025-09-07T23:51:12,974 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/) 2025-09-07T23:51:12,974 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 2025-09-07T23:51:12,974 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/) 2025-09-07T23:51:12,975 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/) 2025-09-07T23:51:12,975 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/) 2025-09-07T23:51:12,975 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/) 2025-09-07T23:51:12,975 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2025-09-07T23:51:12,975 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2025-09-07T23:51:12,975 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/) 2025-09-07T23:51:12,975 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2025-09-07T23:51:12,976 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/) 2025-09-07T23:51:12,976 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/) 2025-09-07T23:51:12,976 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/) 2025-09-07T23:51:12,976 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/) 2025-09-07T23:51:12,976 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/) 2025-09-07T23:51:12,976 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 2025-09-07T23:51:12,977 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:51:12,977 Getting page https://www.piwheels.org/simple/khmer/ 2025-09-07T23:51:12,978 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:51:13,165 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2025-09-07T23:51:13,166 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2025-09-07T23:51:13,167 Skipping link: not a file: https://pypi.org/simple/khmer/ 2025-09-07T23:51:13,204 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2025-09-07T23:51:13,205 Collecting khmer==1.0.1 2025-09-07T23:51:13,206 Created temporary directory: /tmp/pip-unpack-5am038w_ 2025-09-07T23:51:13,368 Downloading khmer-1.0.1.tar.gz (19.0 MB) 2025-09-07T23:51:16,889 Added khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-xdphtxi7' 2025-09-07T23:51:16,890 Running setup.py (path:/tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/setup.py) egg_info for package khmer 2025-09-07T23:51:16,890 Created temporary directory: /tmp/pip-pip-egg-info-4kkmt1ur 2025-09-07T23:51:16,890 Preparing metadata (setup.py): started 2025-09-07T23:51:16,891 Running command python setup.py egg_info 2025-09-07T23:51:17,691 /tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/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. 2025-09-07T23:51:17,691 import pkg_resources 2025-09-07T23:51:18,242 /tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/versioneer.py:324: SyntaxWarning: invalid escape sequence '\s' 2025-09-07T23:51:18,242 mo = re.search(r'=\s*"(.*)"', line) 2025-09-07T23:51:18,354 /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. 2025-09-07T23:51:18,354 !! 2025-09-07T23:51:18,354 ******************************************************************************** 2025-09-07T23:51:18,354 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:51:18,354 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:51:18,354 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:51:18,354 or your builds will no longer be supported. 2025-09-07T23:51:18,355 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:51:18,355 ******************************************************************************** 2025-09-07T23:51:18,355 !! 2025-09-07T23:51:18,355 opt = self._enforce_underscore(opt, section) 2025-09-07T23:51:18,624 /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. 2025-09-07T23:51:18,624 !! 2025-09-07T23:51:18,624 ******************************************************************************** 2025-09-07T23:51:18,624 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:51:18,625 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:51:18,625 (Affected: khmer). 2025-09-07T23:51:18,625 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:51:18,625 or your builds will no longer be supported. 2025-09-07T23:51:18,625 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:51:18,625 ******************************************************************************** 2025-09-07T23:51:18,625 !! 2025-09-07T23:51:18,625 opt = self._enforce_underscore(opt, section) 2025-09-07T23:51:18,626 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:51:18,626 !! 2025-09-07T23:51:18,626 ******************************************************************************** 2025-09-07T23:51:18,626 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:51:18,626 License :: OSI Approved :: BSD License 2025-09-07T23:51:18,626 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:51:18,626 ******************************************************************************** 2025-09-07T23:51:18,627 !! 2025-09-07T23:51:18,627 self._finalize_license_expression() 2025-09-07T23:51:18,699 running egg_info 2025-09-07T23:51:18,770 creating /tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info 2025-09-07T23:51:18,771 writing /tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info/PKG-INFO 2025-09-07T23:51:18,773 writing dependency_links to /tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info/dependency_links.txt 2025-09-07T23:51:18,775 writing requirements to /tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info/requires.txt 2025-09-07T23:51:18,775 writing top-level names to /tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info/top_level.txt 2025-09-07T23:51:18,775 writing manifest file '/tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info/SOURCES.txt' 2025-09-07T23:51:18,854 dependency lib/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,854 dependency lib/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,854 dependency lib/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,855 dependency lib/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,855 dependency lib/zlib/gzclose.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,855 dependency lib/zlib/gzlib.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,855 dependency lib/zlib/gzread.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,856 dependency lib/zlib/gzwrite.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,856 dependency lib/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,856 dependency lib/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,857 dependency lib/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,857 dependency lib/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,857 dependency lib/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,857 dependency lib/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,858 dependency lib/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,858 dependency lib/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,858 dependency lib/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,858 dependency lib/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,859 dependency lib/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,859 dependency lib/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,859 dependency lib/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:18,859 dependency lib/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:19,007 reading manifest file '/tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info/SOURCES.txt' 2025-09-07T23:51:19,007 reading manifest template 'MANIFEST.in' 2025-09-07T23:51:19,262 warning: no previously-included files found matching 'lib/zlib/Makefile' 2025-09-07T23:51:19,262 warning: no previously-included files found matching 'lib/zlib/zconf.h' 2025-09-07T23:51:19,267 no previously-included directories found matching 'doc/doxygen' 2025-09-07T23:51:19,273 warning: no previously-included files matching '*.orig' found anywhere in distribution 2025-09-07T23:51:19,274 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-07T23:51:19,275 adding license file 'LICENSE' 2025-09-07T23:51:19,288 writing manifest file '/tmp/pip-pip-egg-info-4kkmt1ur/khmer.egg-info/SOURCES.txt' 2025-09-07T23:51:19,414 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:51:19,419 Source in /tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05 has version 1.0.1, which satisfies requirement khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz 2025-09-07T23:51:19,419 Removed khmer==1.0.1 from https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-xdphtxi7' 2025-09-07T23:51:19,424 Created temporary directory: /tmp/pip-unpack-ylk38yem 2025-09-07T23:51:19,424 Created temporary directory: /tmp/pip-unpack-_9u5wxmf 2025-09-07T23:51:19,424 Building wheels for collected packages: khmer 2025-09-07T23:51:19,426 Created temporary directory: /tmp/pip-wheel-xpubgot0 2025-09-07T23:51:19,426 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 2025-09-07T23:51:19,427 Building wheel for khmer (setup.py): started 2025-09-07T23:51:19,428 Destination directory: /tmp/pip-wheel-xpubgot0 2025-09-07T23:51:19,428 Running command python setup.py bdist_wheel 2025-09-07T23:51:19,966 /tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/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. 2025-09-07T23:51:19,967 import pkg_resources 2025-09-07T23:51:20,621 /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. 2025-09-07T23:51:20,621 !! 2025-09-07T23:51:20,622 ******************************************************************************** 2025-09-07T23:51:20,622 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:51:20,622 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:51:20,622 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:51:20,622 or your builds will no longer be supported. 2025-09-07T23:51:20,622 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:51:20,622 ******************************************************************************** 2025-09-07T23:51:20,623 !! 2025-09-07T23:51:20,623 opt = self._enforce_underscore(opt, section) 2025-09-07T23:51:20,893 /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. 2025-09-07T23:51:20,893 !! 2025-09-07T23:51:20,893 ******************************************************************************** 2025-09-07T23:51:20,893 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:51:20,893 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:51:20,893 (Affected: khmer). 2025-09-07T23:51:20,893 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:51:20,894 or your builds will no longer be supported. 2025-09-07T23:51:20,894 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:51:20,894 ******************************************************************************** 2025-09-07T23:51:20,894 !! 2025-09-07T23:51:20,894 opt = self._enforce_underscore(opt, section) 2025-09-07T23:51:20,894 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:51:20,894 !! 2025-09-07T23:51:20,895 ******************************************************************************** 2025-09-07T23:51:20,895 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:51:20,895 License :: OSI Approved :: BSD License 2025-09-07T23:51:20,895 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:51:20,895 ******************************************************************************** 2025-09-07T23:51:20,895 !! 2025-09-07T23:51:20,895 self._finalize_license_expression() 2025-09-07T23:51:20,896 running bdist_wheel 2025-09-07T23:51:21,116 running build 2025-09-07T23:51:21,116 got version from file /tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/khmer/_version.py {'version': '1.0.1', 'full': '53a97858f0b445a323419829a0c5baef5f242e4e'} 2025-09-07T23:51:21,116 running build_py 2025-09-07T23:51:21,193 creating build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,193 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,194 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,194 copying khmer/load_pe.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,195 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,195 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,196 copying khmer/file.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,196 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,197 copying khmer/threading_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,197 running egg_info 2025-09-07T23:51:21,272 creating khmer.egg-info 2025-09-07T23:51:21,272 writing khmer.egg-info/PKG-INFO 2025-09-07T23:51:21,275 writing dependency_links to khmer.egg-info/dependency_links.txt 2025-09-07T23:51:21,276 writing requirements to khmer.egg-info/requires.txt 2025-09-07T23:51:21,276 writing top-level names to khmer.egg-info/top_level.txt 2025-09-07T23:51:21,277 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:51:21,280 dependency lib/zlib/adler32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,280 dependency lib/zlib/compress.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,280 dependency lib/zlib/crc32.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,281 dependency lib/zlib/deflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,281 dependency lib/zlib/gzclose.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,281 dependency lib/zlib/gzlib.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,281 dependency lib/zlib/gzread.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,282 dependency lib/zlib/gzwrite.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,282 dependency lib/zlib/infback.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,282 dependency lib/zlib/inffast.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,283 dependency lib/zlib/inflate.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,283 dependency lib/zlib/inftrees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,283 dependency lib/zlib/trees.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,283 dependency lib/zlib/uncompr.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,284 dependency lib/zlib/zutil.lo won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,284 dependency lib/bzip2/blocksort.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,284 dependency lib/bzip2/huffman.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,284 dependency lib/bzip2/crctable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,285 dependency lib/bzip2/randtable.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,285 dependency lib/bzip2/compress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,285 dependency lib/bzip2/decompress.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,285 dependency lib/bzip2/bzlib.o won't be automatically included in the manifest: the path doesn't exist 2025-09-07T23:51:21,359 reading manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:51:21,360 reading manifest template 'MANIFEST.in' 2025-09-07T23:51:21,615 warning: no previously-included files found matching 'lib/zlib/Makefile' 2025-09-07T23:51:21,616 warning: no previously-included files found matching 'lib/zlib/zconf.h' 2025-09-07T23:51:21,620 no previously-included directories found matching 'doc/doxygen' 2025-09-07T23:51:21,625 warning: no previously-included files matching '*.orig' found anywhere in distribution 2025-09-07T23:51:21,626 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-07T23:51:21,627 adding license file 'LICENSE' 2025-09-07T23:51:21,640 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-07T23:51:21,647 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-07T23:51:21,649 running build_ext 2025-09-07T23:51:21,649 bash -c "cd lib/zlib && ( test Makefile -nt configure || bash ./configure --static ) && make -f Makefile.pic PIC" 2025-09-07T23:51:21,769 Checking for gcc... 2025-09-07T23:51:22,026 Building static library libz.a version 1.2.8 with gcc. 2025-09-07T23:51:22,133 Checking for off64_t... Yes. 2025-09-07T23:51:22,143 Checking for fseeko... Yes. 2025-09-07T23:51:22,366 Checking for strerror... Yes. 2025-09-07T23:51:22,508 Checking for unistd.h... Yes. 2025-09-07T23:51:22,631 Checking for stdarg.h... Yes. 2025-09-07T23:51:22,782 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). 2025-09-07T23:51:23,013 Checking for vsnprintf() in stdio.h... Yes. 2025-09-07T23:51:23,136 Checking for return value of vsnprintf()... Yes. 2025-09-07T23:51:23,239 Checking for attribute(visibility) support... Yes. 2025-09-07T23:51:23,308 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c 2025-09-07T23:51:23,694 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c 2025-09-07T23:51:24,185 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c 2025-09-07T23:51:26,272 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c 2025-09-07T23:51:27,178 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c 2025-09-07T23:51:27,688 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c 2025-09-07T23:51:29,706 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c 2025-09-07T23:51:30,282 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c 2025-09-07T23:51:31,810 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c 2025-09-07T23:51:31,995 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c 2025-09-07T23:51:32,147 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c 2025-09-07T23:51:32,289 gcc -O3 -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c 2025-09-07T23:51:32,338 In file included from /usr/include/features.h:415, 2025-09-07T23:51:32,338 from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2025-09-07T23:51:32,339 from /usr/include/stdio.h:28, 2025-09-07T23:51:32,339 from gzguts.h:21, 2025-09-07T23:51:32,339 from gzclose.c:6: 2025-09-07T23:51:32,339 /usr/include/features-time64.h:26:5: error: #error "_TIME_BITS=64 is allowed only with _FILE_OFFSET_BITS=64" 2025-09-07T23:51:32,339 26 | # error "_TIME_BITS=64 is allowed only with _FILE_OFFSET_BITS=64" 2025-09-07T23:51:32,339 | ^~~~~ 2025-09-07T23:51:32,417 make: *** [Makefile:159: gzclose.lo] Error 1 2025-09-07T23:51:32,418 error: command '/usr/bin/bash' failed with exit code 2 2025-09-07T23:51:32,546 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:51:32,558 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:51:32,558 exec(compile('"'"''"'"''"'"' 2025-09-07T23:51:32,558 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:51:32,558 # 2025-09-07T23:51:32,558 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:51:32,558 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:51:32,558 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:51:32,558 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:51:32,558 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:51:32,558 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:51:32,558 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:51:32,558 import os, sys, tokenize, traceback 2025-09-07T23:51:32,558 2025-09-07T23:51:32,558 try: 2025-09-07T23:51:32,558 import setuptools 2025-09-07T23:51:32,558 except ImportError: 2025-09-07T23:51:32,558 print( 2025-09-07T23:51:32,558 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:51:32,558 "the build environment with exception:", 2025-09-07T23:51:32,558 file=sys.stderr, 2025-09-07T23:51:32,558 ) 2025-09-07T23:51:32,558 traceback.print_exc() 2025-09-07T23:51:32,558 sys.exit(1) 2025-09-07T23:51:32,558 2025-09-07T23:51:32,558 __file__ = %r 2025-09-07T23:51:32,558 sys.argv[0] = __file__ 2025-09-07T23:51:32,558 2025-09-07T23:51:32,558 if os.path.exists(__file__): 2025-09-07T23:51:32,558 filename = __file__ 2025-09-07T23:51:32,558 with tokenize.open(__file__) as f: 2025-09-07T23:51:32,558 setup_py_code = f.read() 2025-09-07T23:51:32,558 else: 2025-09-07T23:51:32,558 filename = "" 2025-09-07T23:51:32,558 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:51:32,558 2025-09-07T23:51:32,558 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:51:32,558 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-xpubgot0[/] 2025-09-07T23:51:32,558 [bold magenta]cwd[/]: /tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/ 2025-09-07T23:51:32,558 Building wheel for khmer (setup.py): finished with status 'error' 2025-09-07T23:51:32,559 ERROR: Failed building wheel for khmer 2025-09-07T23:51:32,559 Running setup.py clean for khmer 2025-09-07T23:51:32,560 Running command python setup.py clean 2025-09-07T23:51:33,101 /tmp/pip-wheel-cwezruyd/khmer_491c9b988bdb40ffaf3bb60adffd9a05/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. 2025-09-07T23:51:33,101 import pkg_resources 2025-09-07T23:51:33,766 /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. 2025-09-07T23:51:33,767 !! 2025-09-07T23:51:33,767 ******************************************************************************** 2025-09-07T23:51:33,767 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:51:33,767 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:51:33,767 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:51:33,767 or your builds will no longer be supported. 2025-09-07T23:51:33,768 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:51:33,768 ******************************************************************************** 2025-09-07T23:51:33,768 !! 2025-09-07T23:51:33,768 opt = self._enforce_underscore(opt, section) 2025-09-07T23:51:34,047 /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. 2025-09-07T23:51:34,047 !! 2025-09-07T23:51:34,047 ******************************************************************************** 2025-09-07T23:51:34,047 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-07T23:51:34,047 versions. Please use the underscore name 'include_dirs' instead. 2025-09-07T23:51:34,047 (Affected: khmer). 2025-09-07T23:51:34,048 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-07T23:51:34,048 or your builds will no longer be supported. 2025-09-07T23:51:34,048 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-07T23:51:34,048 ******************************************************************************** 2025-09-07T23:51:34,048 !! 2025-09-07T23:51:34,048 opt = self._enforce_underscore(opt, section) 2025-09-07T23:51:34,048 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:51:34,048 !! 2025-09-07T23:51:34,049 ******************************************************************************** 2025-09-07T23:51:34,049 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:51:34,049 License :: OSI Approved :: BSD License 2025-09-07T23:51:34,049 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:51:34,049 ******************************************************************************** 2025-09-07T23:51:34,049 !! 2025-09-07T23:51:34,049 self._finalize_license_expression() 2025-09-07T23:51:34,122 running clean 2025-09-07T23:51:34,195 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:51:34,196 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:51:34,196 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:51:34,196 removing 'build' 2025-09-07T23:51:34,321 Failed to build khmer 2025-09-07T23:51:34,322 ERROR: Failed to build one or more wheels 2025-09-07T23:51:34,322 Exception information: 2025-09-07T23:51:34,322 Traceback (most recent call last): 2025-09-07T23:51:34,322 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:51:34,322 status = _inner_run() 2025-09-07T23:51:34,322 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:51:34,322 return self.run(options, args) 2025-09-07T23:51:34,322 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:51:34,322 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:51:34,322 return func(self, options, args) 2025-09-07T23:51:34,322 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:51:34,322 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:51:34,322 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:51:34,327 Removed build tracker: '/tmp/pip-build-tracker-xdphtxi7'