2025-09-08T01:54:39,161 Created temporary directory: /tmp/pip-build-tracker-1hm3q49h
2025-09-08T01:54:39,161 Initialized build tracking at /tmp/pip-build-tracker-1hm3q49h
2025-09-08T01:54:39,162 Created build tracker: /tmp/pip-build-tracker-1hm3q49h
2025-09-08T01:54:39,162 Entered build tracker: /tmp/pip-build-tracker-1hm3q49h
2025-09-08T01:54:39,162 Created temporary directory: /tmp/pip-wheel-2yndp9bd
2025-09-08T01:54:39,165 Created temporary directory: /tmp/pip-ephem-wheel-cache-547yijmr
2025-09-08T01:54:39,224 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-08T01:54:39,226 2 location(s) to search for versions of khmer:
2025-09-08T01:54:39,226 * https://pypi.org/simple/khmer/
2025-09-08T01:54:39,226 * https://www.piwheels.org/simple/khmer/
2025-09-08T01:54:39,227 Fetching project page and analyzing links: https://pypi.org/simple/khmer/
2025-09-08T01:54:39,227 Getting page https://pypi.org/simple/khmer/
2025-09-08T01:54:39,228 Found index url https://pypi.org/simple/
2025-09-08T01:54:39,299 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json
2025-09-08T01:54:39,304   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/)
2025-09-08T01:54:39,304   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/)
2025-09-08T01:54:39,304   Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6
2025-09-08T01:54:39,305   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
2025-09-08T01:54:39,305   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/)
2025-09-08T01:54:39,305   Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7
2025-09-08T01:54:39,305   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/)
2025-09-08T01:54:39,305   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
2025-09-08T01:54:39,305   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/)
2025-09-08T01:54:39,306   Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8
2025-09-08T01:54:39,306   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/)
2025-09-08T01:54:39,306   Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0
2025-09-08T01:54:39,306   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/)
2025-09-08T01:54:39,306   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
2025-09-08T01:54:39,307   Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1
2025-09-08T01:54:39,307   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/)
2025-09-08T01:54:39,307   Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2
2025-09-08T01:54:39,307   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/)
2025-09-08T01:54:39,307   Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3
2025-09-08T01:54:39,307   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/)
2025-09-08T01:54:39,308   Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4
2025-09-08T01:54:39,308   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/)
2025-09-08T01:54:39,308   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/)
2025-09-08T01:54:39,308   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
2025-09-08T01:54:39,308   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/)
2025-09-08T01:54:39,308   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/)
2025-09-08T01:54:39,308   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/)
2025-09-08T01:54:39,309   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/)
2025-09-08T01:54:39,309   Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0
2025-09-08T01:54:39,309   Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3
2025-09-08T01:54:39,309   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/)
2025-09-08T01:54:39,309   Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1
2025-09-08T01:54:39,309   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/)
2025-09-08T01:54:39,310   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/)
2025-09-08T01:54:39,310   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/)
2025-09-08T01:54:39,310   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/)
2025-09-08T01:54:39,310   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/)
2025-09-08T01:54:39,310   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
2025-09-08T01:54:39,310 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/
2025-09-08T01:54:39,311 Getting page https://www.piwheels.org/simple/khmer/
2025-09-08T01:54:39,312 Found index url https://www.piwheels.org/simple/
2025-09-08T01:54:39,397 Fetched page https://www.piwheels.org/simple/khmer/ as text/html
2025-09-08T01:54:39,398 Skipping link: not a file: https://www.piwheels.org/simple/khmer/
2025-09-08T01:54:39,398 Skipping link: not a file: https://pypi.org/simple/khmer/
2025-09-08T01:54:39,426 Given no hashes to check 1 links for project 'khmer': discarding no candidates
2025-09-08T01:54:39,427 Collecting khmer==1.4.1
2025-09-08T01:54:39,428   Created temporary directory: /tmp/pip-unpack-nqbijizg
2025-09-08T01:54:40,193   Downloading khmer-1.4.1.tar.gz (8.6 MB)
2025-09-08T01:54:42,555   Added khmer==1.4.1 from https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz to build tracker '/tmp/pip-build-tracker-1hm3q49h'
2025-09-08T01:54:42,556   Running setup.py (path:/tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/setup.py) egg_info for package khmer
2025-09-08T01:54:42,556   Created temporary directory: /tmp/pip-pip-egg-info-39uo2r53
2025-09-08T01:54:42,557   Preparing metadata (setup.py): started
2025-09-08T01:54:42,557   Running command python setup.py egg_info
2025-09-08T01:54:43,285   /tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/versioneer.py:415: SyntaxWarning: invalid escape sequence '\s'
2025-09-08T01:54:43,285     mo = re.search(r'=\s*"(.*)"', line)
2025-09-08T01:54:43,319   /tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/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.
2025-09-08T01:54:43,319     import pkg_resources
2025-09-08T01:54:44,066   /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.
2025-09-08T01:54:44,066   !!

2025-09-08T01:54:44,066           ********************************************************************************
2025-09-08T01:54:44,066           Usage of dash-separated 'include-dirs' will not be supported in future
2025-09-08T01:54:44,066           versions. Please use the underscore name 'include_dirs' instead.

2025-09-08T01:54:44,066           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T01:54:44,067           or your builds will no longer be supported.

2025-09-08T01:54:44,067           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T01:54:44,067           ********************************************************************************

2025-09-08T01:54:44,067   !!
2025-09-08T01:54:44,067     opt = self._enforce_underscore(opt, section)
2025-09-08T01:54:44,341   /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.
2025-09-08T01:54:44,341   !!

2025-09-08T01:54:44,341           ********************************************************************************
2025-09-08T01:54:44,341           Usage of dash-separated 'include-dirs' will not be supported in future
2025-09-08T01:54:44,342           versions. Please use the underscore name 'include_dirs' instead.
2025-09-08T01:54:44,342           (Affected: khmer).

2025-09-08T01:54:44,342           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T01:54:44,342           or your builds will no longer be supported.

2025-09-08T01:54:44,342           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T01:54:44,342           ********************************************************************************

2025-09-08T01:54:44,342   !!
2025-09-08T01:54:44,342     opt = self._enforce_underscore(opt, section)
2025-09-08T01:54:44,343   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-09-08T01:54:44,343   !!

2025-09-08T01:54:44,343           ********************************************************************************
2025-09-08T01:54:44,343           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-09-08T01:54:44,343           License :: OSI Approved :: BSD License

2025-09-08T01:54:44,343           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-09-08T01:54:44,343           ********************************************************************************

2025-09-08T01:54:44,344   !!
2025-09-08T01:54:44,344     self._finalize_license_expression()
2025-09-08T01:54:44,415   running egg_info
2025-09-08T01:54:44,490   creating /tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info
2025-09-08T01:54:44,491   writing /tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info/PKG-INFO
2025-09-08T01:54:44,494   writing dependency_links to /tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info/dependency_links.txt
2025-09-08T01:54:44,496   writing requirements to /tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info/requires.txt
2025-09-08T01:54:44,496   writing top-level names to /tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info/top_level.txt
2025-09-08T01:54:44,496   writing manifest file '/tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info/SOURCES.txt'
2025-09-08T01:54:44,728   reading manifest file '/tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info/SOURCES.txt'
2025-09-08T01:54:44,729   reading manifest template 'MANIFEST.in'
2025-09-08T01:54:45,308   warning: no previously-included files found matching 'third-party/zlib/Makefile'
2025-09-08T01:54:45,309   warning: no previously-included files found matching 'third-party/zlib/zconf.h'
2025-09-08T01:54:45,318   warning: no previously-included files matching '*.orig' found anywhere in distribution
2025-09-08T01:54:45,321   warning: no previously-included files matching '*.pyc' found anywhere in distribution
2025-09-08T01:54:45,321   adding license file 'LICENSE'
2025-09-08T01:54:45,343   writing manifest file '/tmp/pip-pip-egg-info-39uo2r53/khmer.egg-info/SOURCES.txt'
2025-09-08T01:54:45,470   Preparing metadata (setup.py): finished with status 'done'
2025-09-08T01:54:45,474   Source in /tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512 has version 1.4.1, which satisfies requirement khmer==1.4.1 from https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz
2025-09-08T01:54:45,474   Removed khmer==1.4.1 from https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz from build tracker '/tmp/pip-build-tracker-1hm3q49h'
2025-09-08T01:54:45,481 Created temporary directory: /tmp/pip-unpack-0aoy1k7t
2025-09-08T01:54:45,481 Created temporary directory: /tmp/pip-unpack-xtr4sdhy
2025-09-08T01:54:45,481 Building wheels for collected packages: khmer
2025-09-08T01:54:45,483   Created temporary directory: /tmp/pip-wheel-nwd_twga
2025-09-08T01:54:45,483   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
2025-09-08T01:54:45,484   Building wheel for khmer (setup.py): started
2025-09-08T01:54:45,485   Destination directory: /tmp/pip-wheel-nwd_twga
2025-09-08T01:54:45,485   Running command python setup.py bdist_wheel
2025-09-08T01:54:46,209   /tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/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.
2025-09-08T01:54:46,209     import pkg_resources
2025-09-08T01:54:46,881   /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.
2025-09-08T01:54:46,881   !!

2025-09-08T01:54:46,881           ********************************************************************************
2025-09-08T01:54:46,881           Usage of dash-separated 'include-dirs' will not be supported in future
2025-09-08T01:54:46,881           versions. Please use the underscore name 'include_dirs' instead.

2025-09-08T01:54:46,881           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T01:54:46,881           or your builds will no longer be supported.

2025-09-08T01:54:46,882           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T01:54:46,882           ********************************************************************************

2025-09-08T01:54:46,882   !!
2025-09-08T01:54:46,882     opt = self._enforce_underscore(opt, section)
2025-09-08T01:54:47,153   /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.
2025-09-08T01:54:47,153   !!

2025-09-08T01:54:47,153           ********************************************************************************
2025-09-08T01:54:47,153           Usage of dash-separated 'include-dirs' will not be supported in future
2025-09-08T01:54:47,153           versions. Please use the underscore name 'include_dirs' instead.
2025-09-08T01:54:47,153           (Affected: khmer).

2025-09-08T01:54:47,154           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T01:54:47,154           or your builds will no longer be supported.

2025-09-08T01:54:47,154           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T01:54:47,154           ********************************************************************************

2025-09-08T01:54:47,154   !!
2025-09-08T01:54:47,154     opt = self._enforce_underscore(opt, section)
2025-09-08T01:54:47,155   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-09-08T01:54:47,155   !!

2025-09-08T01:54:47,155           ********************************************************************************
2025-09-08T01:54:47,155           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-09-08T01:54:47,155           License :: OSI Approved :: BSD License

2025-09-08T01:54:47,155           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-09-08T01:54:47,155           ********************************************************************************

2025-09-08T01:54:47,155   !!
2025-09-08T01:54:47,156     self._finalize_license_expression()
2025-09-08T01:54:47,156   running bdist_wheel
2025-09-08T01:54:47,373   running build
2025-09-08T01:54:47,373   got version from file /tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/khmer/_version.py {'version': '1.4.1', 'full': '1e762a3cd8567848b76ff7842c437aaab89d925f'}
2025-09-08T01:54:47,373   running build_py
2025-09-08T01:54:47,450   creating build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:47,450   copying khmer/_version.py -> build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:47,451   copying khmer/utils.py -> build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:47,451   copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:47,452   copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:47,453   copying khmer/kfile.py -> build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:47,453   copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:47,454   creating build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,454   copying tests/test_version.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,455   copying tests/test_threaded_sequence_processor.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,456   copying tests/test_subset_graph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,456   copying tests/test_scripts.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,457   copying tests/test_script_arguments.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,458   copying tests/test_sandbox_scripts.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,458   copying tests/test_read_parsers.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,459   copying tests/test_read_aligner.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,459   copying tests/test_lump.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,460   copying tests/test_labelhash.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,460   copying tests/test_hll.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,461   copying tests/test_hashbits_obj.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,461   copying tests/test_hashbits.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,462   copying tests/test_graph.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,462   copying tests/test_functions.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,463   copying tests/test_filter.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,463   copying tests/test_counting_single.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,464   copying tests/test_counting_hash.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,465   copying tests/khmer_tst_utils.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,465   copying tests/__init__.py -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:47,465   running egg_info
2025-09-08T01:54:47,538   creating khmer.egg-info
2025-09-08T01:54:47,539   writing khmer.egg-info/PKG-INFO
2025-09-08T01:54:47,542   writing dependency_links to khmer.egg-info/dependency_links.txt
2025-09-08T01:54:47,543   writing requirements to khmer.egg-info/requires.txt
2025-09-08T01:54:47,544   writing top-level names to khmer.egg-info/top_level.txt
2025-09-08T01:54:47,544   writing manifest file 'khmer.egg-info/SOURCES.txt'
2025-09-08T01:54:47,622   reading manifest file 'khmer.egg-info/SOURCES.txt'
2025-09-08T01:54:47,623   reading manifest template 'MANIFEST.in'
2025-09-08T01:54:48,211   warning: no previously-included files found matching 'third-party/zlib/Makefile'
2025-09-08T01:54:48,211   warning: no previously-included files found matching 'third-party/zlib/zconf.h'
2025-09-08T01:54:48,221   warning: no previously-included files matching '*.orig' found anywhere in distribution
2025-09-08T01:54:48,223   warning: no previously-included files matching '*.pyc' found anywhere in distribution
2025-09-08T01:54:48,224   adding license file 'LICENSE'
2025-09-08T01:54:48,247   writing manifest file 'khmer.egg-info/SOURCES.txt'
2025-09-08T01:54:48,274   copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-313/khmer
2025-09-08T01:54:48,275   copying tests/.gitignore -> build/lib.linux-armv7l-cpython-313/khmer/tests
2025-09-08T01:54:48,276   creating build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,276   copying tests/test-data/100-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,277   copying tests/test-data/100-reads.fq.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,277   copying tests/test-data/100-reads.fq.truncated.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,278   copying tests/test-data/100-reads.fq.truncated.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,278   copying tests/test-data/all-A.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,279   copying tests/test-data/badversion-k12.ct -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,279   copying tests/test-data/badversion-k12.ht -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,280   copying tests/test-data/badversion-k32.stoptags -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,280   copying tests/test-data/badversion-k32.tagset -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,281   copying tests/test-data/biglump-random-20-a.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,281   copying tests/test-data/casava_18-pe.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,282   copying tests/test-data/combine_parts_1.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,282   copying tests/test-data/empty-file -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,283   copying tests/test-data/fakelump.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,283   copying tests/test-data/fakelump.fa.stoptags.txt -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,284   copying tests/test-data/filter-test-A.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,284   copying tests/test-data/filter-test-B.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,285   copying tests/test-data/goodversion-k12.ht -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,285   copying tests/test-data/goodversion-k12.ht.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,286   copying tests/test-data/goodversion-k32.stoptags -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,286   copying tests/test-data/goodversion-k32.tagset -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,287   copying tests/test-data/normC20k20.ct -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,287   copying tests/test-data/old-style-format-w-comments.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,288   copying tests/test-data/overlap.out -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,289   copying tests/test-data/paired-broken.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,289   copying tests/test-data/paired-broken.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,290   copying tests/test-data/paired-broken2.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,290   copying tests/test-data/paired-broken2.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,291   copying tests/test-data/paired-broken3.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,291   copying tests/test-data/paired-broken3.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,292   copying tests/test-data/paired-mixed-2.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,292   copying tests/test-data/paired-mixed-broken.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,293   copying tests/test-data/paired-mixed.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,293   copying tests/test-data/paired-mixed.fa.pe -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,293   copying tests/test-data/paired-mixed.fa.se -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,294   copying tests/test-data/paired-mixed.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,295   copying tests/test-data/paired-mixed.fq.pe -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,295   copying tests/test-data/paired-mixed.fq.se -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,296   copying tests/test-data/paired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,296   copying tests/test-data/paired.fa.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,297   copying tests/test-data/paired.fa.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,297   copying tests/test-data/paired.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,298   copying tests/test-data/paired.fq.1 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,298   copying tests/test-data/paired.fq.2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,299   copying tests/test-data/random-20-X2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,299   copying tests/test-data/random-20-a.even.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,300   copying tests/test-data/random-20-a.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,300   copying tests/test-data/random-20-a.fa.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,301   copying tests/test-data/random-20-a.fa.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,301   copying tests/test-data/random-20-a.fa.part -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,302   copying tests/test-data/random-20-a.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,302   copying tests/test-data/random-20-a.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,303   copying tests/test-data/random-20-a.fq.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,304   copying tests/test-data/random-20-a.odd.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,304   copying tests/test-data/random-20-b.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,305   copying tests/test-data/random-31-c.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,305   copying tests/test-data/real-partition-small.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,306   copying tests/test-data/real-partition-tiny.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,306   copying tests/test-data/single-read.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,307   copying tests/test-data/test-abund-read-2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,308   copying tests/test-data/test-abund-read-2.fa.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,308   copying tests/test-data/test-abund-read-2.fa.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,309   copying tests/test-data/test-abund-read-2.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,309   copying tests/test-data/test-abund-read-2.paired.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,310   copying tests/test-data/test-abund-read-2.paired2.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,310   copying tests/test-data/test-abund-read-3.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,311   copying tests/test-data/test-abund-read-impaired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,311   copying tests/test-data/test-abund-read-paired.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,312   copying tests/test-data/test-abund-read-paired.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,312   copying tests/test-data/test-abund-read.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,313   copying tests/test-data/test-empty.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,313   copying tests/test-data/test-empty.fa.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,314   copying tests/test-data/test-error-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,314   copying tests/test-data/test-fastq-n-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,315   copying tests/test-data/test-fastq-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,315   copying tests/test-data/test-graph.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,316   copying tests/test-data/test-graph2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,316   copying tests/test-data/test-graph5.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,317   copying tests/test-data/test-labels.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,317   copying tests/test-data/test-large.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,357   copying tests/test-data/test-output-partitions.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,357   copying tests/test-data/test-overlap1.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,363   copying tests/test-data/test-overlap2.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,369   copying tests/test-data/test-reads.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,378   copying tests/test-data/test-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,381   copying tests/test-data/test-reads.fq.gz -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,384   copying tests/test-data/test-short.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,385   copying tests/test-data/test-sweep-contigs.fp -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,385   copying tests/test-data/test-sweep-reads.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,386   copying tests/test-data/test-sweep-reads.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,386   copying tests/test-data/test-transcript.fa -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,387   copying tests/test-data/truncated.fq -> build/lib.linux-armv7l-cpython-313/khmer/tests/test-data
2025-09-08T01:54:48,388   running build_ext
2025-09-08T01:54:48,389   error: ['khmer', 'khmer.tests'] require 64-bit operating system
2025-09-08T01:54:48,514   ERROR: python setup.py bdist_wheel exited with 1
2025-09-08T01:54:48,525   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2025-09-08T01:54:48,525   exec(compile('"'"''"'"''"'"'
2025-09-08T01:54:48,525   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2025-09-08T01:54:48,525   #
2025-09-08T01:54:48,525   # - It imports setuptools before invoking setup.py, to enable projects that directly
2025-09-08T01:54:48,525   #   import from `distutils.core` to work with newer packaging standards.
2025-09-08T01:54:48,525   # - It provides a clear error message when setuptools is not installed.
2025-09-08T01:54:48,525   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2025-09-08T01:54:48,525   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2025-09-08T01:54:48,525   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2025-09-08T01:54:48,525   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2025-09-08T01:54:48,525   import os, sys, tokenize, traceback
2025-09-08T01:54:48,525   
2025-09-08T01:54:48,525   try:
2025-09-08T01:54:48,525       import setuptools
2025-09-08T01:54:48,525   except ImportError:
2025-09-08T01:54:48,525       print(
2025-09-08T01:54:48,525           "ERROR: Can not execute `setup.py` since setuptools failed to import in "
2025-09-08T01:54:48,525           "the build environment with exception:",
2025-09-08T01:54:48,525           file=sys.stderr,
2025-09-08T01:54:48,525       )
2025-09-08T01:54:48,525       traceback.print_exc()
2025-09-08T01:54:48,525       sys.exit(1)
2025-09-08T01:54:48,525   
2025-09-08T01:54:48,525   __file__ = %r
2025-09-08T01:54:48,525   sys.argv[0] = __file__
2025-09-08T01:54:48,525   
2025-09-08T01:54:48,525   if os.path.exists(__file__):
2025-09-08T01:54:48,525       filename = __file__
2025-09-08T01:54:48,525       with tokenize.open(__file__) as f:
2025-09-08T01:54:48,525           setup_py_code = f.read()
2025-09-08T01:54:48,525   else:
2025-09-08T01:54:48,525       filename = "<auto-generated setuptools caller>"
2025-09-08T01:54:48,525       setup_py_code = "from setuptools import setup; setup()"
2025-09-08T01:54:48,525   
2025-09-08T01:54:48,525   exec(compile(setup_py_code, filename, "exec"))
2025-09-08T01:54:48,525   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-nwd_twga[/]
2025-09-08T01:54:48,525   [bold magenta]cwd[/]: /tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/
2025-09-08T01:54:48,526   Building wheel for khmer (setup.py): finished with status 'error'
2025-09-08T01:54:48,527   ERROR: Failed building wheel for khmer
2025-09-08T01:54:48,527   Running setup.py clean for khmer
2025-09-08T01:54:48,528   Running command python setup.py clean
2025-09-08T01:54:49,257   /tmp/pip-wheel-2yndp9bd/khmer_fb46418113414fcca2e15d13d5c48512/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.
2025-09-08T01:54:49,257     import pkg_resources
2025-09-08T01:54:49,940   /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.
2025-09-08T01:54:49,940   !!

2025-09-08T01:54:49,941           ********************************************************************************
2025-09-08T01:54:49,941           Usage of dash-separated 'include-dirs' will not be supported in future
2025-09-08T01:54:49,941           versions. Please use the underscore name 'include_dirs' instead.

2025-09-08T01:54:49,941           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T01:54:49,941           or your builds will no longer be supported.

2025-09-08T01:54:49,941           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T01:54:49,941           ********************************************************************************

2025-09-08T01:54:49,942   !!
2025-09-08T01:54:49,942     opt = self._enforce_underscore(opt, section)
2025-09-08T01:54:50,216   /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.
2025-09-08T01:54:50,216   !!

2025-09-08T01:54:50,216           ********************************************************************************
2025-09-08T01:54:50,216           Usage of dash-separated 'include-dirs' will not be supported in future
2025-09-08T01:54:50,216           versions. Please use the underscore name 'include_dirs' instead.
2025-09-08T01:54:50,216           (Affected: khmer).

2025-09-08T01:54:50,216           By 2026-Mar-03, you need to update your project and remove deprecated calls
2025-09-08T01:54:50,216           or your builds will no longer be supported.

2025-09-08T01:54:50,217           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2025-09-08T01:54:50,217           ********************************************************************************

2025-09-08T01:54:50,217   !!
2025-09-08T01:54:50,217     opt = self._enforce_underscore(opt, section)
2025-09-08T01:54:50,217   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-09-08T01:54:50,217   !!

2025-09-08T01:54:50,217           ********************************************************************************
2025-09-08T01:54:50,218           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-09-08T01:54:50,218           License :: OSI Approved :: BSD License

2025-09-08T01:54:50,218           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-09-08T01:54:50,218           ********************************************************************************

2025-09-08T01:54:50,218   !!
2025-09-08T01:54:50,218     self._finalize_license_expression()
2025-09-08T01:54:50,291   running clean
2025-09-08T01:54:50,365   removing 'build/lib.linux-armv7l-cpython-313' (and everything under it)
2025-09-08T01:54:50,375   'build/bdist.linux-armv7l' does not exist -- can't clean it
2025-09-08T01:54:50,375   'build/scripts-3.13' does not exist -- can't clean it
2025-09-08T01:54:50,376   removing 'build'
2025-09-08T01:54:50,499 Failed to build khmer
2025-09-08T01:54:50,499 ERROR: Failed to build one or more wheels
2025-09-08T01:54:50,500 Exception information:
2025-09-08T01:54:50,500 Traceback (most recent call last):
2025-09-08T01:54:50,500   File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper
2025-09-08T01:54:50,500     status = _inner_run()
2025-09-08T01:54:50,500   File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run
2025-09-08T01:54:50,500     return self.run(options, args)
2025-09-08T01:54:50,500            ~~~~~~~~^^^^^^^^^^^^^^^
2025-09-08T01:54:50,500   File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper
2025-09-08T01:54:50,500     return func(self, options, args)
2025-09-08T01:54:50,500   File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run
2025-09-08T01:54:50,500     raise CommandError("Failed to build one or more wheels")
2025-09-08T01:54:50,500 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2025-09-08T01:54:50,504 Removed build tracker: '/tmp/pip-build-tracker-1hm3q49h'