2025-09-08T02:46:24,035 Created temporary directory: /tmp/pip-build-tracker-9k6hpsbx 2025-09-08T02:46:24,036 Initialized build tracking at /tmp/pip-build-tracker-9k6hpsbx 2025-09-08T02:46:24,036 Created build tracker: /tmp/pip-build-tracker-9k6hpsbx 2025-09-08T02:46:24,036 Entered build tracker: /tmp/pip-build-tracker-9k6hpsbx 2025-09-08T02:46:24,036 Created temporary directory: /tmp/pip-wheel-02c1em4q 2025-09-08T02:46:24,039 Created temporary directory: /tmp/pip-ephem-wheel-cache-twi8m5yj 2025-09-08T02:46:24,098 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T02:46:24,100 2 location(s) to search for versions of khmer: 2025-09-08T02:46:24,100 * https://pypi.org/simple/khmer/ 2025-09-08T02:46:24,100 * https://www.piwheels.org/simple/khmer/ 2025-09-08T02:46:24,101 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2025-09-08T02:46:24,101 Getting page https://pypi.org/simple/khmer/ 2025-09-08T02:46:24,102 Found index url https://pypi.org/simple/ 2025-09-08T02:46:24,171 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2025-09-08T02:46:24,176 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/) 2025-09-08T02:46:24,176 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/) 2025-09-08T02:46:24,176 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2025-09-08T02:46:24,176 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 2025-09-08T02:46:24,177 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/) 2025-09-08T02:46:24,177 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2025-09-08T02:46:24,177 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/) 2025-09-08T02:46:24,177 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 2025-09-08T02:46:24,177 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/) 2025-09-08T02:46:24,177 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2025-09-08T02:46:24,177 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/) 2025-09-08T02:46:24,178 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2025-09-08T02:46:24,178 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/) 2025-09-08T02:46:24,178 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 2025-09-08T02:46:24,178 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2025-09-08T02:46:24,178 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/) 2025-09-08T02:46:24,178 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2025-09-08T02:46:24,179 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/) 2025-09-08T02:46:24,179 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2025-09-08T02:46:24,179 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/) 2025-09-08T02:46:24,179 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2025-09-08T02:46:24,179 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/) 2025-09-08T02:46:24,179 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/) 2025-09-08T02:46:24,180 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 2025-09-08T02:46:24,180 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/) 2025-09-08T02:46:24,180 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/) 2025-09-08T02:46:24,180 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/) 2025-09-08T02:46:24,180 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/) 2025-09-08T02:46:24,180 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2025-09-08T02:46:24,181 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2025-09-08T02:46:24,181 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/) 2025-09-08T02:46:24,181 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2025-09-08T02:46:24,181 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/) 2025-09-08T02:46:24,181 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/) 2025-09-08T02:46:24,181 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/) 2025-09-08T02:46:24,181 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/) 2025-09-08T02:46:24,182 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/) 2025-09-08T02:46:24,182 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 2025-09-08T02:46:24,182 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2025-09-08T02:46:24,182 Getting page https://www.piwheels.org/simple/khmer/ 2025-09-08T02:46:24,183 Found index url https://www.piwheels.org/simple/ 2025-09-08T02:46:24,275 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2025-09-08T02:46:24,276 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2025-09-08T02:46:24,276 Skipping link: not a file: https://pypi.org/simple/khmer/ 2025-09-08T02:46:24,302 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2025-09-08T02:46:24,303 Collecting khmer==2.0 2025-09-08T02:46:24,304 Created temporary directory: /tmp/pip-unpack-jhxmmfgy 2025-09-08T02:46:24,458 Downloading khmer-2.0.tar.gz (8.5 MB) 2025-09-08T02:46:26,995 Added khmer==2.0 from https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz to build tracker '/tmp/pip-build-tracker-9k6hpsbx' 2025-09-08T02:46:26,996 Running setup.py (path:/tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/setup.py) egg_info for package khmer 2025-09-08T02:46:26,997 Created temporary directory: /tmp/pip-pip-egg-info-wtkk99m3 2025-09-08T02:46:26,997 Preparing metadata (setup.py): started 2025-09-08T02:46:26,998 Running command python setup.py egg_info 2025-09-08T02:46:27,701 /tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/versioneer.py:416: SyntaxWarning: invalid escape sequence '\s' 2025-09-08T02:46:27,702 mo = re.search(r'=\s*"(.*)"', line) 2025-09-08T02:46:27,734 /tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/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. 2025-09-08T02:46:27,734 import pkg_resources 2025-09-08T02:46:28,405 /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. 2025-09-08T02:46:28,405 !! 2025-09-08T02:46:28,405 ******************************************************************************** 2025-09-08T02:46:28,405 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-08T02:46:28,405 versions. Please use the underscore name 'include_dirs' instead. 2025-09-08T02:46:28,406 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T02:46:28,406 or your builds will no longer be supported. 2025-09-08T02:46:28,406 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T02:46:28,406 ******************************************************************************** 2025-09-08T02:46:28,406 !! 2025-09-08T02:46:28,406 opt = self._enforce_underscore(opt, section) 2025-09-08T02:46:28,685 /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. 2025-09-08T02:46:28,685 !! 2025-09-08T02:46:28,685 ******************************************************************************** 2025-09-08T02:46:28,685 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-08T02:46:28,685 versions. Please use the underscore name 'include_dirs' instead. 2025-09-08T02:46:28,685 (Affected: khmer). 2025-09-08T02:46:28,686 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T02:46:28,686 or your builds will no longer be supported. 2025-09-08T02:46:28,686 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T02:46:28,686 ******************************************************************************** 2025-09-08T02:46:28,686 !! 2025-09-08T02:46:28,686 opt = self._enforce_underscore(opt, section) 2025-09-08T02:46:28,688 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T02:46:28,688 !! 2025-09-08T02:46:28,688 ******************************************************************************** 2025-09-08T02:46:28,688 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T02:46:28,688 License :: OSI Approved :: BSD License 2025-09-08T02:46:28,689 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T02:46:28,689 ******************************************************************************** 2025-09-08T02:46:28,689 !! 2025-09-08T02:46:28,689 self._finalize_license_expression() 2025-09-08T02:46:28,763 running egg_info 2025-09-08T02:46:28,838 creating /tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info 2025-09-08T02:46:28,839 writing /tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info/PKG-INFO 2025-09-08T02:46:28,842 writing dependency_links to /tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info/dependency_links.txt 2025-09-08T02:46:28,844 writing requirements to /tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info/requires.txt 2025-09-08T02:46:28,845 writing top-level names to /tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info/top_level.txt 2025-09-08T02:46:28,845 writing manifest file '/tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info/SOURCES.txt' 2025-09-08T02:46:29,080 reading manifest file '/tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info/SOURCES.txt' 2025-09-08T02:46:29,081 reading manifest template 'MANIFEST.in' 2025-09-08T02:46:29,560 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2025-09-08T02:46:29,561 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2025-09-08T02:46:29,562 warning: no files found matching 'README.txt' under directory 'scripts' 2025-09-08T02:46:29,569 warning: no previously-included files matching '*.orig' found anywhere in distribution 2025-09-08T02:46:29,571 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-08T02:46:29,572 adding license file 'LICENSE' 2025-09-08T02:46:29,593 writing manifest file '/tmp/pip-pip-egg-info-wtkk99m3/khmer.egg-info/SOURCES.txt' 2025-09-08T02:46:29,719 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T02:46:29,724 Source in /tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72 has version 2.0, which satisfies requirement khmer==2.0 from https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz 2025-09-08T02:46:29,724 Removed khmer==2.0 from https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz from build tracker '/tmp/pip-build-tracker-9k6hpsbx' 2025-09-08T02:46:29,730 Created temporary directory: /tmp/pip-unpack-amp0tq8z 2025-09-08T02:46:29,730 Created temporary directory: /tmp/pip-unpack-m1qqzs9c 2025-09-08T02:46:29,730 Building wheels for collected packages: khmer 2025-09-08T02:46:29,732 Created temporary directory: /tmp/pip-wheel-y8nx55yp 2025-09-08T02:46:29,732 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 2025-09-08T02:46:29,733 Building wheel for khmer (setup.py): started 2025-09-08T02:46:29,734 Destination directory: /tmp/pip-wheel-y8nx55yp 2025-09-08T02:46:29,734 Running command python setup.py bdist_wheel 2025-09-08T02:46:30,456 /tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/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. 2025-09-08T02:46:30,456 import pkg_resources 2025-09-08T02:46:31,128 /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. 2025-09-08T02:46:31,128 !! 2025-09-08T02:46:31,128 ******************************************************************************** 2025-09-08T02:46:31,128 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-08T02:46:31,128 versions. Please use the underscore name 'include_dirs' instead. 2025-09-08T02:46:31,128 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T02:46:31,128 or your builds will no longer be supported. 2025-09-08T02:46:31,129 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T02:46:31,129 ******************************************************************************** 2025-09-08T02:46:31,129 !! 2025-09-08T02:46:31,129 opt = self._enforce_underscore(opt, section) 2025-09-08T02:46:31,405 /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. 2025-09-08T02:46:31,405 !! 2025-09-08T02:46:31,405 ******************************************************************************** 2025-09-08T02:46:31,405 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-08T02:46:31,406 versions. Please use the underscore name 'include_dirs' instead. 2025-09-08T02:46:31,406 (Affected: khmer). 2025-09-08T02:46:31,406 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T02:46:31,406 or your builds will no longer be supported. 2025-09-08T02:46:31,406 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T02:46:31,406 ******************************************************************************** 2025-09-08T02:46:31,406 !! 2025-09-08T02:46:31,406 opt = self._enforce_underscore(opt, section) 2025-09-08T02:46:31,407 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T02:46:31,407 !! 2025-09-08T02:46:31,407 ******************************************************************************** 2025-09-08T02:46:31,407 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T02:46:31,407 License :: OSI Approved :: BSD License 2025-09-08T02:46:31,407 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T02:46:31,407 ******************************************************************************** 2025-09-08T02:46:31,408 !! 2025-09-08T02:46:31,408 self._finalize_license_expression() 2025-09-08T02:46:31,408 running bdist_wheel 2025-09-08T02:46:31,636 running build 2025-09-08T02:46:31,636 got version from file /tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/khmer/_version.py {'version': '2.0', 'full': 'c2cc671127b97083e87989c0822ea036dd8202dc'} 2025-09-08T02:46:31,637 running build_py 2025-09-08T02:46:31,714 creating build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,715 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,715 copying khmer/kfile.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,716 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,716 copying khmer/khmer_logger.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,717 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,718 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,718 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:31,719 creating build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,719 copying tests/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,720 copying tests/khmer_tst_utils.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,721 copying tests/test_countgraph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,721 copying tests/test_counting_single.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,722 copying tests/test_filter.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,722 copying tests/test_functions.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,723 copying tests/test_graph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,723 copying tests/test_hll.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,724 copying tests/test_labelhash.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,724 copying tests/test_lump.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,725 copying tests/test_nodegraph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,726 copying tests/test_normalize_by_median.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,726 copying tests/test_oxli_functions.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,727 copying tests/test_read_aligner.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,727 copying tests/test_read_parsers.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,728 copying tests/test_sandbox_scripts.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,728 copying tests/test_script_arguments.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,729 copying tests/test_scripts.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,730 copying tests/test_streaming_io.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,731 copying tests/test_subset_graph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,731 copying tests/test_threaded_sequence_processor.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,732 copying tests/test_version.py -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:31,733 creating build/lib.linux-armv7l-cpython-313/oxli 2025-09-08T02:46:31,733 copying oxli/__init__.py -> build/lib.linux-armv7l-cpython-313/oxli 2025-09-08T02:46:31,733 copying oxli/build_graph.py -> build/lib.linux-armv7l-cpython-313/oxli 2025-09-08T02:46:31,734 copying oxli/functions.py -> build/lib.linux-armv7l-cpython-313/oxli 2025-09-08T02:46:31,734 running egg_info 2025-09-08T02:46:31,809 creating khmer.egg-info 2025-09-08T02:46:31,809 writing khmer.egg-info/PKG-INFO 2025-09-08T02:46:31,812 writing dependency_links to khmer.egg-info/dependency_links.txt 2025-09-08T02:46:31,814 writing requirements to khmer.egg-info/requires.txt 2025-09-08T02:46:31,815 writing top-level names to khmer.egg-info/top_level.txt 2025-09-08T02:46:31,815 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-08T02:46:31,899 reading manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-08T02:46:31,899 reading manifest template 'MANIFEST.in' 2025-09-08T02:46:32,382 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2025-09-08T02:46:32,383 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2025-09-08T02:46:32,385 warning: no files found matching 'README.txt' under directory 'scripts' 2025-09-08T02:46:32,391 warning: no previously-included files matching '*.orig' found anywhere in distribution 2025-09-08T02:46:32,393 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-08T02:46:32,393 adding license file 'LICENSE' 2025-09-08T02:46:32,414 writing manifest file 'khmer.egg-info/SOURCES.txt' 2025-09-08T02:46:32,440 copying khmer/_khmer.cc -> build/lib.linux-armv7l-cpython-313/khmer 2025-09-08T02:46:32,441 copying tests/.gitignore -> build/lib.linux-armv7l-cpython-313/khmer/tests 2025-09-08T02:46:32,442 creating build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,442 copying tests/test-data/100-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,443 copying tests/test-data/100-reads.fq.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,443 copying tests/test-data/100-reads.fq.truncated.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,444 copying tests/test-data/100-reads.fq.truncated.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,444 copying tests/test-data/all-A.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,445 copying tests/test-data/badversion-k12.ct -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,445 copying tests/test-data/badversion-k12.ht -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,446 copying tests/test-data/badversion-k32.stoptags -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,446 copying tests/test-data/badversion-k32.tagset -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,447 copying tests/test-data/biglump-random-20-a.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,447 copying tests/test-data/casava_18-pe.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,448 copying tests/test-data/combine_parts_1.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,448 copying tests/test-data/dn-test-all-paired-all-keep.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,449 copying tests/test-data/dn-test-none-paired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,449 copying tests/test-data/dn-test-some-paired-all-keep.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,450 copying tests/test-data/empty-file -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,450 copying tests/test-data/empty-file.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,451 copying tests/test-data/empty-file.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,451 copying tests/test-data/fakelump.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,452 copying tests/test-data/fakelump.fa.stoptags.txt -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,452 copying tests/test-data/filter-test-A.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,453 copying tests/test-data/filter-test-B.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,453 copying tests/test-data/goodversion-k12.ht -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,454 copying tests/test-data/goodversion-k12.ht.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,454 copying tests/test-data/goodversion-k32.stoptags -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,455 copying tests/test-data/goodversion-k32.tagset -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,455 copying tests/test-data/multi-output.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,456 copying tests/test-data/normC20k20.ct -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,471 copying tests/test-data/old-style-format-w-comments.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,472 copying tests/test-data/paired-broken.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,472 copying tests/test-data/paired-broken.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,473 copying tests/test-data/paired-broken.fq.badleft -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,473 copying tests/test-data/paired-broken.fq.badright -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,474 copying tests/test-data/paired-broken.fq.paired_bad -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,474 copying tests/test-data/paired-broken2.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,475 copying tests/test-data/paired-broken2.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,475 copying tests/test-data/paired-broken3.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,476 copying tests/test-data/paired-broken3.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,476 copying tests/test-data/paired-broken4.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,477 copying tests/test-data/paired-broken4.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,477 copying tests/test-data/paired-mixed-2.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,478 copying tests/test-data/paired-mixed-broken.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,478 copying tests/test-data/paired-mixed.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,479 copying tests/test-data/paired-mixed.fa.pe -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,479 copying tests/test-data/paired-mixed.fa.se -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,480 copying tests/test-data/paired-mixed.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,480 copying tests/test-data/paired-mixed.fq.pe -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,481 copying tests/test-data/paired-mixed.fq.se -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,481 copying tests/test-data/paired-slash1.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,482 copying tests/test-data/paired-slash1.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,482 copying tests/test-data/paired-slash1.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,483 copying tests/test-data/paired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,483 copying tests/test-data/paired.fa.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,484 copying tests/test-data/paired.fa.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,484 copying tests/test-data/paired.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,485 copying tests/test-data/paired.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,485 copying tests/test-data/paired.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,486 copying tests/test-data/paired_one.base.dif.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,486 copying tests/test-data/random-20-X2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,487 copying tests/test-data/random-20-a.even.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,487 copying tests/test-data/random-20-a.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,488 copying tests/test-data/random-20-a.fa.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,489 copying tests/test-data/random-20-a.fa.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,489 copying tests/test-data/random-20-a.fa.part -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,490 copying tests/test-data/random-20-a.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,490 copying tests/test-data/random-20-a.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,491 copying tests/test-data/random-20-a.fq.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,491 copying tests/test-data/random-20-a.odd.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,492 copying tests/test-data/random-20-b.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,492 copying tests/test-data/random-31-c.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,493 copying tests/test-data/readaligner-default.json -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,494 copying tests/test-data/readaligner-k12.json -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,494 copying tests/test-data/real-partition-small.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,495 copying tests/test-data/real-partition-tiny.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,495 copying tests/test-data/single-read.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,496 copying tests/test-data/test-abund-read-2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,496 copying tests/test-data/test-abund-read-2.fa.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,497 copying tests/test-data/test-abund-read-2.fa.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,497 copying tests/test-data/test-abund-read-2.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,498 copying tests/test-data/test-abund-read-2.paired.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,498 copying tests/test-data/test-abund-read-2.paired2.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,499 copying tests/test-data/test-abund-read-3.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,499 copying tests/test-data/test-abund-read-impaired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,500 copying tests/test-data/test-abund-read-paired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,501 copying tests/test-data/test-abund-read-paired.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,501 copying tests/test-data/test-abund-read.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,502 copying tests/test-data/test-empty.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,502 copying tests/test-data/test-empty.fa.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,503 copying tests/test-data/test-error-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,503 copying tests/test-data/test-fastq-n-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,504 copying tests/test-data/test-fastq-reads.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,504 copying tests/test-data/test-fastq-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,505 copying tests/test-data/test-filter-abund-Ns.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,505 copying tests/test-data/test-graph.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,506 copying tests/test-data/test-graph2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,506 copying tests/test-data/test-graph5.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,507 copying tests/test-data/test-labels.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,507 copying tests/test-data/test-large.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,546 copying tests/test-data/test-multi.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,547 copying tests/test-data/test-output-partitions.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,547 copying tests/test-data/test-overlap1.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,553 copying tests/test-data/test-overlap2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,559 copying tests/test-data/test-reads.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,568 copying tests/test-data/test-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,571 copying tests/test-data/test-reads.fq.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,574 copying tests/test-data/test-short.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,575 copying tests/test-data/test-sweep-contigs.fp -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,576 copying tests/test-data/test-sweep-reads.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,576 copying tests/test-data/test-sweep-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,577 copying tests/test-data/test-transcript.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,577 copying tests/test-data/truncated.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data 2025-09-08T02:46:32,579 running build_ext 2025-09-08T02:46:32,579 error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system 2025-09-08T02:46:32,704 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T02:46:32,716 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T02:46:32,716 exec(compile('"'"''"'"''"'"' 2025-09-08T02:46:32,716 # This is -- a caller that pip uses to run setup.py 2025-09-08T02:46:32,716 # 2025-09-08T02:46:32,716 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T02:46:32,716 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T02:46:32,716 # - It provides a clear error message when setuptools is not installed. 2025-09-08T02:46:32,716 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T02:46:32,716 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T02:46:32,716 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T02:46:32,716 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T02:46:32,716 import os, sys, tokenize, traceback 2025-09-08T02:46:32,716 2025-09-08T02:46:32,716 try: 2025-09-08T02:46:32,716 import setuptools 2025-09-08T02:46:32,716 except ImportError: 2025-09-08T02:46:32,716 print( 2025-09-08T02:46:32,716 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T02:46:32,716 "the build environment with exception:", 2025-09-08T02:46:32,716 file=sys.stderr, 2025-09-08T02:46:32,716 ) 2025-09-08T02:46:32,716 traceback.print_exc() 2025-09-08T02:46:32,716 sys.exit(1) 2025-09-08T02:46:32,716 2025-09-08T02:46:32,716 __file__ = %r 2025-09-08T02:46:32,716 sys.argv[0] = __file__ 2025-09-08T02:46:32,716 2025-09-08T02:46:32,716 if os.path.exists(__file__): 2025-09-08T02:46:32,716 filename = __file__ 2025-09-08T02:46:32,716 with tokenize.open(__file__) as f: 2025-09-08T02:46:32,716 setup_py_code = f.read() 2025-09-08T02:46:32,716 else: 2025-09-08T02:46:32,716 filename = "" 2025-09-08T02:46:32,716 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T02:46:32,716 2025-09-08T02:46:32,716 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T02:46:32,716 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-y8nx55yp[/] 2025-09-08T02:46:32,716 [bold magenta]cwd[/]: /tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/ 2025-09-08T02:46:32,716 Building wheel for khmer (setup.py): finished with status 'error' 2025-09-08T02:46:32,717 ERROR: Failed building wheel for khmer 2025-09-08T02:46:32,718 Running setup.py clean for khmer 2025-09-08T02:46:32,719 Running command python setup.py clean 2025-09-08T02:46:33,450 /tmp/pip-wheel-02c1em4q/khmer_badb65e5889443b3b6af15a7462eda72/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. 2025-09-08T02:46:33,450 import pkg_resources 2025-09-08T02:46:34,116 /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. 2025-09-08T02:46:34,116 !! 2025-09-08T02:46:34,117 ******************************************************************************** 2025-09-08T02:46:34,117 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-08T02:46:34,117 versions. Please use the underscore name 'include_dirs' instead. 2025-09-08T02:46:34,117 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T02:46:34,117 or your builds will no longer be supported. 2025-09-08T02:46:34,117 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T02:46:34,117 ******************************************************************************** 2025-09-08T02:46:34,117 !! 2025-09-08T02:46:34,118 opt = self._enforce_underscore(opt, section) 2025-09-08T02:46:34,396 /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. 2025-09-08T02:46:34,396 !! 2025-09-08T02:46:34,396 ******************************************************************************** 2025-09-08T02:46:34,396 Usage of dash-separated 'include-dirs' will not be supported in future 2025-09-08T02:46:34,396 versions. Please use the underscore name 'include_dirs' instead. 2025-09-08T02:46:34,396 (Affected: khmer). 2025-09-08T02:46:34,396 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T02:46:34,396 or your builds will no longer be supported. 2025-09-08T02:46:34,397 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T02:46:34,397 ******************************************************************************** 2025-09-08T02:46:34,397 !! 2025-09-08T02:46:34,397 opt = self._enforce_underscore(opt, section) 2025-09-08T02:46:34,397 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T02:46:34,397 !! 2025-09-08T02:46:34,397 ******************************************************************************** 2025-09-08T02:46:34,397 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T02:46:34,398 License :: OSI Approved :: BSD License 2025-09-08T02:46:34,398 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T02:46:34,398 ******************************************************************************** 2025-09-08T02:46:34,398 !! 2025-09-08T02:46:34,398 self._finalize_license_expression() 2025-09-08T02:46:34,475 running clean 2025-09-08T02:46:34,550 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T02:46:34,562 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T02:46:34,562 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T02:46:34,563 removing 'build' 2025-09-08T02:46:34,685 Failed to build khmer 2025-09-08T02:46:34,686 ERROR: Failed to build one or more wheels 2025-09-08T02:46:34,687 Exception information: 2025-09-08T02:46:34,687 Traceback (most recent call last): 2025-09-08T02:46:34,687 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T02:46:34,687 status = _inner_run() 2025-09-08T02:46:34,687 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T02:46:34,687 return self.run(options, args) 2025-09-08T02:46:34,687 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T02:46:34,687 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T02:46:34,687 return func(self, options, args) 2025-09-08T02:46:34,687 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T02:46:34,687 raise CommandError("Failed to build one or more wheels") 2025-09-08T02:46:34,687 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T02:46:34,691 Removed build tracker: '/tmp/pip-build-tracker-9k6hpsbx'