2023-09-08T18:07:51,859 Created temporary directory: /tmp/pip-build-tracker-694ud_vd 2023-09-08T18:07:51,860 Initialized build tracking at /tmp/pip-build-tracker-694ud_vd 2023-09-08T18:07:51,861 Created build tracker: /tmp/pip-build-tracker-694ud_vd 2023-09-08T18:07:51,861 Entered build tracker: /tmp/pip-build-tracker-694ud_vd 2023-09-08T18:07:51,862 Created temporary directory: /tmp/pip-wheel-hm4jc300 2023-09-08T18:07:51,865 Created temporary directory: /tmp/pip-ephem-wheel-cache-ooldel80 2023-09-08T18:07:51,887 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T18:07:51,891 2 location(s) to search for versions of khmer: 2023-09-08T18:07:51,891 * https://pypi.org/simple/khmer/ 2023-09-08T18:07:51,891 * https://www.piwheels.org/simple/khmer/ 2023-09-08T18:07:51,891 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2023-09-08T18:07:51,892 Getting page https://pypi.org/simple/khmer/ 2023-09-08T18:07:51,894 Found index url https://pypi.org/simple/ 2023-09-08T18:07:52,041 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2023-09-08T18:07:52,049 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,049 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,050 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2023-09-08T18:07:52,050 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6.1 2023-09-08T18:07:52,051 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,052 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2023-09-08T18:07:52,052 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,053 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7.1 2023-09-08T18:07:52,054 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,055 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2023-09-08T18:07:52,055 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,056 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2023-09-08T18:07:52,057 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,057 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0.1 2023-09-08T18:07:52,058 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2023-09-08T18:07:52,059 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,059 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2023-09-08T18:07:52,060 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,060 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2023-09-08T18:07:52,061 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,061 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2023-09-08T18:07:52,062 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,063 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,063 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4.1 2023-09-08T18:07:52,064 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,065 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,065 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,066 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,067 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2023-09-08T18:07:52,067 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2023-09-08T18:07:52,068 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,069 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2023-09-08T18:07:52,070 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,070 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,071 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,072 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,072 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T18:07:52,073 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1.1 2023-09-08T18:07:52,074 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2023-09-08T18:07:52,075 Getting page https://www.piwheels.org/simple/khmer/ 2023-09-08T18:07:52,076 Found index url https://www.piwheels.org/simple/ 2023-09-08T18:07:52,327 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2023-09-08T18:07:52,329 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2023-09-08T18:07:52,329 Skipping link: not a file: https://pypi.org/simple/khmer/ 2023-09-08T18:07:52,349 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2023-09-08T18:07:52,368 Collecting khmer==1.4 2023-09-08T18:07:52,370 Created temporary directory: /tmp/pip-unpack-ggk0107s 2023-09-08T18:07:53,415 Downloading khmer-1.4.tar.gz (8.6 MB) 2023-09-08T18:07:58,901 Added khmer==1.4 from https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz to build tracker '/tmp/pip-build-tracker-694ud_vd' 2023-09-08T18:07:58,903 Running setup.py (path:/tmp/pip-wheel-hm4jc300/khmer_2082351ae8ca472c83caf6469f8a2bb7/setup.py) egg_info for package khmer 2023-09-08T18:07:58,904 Created temporary directory: /tmp/pip-pip-egg-info-xkby7qhd 2023-09-08T18:07:58,904 Preparing metadata (setup.py): started 2023-09-08T18:07:58,906 Running command python setup.py egg_info 2023-09-08T18:08:00,038 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T18:08:00,038 !! 2023-09-08T18:08:00,040 ******************************************************************************** 2023-09-08T18:08:00,040 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T18:08:00,041 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T18:08:00,042 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T18:08:00,043 or your builds will no longer be supported. 2023-09-08T18:08:00,044 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T18:08:00,044 ******************************************************************************** 2023-09-08T18:08:00,045 !! 2023-09-08T18:08:00,046 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T18:08:00,238 running egg_info 2023-09-08T18:08:00,239 creating /tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info 2023-09-08T18:08:00,266 writing /tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info/PKG-INFO 2023-09-08T18:08:00,271 writing dependency_links to /tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info/dependency_links.txt 2023-09-08T18:08:00,274 writing requirements to /tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info/requires.txt 2023-09-08T18:08:00,275 writing top-level names to /tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info/top_level.txt 2023-09-08T18:08:00,276 writing manifest file '/tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info/SOURCES.txt' 2023-09-08T18:08:00,357 reading manifest file '/tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info/SOURCES.txt' 2023-09-08T18:08:00,359 reading manifest template 'MANIFEST.in' 2023-09-08T18:08:04,169 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2023-09-08T18:08:04,170 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2023-09-08T18:08:04,197 warning: no previously-included files matching '*.orig' found anywhere in distribution 2023-09-08T18:08:04,200 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-09-08T18:08:04,200 adding license file 'LICENSE' 2023-09-08T18:08:04,232 writing manifest file '/tmp/pip-pip-egg-info-xkby7qhd/khmer.egg-info/SOURCES.txt' 2023-09-08T18:08:04,348 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T18:08:04,351 Source in /tmp/pip-wheel-hm4jc300/khmer_2082351ae8ca472c83caf6469f8a2bb7 has version 1.4, which satisfies requirement khmer==1.4 from https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz 2023-09-08T18:08:04,352 Removed khmer==1.4 from https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz from build tracker '/tmp/pip-build-tracker-694ud_vd' 2023-09-08T18:08:04,356 Created temporary directory: /tmp/pip-unpack-95j2km9_ 2023-09-08T18:08:04,358 Created temporary directory: /tmp/pip-unpack-9lj7f9v2 2023-09-08T18:08:04,373 Building wheels for collected packages: khmer 2023-09-08T18:08:04,378 Created temporary directory: /tmp/pip-wheel-8iuadv4l 2023-09-08T18:08:04,379 Building wheel for khmer (setup.py): started 2023-09-08T18:08:04,380 Destination directory: /tmp/pip-wheel-8iuadv4l 2023-09-08T18:08:04,381 Running command python setup.py bdist_wheel 2023-09-08T18:08:05,659 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T18:08:05,659 !! 2023-09-08T18:08:05,660 ******************************************************************************** 2023-09-08T18:08:05,661 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T18:08:05,661 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T18:08:05,662 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T18:08:05,663 or your builds will no longer be supported. 2023-09-08T18:08:05,664 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T18:08:05,664 ******************************************************************************** 2023-09-08T18:08:05,665 !! 2023-09-08T18:08:05,666 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T18:08:05,843 running bdist_wheel 2023-09-08T18:08:05,889 running build 2023-09-08T18:08:05,890 got version from file /tmp/pip-wheel-hm4jc300/khmer_2082351ae8ca472c83caf6469f8a2bb7/khmer/_version.py {'version': '1.4', 'full': 'ffb8865d28ccf584e5de3362f9150a6b020eaa11'} 2023-09-08T18:08:05,891 running build_py 2023-09-08T18:08:05,916 creating build 2023-09-08T18:08:05,917 creating build/lib.linux-armv7l-cpython-311 2023-09-08T18:08:05,918 creating build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:05,919 copying khmer/khmer_args.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:05,921 copying khmer/kfile.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:05,923 copying khmer/utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:05,925 copying khmer/thread_utils.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:05,927 copying khmer/_version.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:05,928 copying khmer/__init__.py -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:05,931 creating build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,932 copying tests/test_subset_graph.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,934 copying tests/test_scripts.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,938 copying tests/test_lump.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,940 copying tests/test_counting_single.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,942 copying tests/test_hashbits_obj.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,944 copying tests/test_filter.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,946 copying tests/test_counting_hash.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,948 copying tests/test_version.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,950 copying tests/test_read_aligner.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,952 copying tests/test_threaded_sequence_processor.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,954 copying tests/test_labelhash.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,956 copying tests/test_graph.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,959 copying tests/test_hll.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,961 copying tests/test_read_parsers.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,963 copying tests/test_functions.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,965 copying tests/test_sandbox_scripts.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,967 copying tests/khmer_tst_utils.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,969 copying tests/test_hashbits.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,971 copying tests/__init__.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,972 copying tests/test_script_arguments.py -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:05,974 running egg_info 2023-09-08T18:08:06,007 creating khmer.egg-info 2023-09-08T18:08:06,031 writing khmer.egg-info/PKG-INFO 2023-09-08T18:08:06,036 writing dependency_links to khmer.egg-info/dependency_links.txt 2023-09-08T18:08:06,039 writing requirements to khmer.egg-info/requires.txt 2023-09-08T18:08:06,040 writing top-level names to khmer.egg-info/top_level.txt 2023-09-08T18:08:06,041 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T18:08:06,072 reading manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T18:08:06,073 reading manifest template 'MANIFEST.in' 2023-09-08T18:08:10,101 warning: no previously-included files found matching 'third-party/zlib/Makefile' 2023-09-08T18:08:10,101 warning: no previously-included files found matching 'third-party/zlib/zconf.h' 2023-09-08T18:08:10,125 warning: no previously-included files matching '*.orig' found anywhere in distribution 2023-09-08T18:08:10,127 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-09-08T18:08:10,128 adding license file 'LICENSE' 2023-09-08T18:08:10,152 writing manifest file 'khmer.egg-info/SOURCES.txt' 2023-09-08T18:08:10,188 copying khmer/_khmermodule.cc -> build/lib.linux-armv7l-cpython-311/khmer 2023-09-08T18:08:10,192 copying tests/.gitignore -> build/lib.linux-armv7l-cpython-311/khmer/tests 2023-09-08T18:08:10,194 creating build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,195 copying tests/test-data/100-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,198 copying tests/test-data/100-reads.fq.gz -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,201 copying tests/test-data/100-reads.fq.truncated.bz2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,203 copying tests/test-data/100-reads.fq.truncated.gz -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,206 copying tests/test-data/all-A.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,208 copying tests/test-data/badversion-k12.ct -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,211 copying tests/test-data/badversion-k12.ht -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,213 copying tests/test-data/badversion-k32.stoptags -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,216 copying tests/test-data/badversion-k32.tagset -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,218 copying tests/test-data/biglump-random-20-a.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,221 copying tests/test-data/casava_18-pe.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,223 copying tests/test-data/combine_parts_1.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,225 copying tests/test-data/empty-file -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,227 copying tests/test-data/fakelump.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,229 copying tests/test-data/fakelump.fa.stoptags.txt -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,232 copying tests/test-data/filter-test-A.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,234 copying tests/test-data/filter-test-B.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,237 copying tests/test-data/goodversion-k12.ht -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,239 copying tests/test-data/goodversion-k12.ht.gz -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,241 copying tests/test-data/goodversion-k32.stoptags -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,244 copying tests/test-data/goodversion-k32.tagset -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,246 copying tests/test-data/normC20k20.ct -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,250 copying tests/test-data/old-style-format-w-comments.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,252 copying tests/test-data/overlap.out -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,254 copying tests/test-data/paired-broken.fq.1 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,257 copying tests/test-data/paired-broken.fq.2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,259 copying tests/test-data/paired-broken2.fq.1 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,262 copying tests/test-data/paired-broken2.fq.2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,264 copying tests/test-data/paired-broken3.fq.1 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,266 copying tests/test-data/paired-broken3.fq.2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,269 copying tests/test-data/paired-mixed-2.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,271 copying tests/test-data/paired-mixed-broken.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,274 copying tests/test-data/paired-mixed.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,276 copying tests/test-data/paired-mixed.fa.pe -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,278 copying tests/test-data/paired-mixed.fa.se -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,281 copying tests/test-data/paired-mixed.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,283 copying tests/test-data/paired-mixed.fq.pe -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,285 copying tests/test-data/paired-mixed.fq.se -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,288 copying tests/test-data/paired.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,290 copying tests/test-data/paired.fa.1 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,293 copying tests/test-data/paired.fa.2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,295 copying tests/test-data/paired.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,298 copying tests/test-data/paired.fq.1 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,300 copying tests/test-data/paired.fq.2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,302 copying tests/test-data/random-20-X2.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,306 copying tests/test-data/random-20-a.even.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,309 copying tests/test-data/random-20-a.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,312 copying tests/test-data/random-20-a.fa.bz2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,314 copying tests/test-data/random-20-a.fa.gz -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,316 copying tests/test-data/random-20-a.fa.part -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,319 copying tests/test-data/random-20-a.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,322 copying tests/test-data/random-20-a.fq.bz2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,324 copying tests/test-data/random-20-a.fq.gz -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,326 copying tests/test-data/random-20-a.odd.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,328 copying tests/test-data/random-20-b.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,331 copying tests/test-data/random-31-c.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,335 copying tests/test-data/real-partition-small.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,337 copying tests/test-data/real-partition-tiny.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,339 copying tests/test-data/single-read.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,341 copying tests/test-data/test-abund-read-2.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,344 copying tests/test-data/test-abund-read-2.fa.bz2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,346 copying tests/test-data/test-abund-read-2.fa.gz -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,348 copying tests/test-data/test-abund-read-2.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,352 copying tests/test-data/test-abund-read-2.paired.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,354 copying tests/test-data/test-abund-read-2.paired2.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,356 copying tests/test-data/test-abund-read-3.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,358 copying tests/test-data/test-abund-read-impaired.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,360 copying tests/test-data/test-abund-read-paired.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,362 copying tests/test-data/test-abund-read-paired.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,364 copying tests/test-data/test-abund-read.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,366 copying tests/test-data/test-empty.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,368 copying tests/test-data/test-empty.fa.bz2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,370 copying tests/test-data/test-error-reads.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,372 copying tests/test-data/test-fastq-n-reads.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,375 copying tests/test-data/test-fastq-reads.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,378 copying tests/test-data/test-graph.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,380 copying tests/test-data/test-graph2.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,382 copying tests/test-data/test-graph5.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,384 copying tests/test-data/test-labels.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,386 copying tests/test-data/test-large.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,545 copying tests/test-data/test-output-partitions.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,547 copying tests/test-data/test-overlap1.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,578 copying tests/test-data/test-overlap2.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,638 copying tests/test-data/test-reads.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,703 copying tests/test-data/test-reads.fq.bz2 -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,729 copying tests/test-data/test-reads.fq.gz -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,758 copying tests/test-data/test-short.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,765 copying tests/test-data/test-sweep-contigs.fp -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,772 copying tests/test-data/test-sweep-reads.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,779 copying tests/test-data/test-sweep-reads.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,785 copying tests/test-data/test-transcript.fa -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,792 copying tests/test-data/truncated.fq -> build/lib.linux-armv7l-cpython-311/khmer/tests/test-data 2023-09-08T18:08:10,802 running build_ext 2023-09-08T18:08:10,804 error: ['khmer', 'khmer.tests'] require 64-bit operating system 2023-09-08T18:08:10,918 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T18:08:10,931 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T18:08:10,931 exec(compile('"'"''"'"''"'"' 2023-09-08T18:08:10,931 # This is -- a caller that pip uses to run setup.py 2023-09-08T18:08:10,931 # 2023-09-08T18:08:10,931 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T18:08:10,931 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T18:08:10,931 # - It provides a clear error message when setuptools is not installed. 2023-09-08T18:08:10,931 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T18:08:10,931 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T18:08:10,931 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T18:08:10,931 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T18:08:10,931 import os, sys, tokenize 2023-09-08T18:08:10,931 2023-09-08T18:08:10,931 try: 2023-09-08T18:08:10,931 import setuptools 2023-09-08T18:08:10,931 except ImportError as error: 2023-09-08T18:08:10,931 print( 2023-09-08T18:08:10,931 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T18:08:10,931 "the build environment.", 2023-09-08T18:08:10,931 file=sys.stderr, 2023-09-08T18:08:10,931 ) 2023-09-08T18:08:10,931 sys.exit(1) 2023-09-08T18:08:10,931 2023-09-08T18:08:10,931 __file__ = %r 2023-09-08T18:08:10,931 sys.argv[0] = __file__ 2023-09-08T18:08:10,931 2023-09-08T18:08:10,931 if os.path.exists(__file__): 2023-09-08T18:08:10,931 filename = __file__ 2023-09-08T18:08:10,931 with tokenize.open(__file__) as f: 2023-09-08T18:08:10,931 setup_py_code = f.read() 2023-09-08T18:08:10,931 else: 2023-09-08T18:08:10,931 filename = "" 2023-09-08T18:08:10,931 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T18:08:10,931 2023-09-08T18:08:10,931 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T18:08:10,931 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-hm4jc300/khmer_2082351ae8ca472c83caf6469f8a2bb7/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-8iuadv4l[/] 2023-09-08T18:08:10,931 [bold magenta]cwd[/]: /tmp/pip-wheel-hm4jc300/khmer_2082351ae8ca472c83caf6469f8a2bb7/ 2023-09-08T18:08:10,932 Building wheel for khmer (setup.py): finished with status 'error' 2023-09-08T18:08:10,933 ERROR: Failed building wheel for khmer 2023-09-08T18:08:10,935 Running setup.py clean for khmer 2023-09-08T18:08:10,936 Running command python setup.py clean 2023-09-08T18:08:12,015 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:510: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-09-08T18:08:12,015 !! 2023-09-08T18:08:12,016 ******************************************************************************** 2023-09-08T18:08:12,017 Usage of dash-separated 'include-dirs' will not be supported in future 2023-09-08T18:08:12,017 versions. Please use the underscore name 'include_dirs' instead. 2023-09-08T18:08:12,018 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-09-08T18:08:12,019 or your builds will no longer be supported. 2023-09-08T18:08:12,020 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-09-08T18:08:12,020 ******************************************************************************** 2023-09-08T18:08:12,021 !! 2023-09-08T18:08:12,022 opt = self.warn_dash_deprecation(opt, section) 2023-09-08T18:08:12,204 running clean 2023-09-08T18:08:12,227 removing 'build/lib.linux-armv7l-cpython-311' (and everything under it) 2023-09-08T18:08:12,265 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-08T18:08:12,266 'build/scripts-3.11' does not exist -- can't clean it 2023-09-08T18:08:12,266 removing 'build' 2023-09-08T18:08:12,379 Failed to build khmer 2023-09-08T18:08:12,381 ERROR: Failed to build one or more wheels 2023-09-08T18:08:12,382 Exception information: 2023-09-08T18:08:12,382 Traceback (most recent call last): 2023-09-08T18:08:12,382 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T18:08:12,382 status = run_func(*args) 2023-09-08T18:08:12,382 ^^^^^^^^^^^^^^^ 2023-09-08T18:08:12,382 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T18:08:12,382 return func(self, options, args) 2023-09-08T18:08:12,382 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T18:08:12,382 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T18:08:12,382 raise CommandError("Failed to build one or more wheels") 2023-09-08T18:08:12,382 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T18:08:12,385 Removed build tracker: '/tmp/pip-build-tracker-694ud_vd'