2025-09-09T07:38:01,900 Created temporary directory: /tmp/pip-build-tracker-_oihj3pl 2025-09-09T07:38:01,900 Initialized build tracking at /tmp/pip-build-tracker-_oihj3pl 2025-09-09T07:38:01,901 Created build tracker: /tmp/pip-build-tracker-_oihj3pl 2025-09-09T07:38:01,901 Entered build tracker: /tmp/pip-build-tracker-_oihj3pl 2025-09-09T07:38:01,901 Created temporary directory: /tmp/pip-wheel-et2okxsj 2025-09-09T07:38:01,904 Created temporary directory: /tmp/pip-ephem-wheel-cache-o_tbb8rw 2025-09-09T07:38:01,964 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-09T07:38:01,966 2 location(s) to search for versions of ont-bonito: 2025-09-09T07:38:01,966 * https://pypi.org/simple/ont-bonito/ 2025-09-09T07:38:01,966 * https://www.piwheels.org/simple/ont-bonito/ 2025-09-09T07:38:01,967 Fetching project page and analyzing links: https://pypi.org/simple/ont-bonito/ 2025-09-09T07:38:01,967 Getting page https://pypi.org/simple/ont-bonito/ 2025-09-09T07:38:01,968 Found index url https://pypi.org/simple/ 2025-09-09T07:38:02,037 Fetched page https://pypi.org/simple/ont-bonito/ as application/vnd.pypi.simple.v1+json 2025-09-09T07:38:02,044 Found link https://files.pythonhosted.org/packages/d9/db/561675d546075abac5f22cd30a78c084af0cf6aa376ace242405b801658f/ont-bonito-0.0.1.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.0.1 2025-09-09T07:38:02,044 Found link https://files.pythonhosted.org/packages/1e/d1/8e91e83711e166c9da2dd39017c9ac471c516b87b48bcdc0e25a4cb12d95/ont-bonito-0.0.3.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.0.3 2025-09-09T07:38:02,044 Found link https://files.pythonhosted.org/packages/e6/97/ee764ddc586c5fcf9be804289a26d80ce31a1eabfd550b1276dead9b9de1/ont-bonito-0.0.4.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.0.4 2025-09-09T07:38:02,044 Found link https://files.pythonhosted.org/packages/51/2a/771af15029be16025022b91ee7675af7945fc0350e3c1190c7d1cad934d3/ont-bonito-0.0.5.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.0.5 2025-09-09T07:38:02,045 Found link https://files.pythonhosted.org/packages/60/99/f9b4e7db2b81d07ca49873fef96a1d3378248ee8730cf07fda1231cd8910/ont-bonito-0.0.7.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.0.7 2025-09-09T07:38:02,045 Found link https://files.pythonhosted.org/packages/3a/cc/a64e90955addd8b831e43decc9ee2cd8f8395c7c44ceef250bc60f2550f8/ont-bonito-0.0.8.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.0.8 2025-09-09T07:38:02,045 Found link https://files.pythonhosted.org/packages/29/db/59fef46c323e86347b7558ad3c5a775037ef6923bc62b7e15173fefeed82/ont-bonito-0.1.0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.1.0 2025-09-09T07:38:02,045 Found link https://files.pythonhosted.org/packages/78/52/9f978f27aa96ccbb07ed86f25d599c28c80f41f6414f8035372e7acc00f6/ont-bonito-0.1.2.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.1.2 2025-09-09T07:38:02,046 Found link https://files.pythonhosted.org/packages/9c/53/044d2ab2e0d2c00f5331aa4f1623c888dbc818c7fba70d069d80529ed113/ont-bonito-0.1.3.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.1.3 2025-09-09T07:38:02,046 Found link https://files.pythonhosted.org/packages/59/8d/0c2eb31f833160e51648eae8d49bd6610bd6fad6ae5879e22a76187b5979/ont-bonito-0.1.4.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.1.4 2025-09-09T07:38:02,046 Found link https://files.pythonhosted.org/packages/95/fa/8a178168ee44c7f66a4239e4a2a1569896e787397080d1e1e0c2b1a331c2/ont-bonito-0.1.5.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.1.5 2025-09-09T07:38:02,046 Found link https://files.pythonhosted.org/packages/43/3a/37759ab5cca2b641f6e8000ad79cf4c86708efd3a1a1cafd4112ca7abcc7/ont-bonito-0.2.0a1.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.0a1 2025-09-09T07:38:02,046 Found link https://files.pythonhosted.org/packages/9f/92/8bc665b17c156ddd88ca5d5aab8a0df099ffb508068ca6b773aa5695973b/ont-bonito-0.2.0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.0 2025-09-09T07:38:02,047 Found link https://files.pythonhosted.org/packages/41/fc/a2d21c9eeca274194294321505035094e407f3eed3466a831eb6de657912/ont-bonito-0.2.1a0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.1a0 2025-09-09T07:38:02,047 Found link https://files.pythonhosted.org/packages/8d/1e/b5ea1a1ddcd184c797ebfe251ecbf23fa97850515acc175c8671d1f425d2/ont-bonito-0.2.1.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.1 2025-09-09T07:38:02,047 Found link https://files.pythonhosted.org/packages/9b/3f/5cc8fa4703f5322956fff3d14c50d10a4bc46cd116bb77afc107f9213377/ont-bonito-0.2.2a0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.2a0 2025-09-09T07:38:02,047 Found link https://files.pythonhosted.org/packages/b4/38/79e98f2506fd0152989541ca93f25838e4017526c54e2b9b57df806ab28e/ont-bonito-0.2.2.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.2 2025-09-09T07:38:02,048 Found link https://files.pythonhosted.org/packages/7b/5c/c58113d696ef7b470cae9308134d039a156de85bca856fab94f2024e5e7c/ont-bonito-0.2.3a0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.3a0 2025-09-09T07:38:02,048 Found link https://files.pythonhosted.org/packages/08/7f/c156a67a0aeb65da44d42c877d277e3135c79d934c943a64cff626fd317e/ont-bonito-0.2.3.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.2.3 2025-09-09T07:38:02,048 Found link 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https://files.pythonhosted.org/packages/8a/1e/66b8a54e3a834ace2ca7da0cdcddb8e8aba6378a1138eae8d23a69717365/ont-bonito-0.5.0a0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.5.0a0 2025-09-09T07:38:02,052 Found link https://files.pythonhosted.org/packages/c0/67/767711facb8ba83705205c97200da7c38ee237ea4f75ac238837a34470d7/ont-bonito-0.5.0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.5.0 2025-09-09T07:38:02,052 Found link https://files.pythonhosted.org/packages/c3/83/92100e7d0d0c2f6fe308e0b59abca48abbc0964ae8ebe7ba3661db363d3f/ont-bonito-0.5.1a0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.5.1a0 2025-09-09T07:38:02,052 Found link https://files.pythonhosted.org/packages/83/01/fd86e1b52f88835a57a95fffd87310b45943c2638d7f0d5ddc5d5d79f963/ont-bonito-0.5.1.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.5.1 2025-09-09T07:38:02,052 Found link https://files.pythonhosted.org/packages/fb/c4/ac0604938255e78079971e40d5c3f899c8a4da86b55555459cdcf84800ef/ont-bonito-0.5.2.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.5.2 2025-09-09T07:38:02,053 Found link https://files.pythonhosted.org/packages/c7/56/99ed87537a1bca4e37db92bc863e5b930911b12c5326da698f2250b0ca78/ont-bonito-0.5.3.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.5.3 2025-09-09T07:38:02,053 Found link https://files.pythonhosted.org/packages/5c/88/be3977f52a9f5d4c220ce5ba1c2ee13b86e190f1fec97fc1c7a8c1f38cbc/ont-bonito-0.6.0a0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.6.0a0 2025-09-09T07:38:02,053 Found link https://files.pythonhosted.org/packages/76/c6/80785be7f0c43e8547741e2e39c3ce03fc46bced660fe92662830b70fc39/ont-bonito-0.6.0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.6.0 2025-09-09T07:38:02,053 Found link https://files.pythonhosted.org/packages/44/81/fd2d05d745a203673a8540581af478b9c9e512e866e813efde040816a9dd/ont-bonito-0.6.1.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.6.1 2025-09-09T07:38:02,054 Found link https://files.pythonhosted.org/packages/4a/65/64a411f93b81cacf9df362e6b287fc0558cbf39aa00749e960446aa9d6d5/ont-bonito-0.6.2.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.6.2 2025-09-09T07:38:02,054 Found link https://files.pythonhosted.org/packages/25/93/edefed8f84d0d26f786ceac1127f34994d83d3bd9008cc36417628b52a29/ont-bonito-0.7.0.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.7.0 2025-09-09T07:38:02,054 Found link https://files.pythonhosted.org/packages/ef/ad/ebed4ae6c1b2a7ddeb2c5af2c6fc84ad964cc2f326970dafbb0e75d9d18b/ont-bonito-0.7.1.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.7.1 2025-09-09T07:38:02,054 Found link https://files.pythonhosted.org/packages/c8/fe/dbe281544dff26a76fc448d50eaa05b45a6bcf114f48485db4e0d90bb0d4/ont-bonito-0.7.2.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.7.2 2025-09-09T07:38:02,054 Found link https://files.pythonhosted.org/packages/f9/c5/0809ab32bc8e8df3b68de4c58a385541fa25f16ff909084ce59d6a2c3410/ont-bonito-0.7.3.tar.gz (from https://pypi.org/simple/ont-bonito/), version: 0.7.3 2025-09-09T07:38:02,055 Found link https://files.pythonhosted.org/packages/f2/e9/2310bc3981df09815f6899a70792e6799233e7aa2b931f70b0aa60376816/ont-bonito-0.8.1.tar.gz (from https://pypi.org/simple/ont-bonito/) (requires-python:>=3.8), version: 0.8.1 2025-09-09T07:38:02,056 Found link https://files.pythonhosted.org/packages/f3/7c/54fa467d6de3e141d53a28b9d558bcd9958312c6b0b25e434b9056c1e18b/ont_bonito-0.9.0.tar.gz (from https://pypi.org/simple/ont-bonito/) (requires-python:>=3.9), version: 0.9.0 2025-09-09T07:38:02,056 Fetching project page and analyzing links: 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https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.7.3-py3-none-any.whl#sha256=2a040524fb3f100169ba217feb08e6383466ac11255d28af8456eb81ce3b6bec (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,328 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.7.2-py3-none-any.whl#sha256=21828a2841dad02c1c00096115aa095586dc8291a8cecb0c22ee2f349226b3ed (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,328 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.7.1-py3-none-any.whl#sha256=cbd03457f597f585bc1d64424fd28426169a3887581b90d25419fbe2fcf04a71 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,329 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.7.0-py3-none-any.whl#sha256=8eaedaf827f39cbeceb85498561289f0d3ec178dbae355b36a71babf8cdb60ab 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https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.6.0a0-py3-none-any.whl#sha256=967f4e93c409e78e0804ae584c2cdee2b8a5a2a4a19c719cbb56c22fdefb96a1 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,330 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.5.1-py3-none-any.whl#sha256=adadb15fb95437b8aa445ad488ed159f8234ded4346696175449c532384b539f (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,331 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.5.1a0-py3-none-any.whl#sha256=a52542c89d1a7a0fc321906b26a4dd42565047099063019ed690a8450c42e54a (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,331 Skipping link: No binaries permitted for ont-bonito: 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https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.2.3-py3-none-any.whl#sha256=9d1f667cbe5f8cb1376ee7ca89763d691b11d20fb11348a84e25ca31e2fa9dd3 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,332 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.2.3a0-py3-none-any.whl#sha256=3f6cfda8101ae11440f5416df9056a109d43edf85bb04d21acf4b516c931f0d8 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,333 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.2.2-py3-none-any.whl#sha256=3da544c8dbe1554efc330e34bfc4916660581d2dad83b32cecf963c08dbf6067 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,334 Skipping link: No binaries permitted for ont-bonito: 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https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.2.0-py3-none-any.whl#sha256=af94713a499bd2aa542914d7de4c2e6a3bf5ba4b6c69467962e92e43b17c7bbb (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,335 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.2.0a1-py3-none-any.whl#sha256=d85713e49bbe28aba61e6ece58049327e2ed591ab836a3dee332f7492440f60c (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,335 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.1.5-py3-none-any.whl#sha256=8f8b6261f20a0fd4acd119cb9292de2a1592aca4205d52e5bf2b869888d1c34b (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,335 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.1.4-py3-none-any.whl#sha256=95ecf6751cac2e62cafedee8c7fd36395aa3d06683b465f05f38fc63217c76ec (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,336 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.1.3-py3-none-any.whl#sha256=aa5a1ad050f416a356a275ff7c1edf434f2536ecaedf39868c17e6e03612f80c (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,336 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.1.2-py3-none-any.whl#sha256=c19ce7dd24737098ed21721c2119fcf05495d6c6f1f28ce34bbe4e5381a1cb6d (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,336 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.1.0-py3-none-any.whl#sha256=d8530f0cab49e0a617c041c69b5ff3072e12bdf71c5791223aa6840bb03c563a (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,337 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.0.8-py3-none-any.whl#sha256=e9789f86f9f4fdcf93e943b22612c247b9799881bab9917132d5b31213115818 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,337 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.0.7-py3-none-any.whl#sha256=d67d2643174f008c4147a21f3d48f5ea6e0c8f6d24cf04f8e56c9d41c7ad3a11 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,337 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.0.5-py3-none-any.whl#sha256=dba97dc16615c6084af661cdd650c990dc6f5e801b977d586b3984fbf9cd9cc0 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,338 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.0.4-py3-none-any.whl#sha256=f4296580ddbea57bc95225cf1970b24bd6399bbe45db8e332e7b2526154213d2 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,338 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.0.3-py3-none-any.whl#sha256=7627466cf3e20b953515974d554131dfc7328da352874e47149686dfb162947a (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,338 Skipping link: No binaries permitted for ont-bonito: https://archive1.piwheels.org/simple/ont-bonito/ont_bonito-0.0.1-py3-none-any.whl#sha256=921810adb533b8964600c2600af50dba5338d8585fc4dfdaa32b482a3585bd20 (from https://www.piwheels.org/simple/ont-bonito/) 2025-09-09T07:38:02,339 Skipping link: not a file: https://www.piwheels.org/simple/ont-bonito/ 2025-09-09T07:38:02,339 Skipping link: not a file: https://pypi.org/simple/ont-bonito/ 2025-09-09T07:38:02,366 Given no hashes to check 1 links for project 'ont-bonito': discarding no candidates 2025-09-09T07:38:02,367 Collecting ont-bonito==0.3.2 2025-09-09T07:38:02,369 Created temporary directory: /tmp/pip-unpack-_70bg6x0 2025-09-09T07:38:02,516 Downloading ont-bonito-0.3.2.tar.gz (36 kB) 2025-09-09T07:38:02,564 Added ont-bonito==0.3.2 from https://files.pythonhosted.org/packages/33/5e/124215a3710a22980a3c6eb6af39a26550141e174452e7f38809a4738f21/ont-bonito-0.3.2.tar.gz to build tracker '/tmp/pip-build-tracker-_oihj3pl' 2025-09-09T07:38:02,565 Running setup.py (path:/tmp/pip-wheel-et2okxsj/ont-bonito_06026b089dd24e8dbc2345a09dbb268d/setup.py) egg_info for package ont-bonito 2025-09-09T07:38:02,565 Created temporary directory: /tmp/pip-pip-egg-info-nwdt0fu4 2025-09-09T07:38:02,565 Preparing metadata (setup.py): started 2025-09-09T07:38:02,566 Running command python setup.py egg_info 2025-09-09T07:38:03,801 running egg_info 2025-09-09T07:38:03,874 creating /tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info 2025-09-09T07:38:03,874 writing /tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/PKG-INFO 2025-09-09T07:38:03,876 writing dependency_links to /tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/dependency_links.txt 2025-09-09T07:38:03,876 writing entry points to /tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/entry_points.txt 2025-09-09T07:38:03,877 writing requirements to /tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/requires.txt 2025-09-09T07:38:03,877 writing top-level names to /tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/top_level.txt 2025-09-09T07:38:03,878 writing manifest file '/tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/SOURCES.txt' 2025-09-09T07:38:04,100 reading manifest file '/tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/SOURCES.txt' 2025-09-09T07:38:04,100 reading manifest template 'MANIFEST.in' 2025-09-09T07:38:04,102 adding license file 'LICENCE.txt' 2025-09-09T07:38:04,105 writing manifest file '/tmp/pip-pip-egg-info-nwdt0fu4/ont_bonito.egg-info/SOURCES.txt' 2025-09-09T07:38:04,217 Preparing metadata (setup.py): finished with status 'done' 2025-09-09T07:38:04,222 Source in /tmp/pip-wheel-et2okxsj/ont-bonito_06026b089dd24e8dbc2345a09dbb268d has version 0.3.2, which satisfies requirement ont-bonito==0.3.2 from https://files.pythonhosted.org/packages/33/5e/124215a3710a22980a3c6eb6af39a26550141e174452e7f38809a4738f21/ont-bonito-0.3.2.tar.gz 2025-09-09T07:38:04,222 Removed ont-bonito==0.3.2 from https://files.pythonhosted.org/packages/33/5e/124215a3710a22980a3c6eb6af39a26550141e174452e7f38809a4738f21/ont-bonito-0.3.2.tar.gz from build tracker '/tmp/pip-build-tracker-_oihj3pl' 2025-09-09T07:38:04,230 Created temporary directory: /tmp/pip-unpack-c3h_wok0 2025-09-09T07:38:04,231 Created temporary directory: /tmp/pip-unpack-mc4k4mwe 2025-09-09T07:38:04,231 Building wheels for collected packages: ont-bonito 2025-09-09T07:38:04,232 Created temporary directory: /tmp/pip-wheel-ehp2bq_n 2025-09-09T07:38:04,233 DEPRECATION: Building 'ont-bonito' 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 'ont-bonito'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-09T07:38:04,234 Building wheel for ont-bonito (setup.py): started 2025-09-09T07:38:04,235 Destination directory: /tmp/pip-wheel-ehp2bq_n 2025-09-09T07:38:04,235 Running command python setup.py bdist_wheel 2025-09-09T07:38:05,321 running bdist_wheel 2025-09-09T07:38:05,684 running build 2025-09-09T07:38:05,685 running build_py 2025-09-09T07:38:05,762 creating build/lib/bonito 2025-09-09T07:38:05,762 copying bonito/training.py -> build/lib/bonito 2025-09-09T07:38:05,763 copying bonito/__init__.py -> build/lib/bonito 2025-09-09T07:38:05,764 copying bonito/fast5.py -> build/lib/bonito 2025-09-09T07:38:05,764 copying bonito/multiprocessing.py -> build/lib/bonito 2025-09-09T07:38:05,765 copying bonito/aligner.py -> build/lib/bonito 2025-09-09T07:38:05,765 copying bonito/io.py -> build/lib/bonito 2025-09-09T07:38:05,766 copying bonito/util.py -> build/lib/bonito 2025-09-09T07:38:05,766 copying bonito/nn.py -> build/lib/bonito 2025-09-09T07:38:05,767 creating build/lib/bonito/crf 2025-09-09T07:38:05,767 copying bonito/crf/model.py -> build/lib/bonito/crf 2025-09-09T07:38:05,768 copying bonito/crf/__init__.py -> build/lib/bonito/crf 2025-09-09T07:38:05,768 copying bonito/crf/basecall.py -> build/lib/bonito/crf 2025-09-09T07:38:05,769 creating build/lib/bonito/ctc 2025-09-09T07:38:05,769 copying bonito/ctc/model.py -> build/lib/bonito/ctc 2025-09-09T07:38:05,770 copying bonito/ctc/__init__.py -> build/lib/bonito/ctc 2025-09-09T07:38:05,770 copying bonito/ctc/basecall.py -> build/lib/bonito/ctc 2025-09-09T07:38:05,771 creating build/lib/bonito/cli 2025-09-09T07:38:05,771 copying bonito/cli/pair.py -> build/lib/bonito/cli 2025-09-09T07:38:05,772 copying bonito/cli/convert.py -> build/lib/bonito/cli 2025-09-09T07:38:05,772 copying bonito/cli/view.py -> build/lib/bonito/cli 2025-09-09T07:38:05,773 copying bonito/cli/__init__.py -> build/lib/bonito/cli 2025-09-09T07:38:05,773 copying bonito/cli/train.py -> build/lib/bonito/cli 2025-09-09T07:38:05,774 copying bonito/cli/evaluate.py -> build/lib/bonito/cli 2025-09-09T07:38:05,774 copying bonito/cli/tune.py -> build/lib/bonito/cli 2025-09-09T07:38:05,775 copying bonito/cli/basecaller.py -> build/lib/bonito/cli 2025-09-09T07:38:05,775 copying bonito/cli/download.py -> build/lib/bonito/cli 2025-09-09T07:38:05,776 running egg_info 2025-09-09T07:38:05,849 writing ont_bonito.egg-info/PKG-INFO 2025-09-09T07:38:05,851 writing dependency_links to ont_bonito.egg-info/dependency_links.txt 2025-09-09T07:38:05,851 writing entry points to ont_bonito.egg-info/entry_points.txt 2025-09-09T07:38:05,852 writing requirements to ont_bonito.egg-info/requires.txt 2025-09-09T07:38:05,852 writing top-level names to ont_bonito.egg-info/top_level.txt 2025-09-09T07:38:05,929 reading manifest file 'ont_bonito.egg-info/SOURCES.txt' 2025-09-09T07:38:05,932 reading manifest template 'MANIFEST.in' 2025-09-09T07:38:05,933 adding license file 'LICENCE.txt' 2025-09-09T07:38:05,937 writing manifest file 'ont_bonito.egg-info/SOURCES.txt' 2025-09-09T07:38:05,938 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'bonito.data' is absent from the `packages` configuration. 2025-09-09T07:38:05,938 !! 2025-09-09T07:38:05,938 ******************************************************************************** 2025-09-09T07:38:05,939 ############################ 2025-09-09T07:38:05,939 # Package would be ignored # 2025-09-09T07:38:05,939 ############################ 2025-09-09T07:38:05,939 Python recognizes 'bonito.data' as an importable package[^1], 2025-09-09T07:38:05,939 but it is absent from setuptools' `packages` configuration. 2025-09-09T07:38:05,939 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-09T07:38:05,939 package, please make sure that 'bonito.data' is explicitly added 2025-09-09T07:38:05,939 to the `packages` configuration field. 2025-09-09T07:38:05,939 Alternatively, you can also rely on setuptools' discovery methods 2025-09-09T07:38:05,939 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-09T07:38:05,940 instead of `find_packages(...)`/`find:`). 2025-09-09T07:38:05,940 You can read more about "package discovery" on setuptools documentation page: 2025-09-09T07:38:05,940 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-09T07:38:05,940 If you don't want 'bonito.data' to be distributed and are 2025-09-09T07:38:05,940 already explicitly excluding 'bonito.data' via 2025-09-09T07:38:05,940 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-09T07:38:05,940 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-09T07:38:05,940 combination with a more fine grained `package-data` configuration. 2025-09-09T07:38:05,941 You can read more about "package data files" on setuptools documentation page: 2025-09-09T07:38:05,941 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-09T07:38:05,941 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-09T07:38:05,941 even if it does not contain any `.py` files. 2025-09-09T07:38:05,941 On the other hand, currently there is no concept of package data 2025-09-09T07:38:05,941 directory, all directories are treated like packages. 2025-09-09T07:38:05,941 ******************************************************************************** 2025-09-09T07:38:05,942 !! 2025-09-09T07:38:05,942 check.warn(importable) 2025-09-09T07:38:05,942 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'bonito.models' is absent from the `packages` configuration. 2025-09-09T07:38:05,942 !! 2025-09-09T07:38:05,942 ******************************************************************************** 2025-09-09T07:38:05,942 ############################ 2025-09-09T07:38:05,942 # Package would be ignored # 2025-09-09T07:38:05,942 ############################ 2025-09-09T07:38:05,943 Python recognizes 'bonito.models' as an importable package[^1], 2025-09-09T07:38:05,943 but it is absent from setuptools' `packages` configuration. 2025-09-09T07:38:05,943 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-09T07:38:05,943 package, please make sure that 'bonito.models' is explicitly added 2025-09-09T07:38:05,943 to the `packages` configuration field. 2025-09-09T07:38:05,943 Alternatively, you can also rely on setuptools' discovery methods 2025-09-09T07:38:05,943 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-09T07:38:05,943 instead of `find_packages(...)`/`find:`). 2025-09-09T07:38:05,944 You can read more about "package discovery" on setuptools documentation page: 2025-09-09T07:38:05,944 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-09T07:38:05,944 If you don't want 'bonito.models' to be distributed and are 2025-09-09T07:38:05,944 already explicitly excluding 'bonito.models' via 2025-09-09T07:38:05,944 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-09T07:38:05,944 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-09T07:38:05,944 combination with a more fine grained `package-data` configuration. 2025-09-09T07:38:05,944 You can read more about "package data files" on setuptools documentation page: 2025-09-09T07:38:05,945 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-09T07:38:05,945 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-09T07:38:05,945 even if it does not contain any `.py` files. 2025-09-09T07:38:05,945 On the other hand, currently there is no concept of package data 2025-09-09T07:38:05,945 directory, all directories are treated like packages. 2025-09-09T07:38:05,945 ******************************************************************************** 2025-09-09T07:38:05,945 !! 2025-09-09T07:38:05,946 check.warn(importable) 2025-09-09T07:38:05,946 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'bonito.models.configs' is absent from the `packages` configuration. 2025-09-09T07:38:05,946 !! 2025-09-09T07:38:05,946 ******************************************************************************** 2025-09-09T07:38:05,946 ############################ 2025-09-09T07:38:05,946 # Package would be ignored # 2025-09-09T07:38:05,946 ############################ 2025-09-09T07:38:05,946 Python recognizes 'bonito.models.configs' as an importable package[^1], 2025-09-09T07:38:05,946 but it is absent from setuptools' `packages` configuration. 2025-09-09T07:38:05,947 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-09T07:38:05,947 package, please make sure that 'bonito.models.configs' is explicitly added 2025-09-09T07:38:05,947 to the `packages` configuration field. 2025-09-09T07:38:05,947 Alternatively, you can also rely on setuptools' discovery methods 2025-09-09T07:38:05,947 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-09T07:38:05,947 instead of `find_packages(...)`/`find:`). 2025-09-09T07:38:05,947 You can read more about "package discovery" on setuptools documentation page: 2025-09-09T07:38:05,948 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-09T07:38:05,948 If you don't want 'bonito.models.configs' to be distributed and are 2025-09-09T07:38:05,948 already explicitly excluding 'bonito.models.configs' via 2025-09-09T07:38:05,948 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-09T07:38:05,948 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-09T07:38:05,948 combination with a more fine grained `package-data` configuration. 2025-09-09T07:38:05,948 You can read more about "package data files" on setuptools documentation page: 2025-09-09T07:38:05,948 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-09T07:38:05,949 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-09T07:38:05,949 even if it does not contain any `.py` files. 2025-09-09T07:38:05,949 On the other hand, currently there is no concept of package data 2025-09-09T07:38:05,949 directory, all directories are treated like packages. 2025-09-09T07:38:05,949 ******************************************************************************** 2025-09-09T07:38:05,949 !! 2025-09-09T07:38:05,949 check.warn(importable) 2025-09-09T07:38:05,949 creating build/lib/bonito/data 2025-09-09T07:38:05,949 copying bonito/data/README.md -> build/lib/bonito/data 2025-09-09T07:38:05,950 creating build/lib/bonito/models 2025-09-09T07:38:05,950 copying bonito/models/README.md -> build/lib/bonito/models 2025-09-09T07:38:05,950 creating build/lib/bonito/models/configs 2025-09-09T07:38:05,950 copying bonito/models/configs/dna_r9.4.1@v1.toml -> build/lib/bonito/models/configs 2025-09-09T07:38:05,950 copying bonito/models/configs/dna_r9.4.1@v2.toml -> build/lib/bonito/models/configs 2025-09-09T07:38:05,950 copying bonito/models/configs/dna_r9.4.1@v3.toml -> build/lib/bonito/models/configs 2025-09-09T07:38:05,950 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-09T07:38:05,950 !! 2025-09-09T07:38:05,950 ******************************************************************************** 2025-09-09T07:38:05,951 Please avoid running ``setup.py`` directly. 2025-09-09T07:38:05,951 Instead, use pypa/build, pypa/installer or other 2025-09-09T07:38:05,951 standards-based tools. 2025-09-09T07:38:05,951 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-09T07:38:05,951 or your builds will no longer be supported. 2025-09-09T07:38:05,951 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-09T07:38:05,951 ******************************************************************************** 2025-09-09T07:38:05,951 !! 2025-09-09T07:38:05,951 self.initialize_options() 2025-09-09T07:38:06,021 installing to build/bdist.linux-armv7l/wheel 2025-09-09T07:38:06,021 running install 2025-09-09T07:38:06,044 running install_lib 2025-09-09T07:38:06,117 creating build/bdist.linux-armv7l/wheel 2025-09-09T07:38:06,118 creating build/bdist.linux-armv7l/wheel/bonito 2025-09-09T07:38:06,118 creating build/bdist.linux-armv7l/wheel/bonito/models 2025-09-09T07:38:06,118 creating build/bdist.linux-armv7l/wheel/bonito/models/configs 2025-09-09T07:38:06,119 copying build/lib/bonito/models/configs/dna_r9.4.1@v3.toml -> build/bdist.linux-armv7l/wheel/./bonito/models/configs 2025-09-09T07:38:06,119 copying build/lib/bonito/models/configs/dna_r9.4.1@v2.toml -> build/bdist.linux-armv7l/wheel/./bonito/models/configs 2025-09-09T07:38:06,120 copying build/lib/bonito/models/configs/dna_r9.4.1@v1.toml -> build/bdist.linux-armv7l/wheel/./bonito/models/configs 2025-09-09T07:38:06,120 copying build/lib/bonito/models/README.md -> build/bdist.linux-armv7l/wheel/./bonito/models 2025-09-09T07:38:06,120 creating build/bdist.linux-armv7l/wheel/bonito/data 2025-09-09T07:38:06,121 copying build/lib/bonito/data/README.md -> build/bdist.linux-armv7l/wheel/./bonito/data 2025-09-09T07:38:06,121 creating build/bdist.linux-armv7l/wheel/bonito/cli 2025-09-09T07:38:06,121 copying build/lib/bonito/cli/download.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,122 copying build/lib/bonito/cli/basecaller.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,122 copying build/lib/bonito/cli/tune.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,123 copying build/lib/bonito/cli/evaluate.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,123 copying build/lib/bonito/cli/train.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,123 copying build/lib/bonito/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,124 copying build/lib/bonito/cli/view.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,124 copying build/lib/bonito/cli/convert.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,124 copying build/lib/bonito/cli/pair.py -> build/bdist.linux-armv7l/wheel/./bonito/cli 2025-09-09T07:38:06,125 creating build/bdist.linux-armv7l/wheel/bonito/ctc 2025-09-09T07:38:06,125 copying build/lib/bonito/ctc/basecall.py -> build/bdist.linux-armv7l/wheel/./bonito/ctc 2025-09-09T07:38:06,126 copying build/lib/bonito/ctc/__init__.py -> build/bdist.linux-armv7l/wheel/./bonito/ctc 2025-09-09T07:38:06,126 copying build/lib/bonito/ctc/model.py -> build/bdist.linux-armv7l/wheel/./bonito/ctc 2025-09-09T07:38:06,126 creating build/bdist.linux-armv7l/wheel/bonito/crf 2025-09-09T07:38:06,127 copying build/lib/bonito/crf/basecall.py -> build/bdist.linux-armv7l/wheel/./bonito/crf 2025-09-09T07:38:06,127 copying build/lib/bonito/crf/__init__.py -> build/bdist.linux-armv7l/wheel/./bonito/crf 2025-09-09T07:38:06,127 copying build/lib/bonito/crf/model.py -> build/bdist.linux-armv7l/wheel/./bonito/crf 2025-09-09T07:38:06,128 copying build/lib/bonito/nn.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,128 copying build/lib/bonito/util.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,129 copying build/lib/bonito/io.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,129 copying build/lib/bonito/aligner.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,129 copying build/lib/bonito/multiprocessing.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,130 copying build/lib/bonito/fast5.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,130 copying build/lib/bonito/__init__.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,130 copying build/lib/bonito/training.py -> build/bdist.linux-armv7l/wheel/./bonito 2025-09-09T07:38:06,131 running install_egg_info 2025-09-09T07:38:06,208 Copying ont_bonito.egg-info to build/bdist.linux-armv7l/wheel/./ont_bonito-0.3.2-py3.13.egg-info 2025-09-09T07:38:06,210 running install_scripts 2025-09-09T07:38:06,212 error: [Errno 2] No such file or directory: 'bonito' 2025-09-09T07:38:06,327 ERROR: python setup.py bdist_wheel exited with 1 2025-09-09T07:38:06,340 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-09T07:38:06,340 exec(compile('"'"''"'"''"'"' 2025-09-09T07:38:06,340 # This is -- a caller that pip uses to run setup.py 2025-09-09T07:38:06,340 # 2025-09-09T07:38:06,340 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-09T07:38:06,340 # import from `distutils.core` to work with newer packaging standards. 2025-09-09T07:38:06,340 # - It provides a clear error message when setuptools is not installed. 2025-09-09T07:38:06,340 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-09T07:38:06,340 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-09T07:38:06,340 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-09T07:38:06,340 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-09T07:38:06,340 import os, sys, tokenize, traceback 2025-09-09T07:38:06,340 2025-09-09T07:38:06,340 try: 2025-09-09T07:38:06,340 import setuptools 2025-09-09T07:38:06,340 except ImportError: 2025-09-09T07:38:06,340 print( 2025-09-09T07:38:06,340 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-09T07:38:06,340 "the build environment with exception:", 2025-09-09T07:38:06,340 file=sys.stderr, 2025-09-09T07:38:06,340 ) 2025-09-09T07:38:06,340 traceback.print_exc() 2025-09-09T07:38:06,340 sys.exit(1) 2025-09-09T07:38:06,340 2025-09-09T07:38:06,340 __file__ = %r 2025-09-09T07:38:06,340 sys.argv[0] = __file__ 2025-09-09T07:38:06,340 2025-09-09T07:38:06,340 if os.path.exists(__file__): 2025-09-09T07:38:06,340 filename = __file__ 2025-09-09T07:38:06,340 with tokenize.open(__file__) as f: 2025-09-09T07:38:06,340 setup_py_code = f.read() 2025-09-09T07:38:06,340 else: 2025-09-09T07:38:06,340 filename = "" 2025-09-09T07:38:06,340 setup_py_code = "from setuptools import setup; setup()" 2025-09-09T07:38:06,340 2025-09-09T07:38:06,340 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T07:38:06,340 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-et2okxsj/ont-bonito_06026b089dd24e8dbc2345a09dbb268d/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ehp2bq_n[/] 2025-09-09T07:38:06,340 [bold magenta]cwd[/]: /tmp/pip-wheel-et2okxsj/ont-bonito_06026b089dd24e8dbc2345a09dbb268d/ 2025-09-09T07:38:06,340 Building wheel for ont-bonito (setup.py): finished with status 'error' 2025-09-09T07:38:06,341 ERROR: Failed building wheel for ont-bonito 2025-09-09T07:38:06,342 Running setup.py clean for ont-bonito 2025-09-09T07:38:06,343 Running command python setup.py clean 2025-09-09T07:38:07,494 running clean 2025-09-09T07:38:07,635 removing 'build/lib' (and everything under it) 2025-09-09T07:38:07,637 removing 'build/bdist.linux-armv7l' (and everything under it) 2025-09-09T07:38:07,638 'build/scripts-3.13' does not exist -- can't clean it 2025-09-09T07:38:07,639 removing 'build' 2025-09-09T07:38:07,751 Failed to build ont-bonito 2025-09-09T07:38:07,752 ERROR: Failed to build one or more wheels 2025-09-09T07:38:07,753 Exception information: 2025-09-09T07:38:07,753 Traceback (most recent call last): 2025-09-09T07:38:07,753 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-09T07:38:07,753 status = _inner_run() 2025-09-09T07:38:07,753 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-09T07:38:07,753 return self.run(options, args) 2025-09-09T07:38:07,753 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-09T07:38:07,753 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-09T07:38:07,753 return func(self, options, args) 2025-09-09T07:38:07,753 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-09T07:38:07,753 raise CommandError("Failed to build one or more wheels") 2025-09-09T07:38:07,753 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-09T07:38:07,757 Removed build tracker: '/tmp/pip-build-tracker-_oihj3pl'