2026-02-08T22:19:20,008 Created temporary directory: /tmp/pip-ephem-wheel-cache-uygycgwj 2026-02-08T22:19:20,010 Created temporary directory: /tmp/pip-build-tracker-z_l83ki9 2026-02-08T22:19:20,011 Initialized build tracking at /tmp/pip-build-tracker-z_l83ki9 2026-02-08T22:19:20,012 Created build tracker: /tmp/pip-build-tracker-z_l83ki9 2026-02-08T22:19:20,012 Entered build tracker: /tmp/pip-build-tracker-z_l83ki9 2026-02-08T22:19:20,013 Created temporary directory: /tmp/pip-wheel-9hine5qf 2026-02-08T22:19:20,016 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-08T22:19:20,018 Created temporary directory: /tmp/pip-ephem-wheel-cache-ml88c83z 2026-02-08T22:19:20,041 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-08T22:19:20,044 2 location(s) to search for versions of scbamtools: 2026-02-08T22:19:20,044 * https://pypi.org/simple/scbamtools/ 2026-02-08T22:19:20,044 * https://www.piwheels.org/simple/scbamtools/ 2026-02-08T22:19:20,045 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/ 2026-02-08T22:19:20,046 Getting page https://pypi.org/simple/scbamtools/ 2026-02-08T22:19:20,047 Found index url https://pypi.org/simple 2026-02-08T22:19:20,264 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json 2026-02-08T22:19:20,267 Found link https://files.pythonhosted.org/packages/90/98/a7355f2097b73330b58718e0c6e83ee7b93bee0d6a00a010db3eaea2fbd5/scbamtools-0.1.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10), version: 0.1 2026-02-08T22:19:20,269 Found link https://files.pythonhosted.org/packages/24/fa/fd646836da42c49f38967ac48eaf7b6e360da3f50b94a305ef06f093a6ba/scbamtools-0.2.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10), version: 0.2 2026-02-08T22:19:20,270 Found link https://files.pythonhosted.org/packages/60/fe/4740173cbc7a3bc2c6b041d19db568741f4e5339a3bb12951bb652467fd1/scbamtools-0.5.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.5 2026-02-08T22:19:20,270 Found link https://files.pythonhosted.org/packages/77/33/b3f2ccfca129f9a1135d936e8ad2030b88bef0e859bf281620d9af5d6b0c/scbamtools-0.6.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.6 2026-02-08T22:19:20,272 Found link https://files.pythonhosted.org/packages/ed/c4/49dabbc8f6e5a6957f3451ec60363c7f804b1bcd2ad95eed323faa9fd6ba/scbamtools-0.8.1.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.1 2026-02-08T22:19:20,273 Found link https://files.pythonhosted.org/packages/f4/e3/382060f419dfa54214c760869e2272bf621f794cfabc13183ce0430f8539/scbamtools-0.8.2.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.2 2026-02-08T22:19:20,274 Found link https://files.pythonhosted.org/packages/58/a8/a17afb0e466cf567d8c13497d0f025c286b28da8ade10f7bb4697652cdec/scbamtools-0.8.3.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.3 2026-02-08T22:19:20,275 Found link https://files.pythonhosted.org/packages/f7/c0/d98768b070c431f1c02c5d08bd1e9b5bf59e6b8e0513ef157ff6aa604673/scbamtools-0.8.5.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.5 2026-02-08T22:19:20,276 Found link https://files.pythonhosted.org/packages/15/99/167036ec2645eb2793461a74cae353ea51708aa75af11e71db641e7fa0ac/scbamtools-0.8.6.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.6 2026-02-08T22:19:20,277 Found link https://files.pythonhosted.org/packages/d9/80/be7b6ed952e6f9c6d31b49f937ff6ce6c87183c6c8da3d7367703145bdc4/scbamtools-0.8.7.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.7 2026-02-08T22:19:20,278 Skipping link: No binaries permitted for scbamtools: https://files.pythonhosted.org/packages/de/43/54c74b3821005050acbd40788206b62177e6b938bfb5c095cca50b4f64dc/scbamtools-0.8.8-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,279 Found link https://files.pythonhosted.org/packages/ac/ac/814920459689b676193f71f87d40fd1ce45ff7338c05c6efde95a2c2f37a/scbamtools-0.8.8.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.8 2026-02-08T22:19:20,279 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/ 2026-02-08T22:19:20,280 Getting page https://www.piwheels.org/simple/scbamtools/ 2026-02-08T22:19:20,281 Found index url https://www.piwheels.org/simple 2026-02-08T22:19:20,438 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html 2026-02-08T22:19:20,449 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.6-cp311-cp311-linux_armv6l.whl#sha256=e06d1f685481047d82616faced558ab95931ad4825326ad183cd4e3215948b53 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,450 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.6-cp311-cp311-linux_armv7l.whl#sha256=e06d1f685481047d82616faced558ab95931ad4825326ad183cd4e3215948b53 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,450 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.6-cp39-cp39-linux_armv6l.whl#sha256=0851593cb51a03b62d82bc7f48425f94d49b577ddc26ae3fef36fba7f22f65b7 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,451 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.6-cp39-cp39-linux_armv7l.whl#sha256=0851593cb51a03b62d82bc7f48425f94d49b577ddc26ae3fef36fba7f22f65b7 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,451 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.5-cp311-cp311-linux_armv6l.whl#sha256=7fbc4b6e883667481fe381c8b7a08074a1cd79eacf7fafc9a0ccbab4777bcfb6 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,452 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.5-cp311-cp311-linux_armv7l.whl#sha256=7fbc4b6e883667481fe381c8b7a08074a1cd79eacf7fafc9a0ccbab4777bcfb6 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,453 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.5-cp313-cp313-linux_armv6l.whl#sha256=abd75a5202ccdec3943c4fcc637e6bd81474ccdd26f078e39e7a4772151e3e75 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,453 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.5-cp313-cp313-linux_armv7l.whl#sha256=abd75a5202ccdec3943c4fcc637e6bd81474ccdd26f078e39e7a4772151e3e75 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,454 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.5-cp39-cp39-linux_armv6l.whl#sha256=e7e68165307d327899b4331dbdebfc6c29e65cd71228acd5bd43ddfa66a0415f (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,454 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.5-cp39-cp39-linux_armv7l.whl#sha256=e7e68165307d327899b4331dbdebfc6c29e65cd71228acd5bd43ddfa66a0415f (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,455 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.3-cp39-cp39-linux_armv6l.whl#sha256=4614242a2712f562214b67d63697ed805021b00a5c08f5ca06ce3744450be271 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,456 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.3-cp39-cp39-linux_armv7l.whl#sha256=4614242a2712f562214b67d63697ed805021b00a5c08f5ca06ce3744450be271 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,456 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.3-cp311-cp311-linux_armv6l.whl#sha256=3ddd860d448ff4a31cc207ae510f4e9e192c849c0de2d148730e7084ce32a701 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,457 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.3-cp311-cp311-linux_armv7l.whl#sha256=3ddd860d448ff4a31cc207ae510f4e9e192c849c0de2d148730e7084ce32a701 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,457 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.2-cp39-cp39-linux_armv6l.whl#sha256=846d5029f6faf1dea94698c84d715ea5f05b9cf62f3bdd22a6ec18f7d3ea1373 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,458 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.2-cp39-cp39-linux_armv7l.whl#sha256=846d5029f6faf1dea94698c84d715ea5f05b9cf62f3bdd22a6ec18f7d3ea1373 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,458 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.2-cp311-cp311-linux_armv6l.whl#sha256=b4f10cfcbe618096f93e1c251428cff5983bd3752c3e358d36d2c27ce52df5ac (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,459 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.2-cp311-cp311-linux_armv7l.whl#sha256=b4f10cfcbe618096f93e1c251428cff5983bd3752c3e358d36d2c27ce52df5ac (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,460 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.1-cp311-cp311-linux_armv6l.whl#sha256=3002fafc54998bad2b456d0f0ac48b7a694c25f60dc26d234cde386d51f7bcbc (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,460 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.1-cp311-cp311-linux_armv7l.whl#sha256=3002fafc54998bad2b456d0f0ac48b7a694c25f60dc26d234cde386d51f7bcbc (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,461 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.1-cp39-cp39-linux_armv6l.whl#sha256=203190fcc7420b31eef2cb4b3cd8db5182b661e2056a5f6357d818fe1519224e (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,462 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.1-cp39-cp39-linux_armv7l.whl#sha256=203190fcc7420b31eef2cb4b3cd8db5182b661e2056a5f6357d818fe1519224e (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,462 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.1-cp313-cp313-linux_armv6l.whl#sha256=2e561934a526f42cef8e2295404e2f3f89ea513c7615e33a6bfc8cb75a9a689d (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,463 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.8.1-cp313-cp313-linux_armv7l.whl#sha256=2e561934a526f42cef8e2295404e2f3f89ea513c7615e33a6bfc8cb75a9a689d (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,464 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.6-cp311-cp311-linux_armv6l.whl#sha256=9288a1e72295542d124c65f92013e3c61eedae50599500c2ac00821300907afb (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,464 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.6-cp311-cp311-linux_armv7l.whl#sha256=9288a1e72295542d124c65f92013e3c61eedae50599500c2ac00821300907afb (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,465 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.6-cp39-cp39-linux_armv6l.whl#sha256=404de3ce08ae3d71ac8cb8a1eb1765fd44623031d1c6dddf6ac18e89cd1599d9 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,465 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.6-cp39-cp39-linux_armv7l.whl#sha256=404de3ce08ae3d71ac8cb8a1eb1765fd44623031d1c6dddf6ac18e89cd1599d9 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,466 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.6-cp313-cp313-linux_armv6l.whl#sha256=e9664700db741247419883b5d50404f92145df6410d1f31e295ac2d4bef633bc (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,466 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.6-cp313-cp313-linux_armv7l.whl#sha256=e9664700db741247419883b5d50404f92145df6410d1f31e295ac2d4bef633bc (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,467 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp311-cp311-linux_armv6l.whl#sha256=9eeb10371047b47673bf1fa28614f1f47c0b6089fd1cf486ed8be089efd51140 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,467 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp311-cp311-linux_armv7l.whl#sha256=9eeb10371047b47673bf1fa28614f1f47c0b6089fd1cf486ed8be089efd51140 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,468 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp39-cp39-linux_armv6l.whl#sha256=44ad821dcd492f55a691e24b59160b6016e170304ae897bde1333049698ef26b (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,469 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp39-cp39-linux_armv7l.whl#sha256=44ad821dcd492f55a691e24b59160b6016e170304ae897bde1333049698ef26b (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,469 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp313-cp313-linux_armv6l.whl#sha256=69b2f634075f82e42e3725c16b49f3d54b4c054997bbf4ffe0c013f0efe1b343 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,470 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp313-cp313-linux_armv7l.whl#sha256=69b2f634075f82e42e3725c16b49f3d54b4c054997bbf4ffe0c013f0efe1b343 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-08T22:19:20,471 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/ 2026-02-08T22:19:20,472 Skipping link: not a file: https://pypi.org/simple/scbamtools/ 2026-02-08T22:19:20,492 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates 2026-02-08T22:19:20,510 Collecting scbamtools==0.8.7 2026-02-08T22:19:20,512 Created temporary directory: /tmp/pip-unpack-4dapgwxv 2026-02-08T22:19:20,727 Downloading scbamtools-0.8.7.tar.gz (619 kB) 2026-02-08T22:19:21,083 Added scbamtools==0.8.7 from https://files.pythonhosted.org/packages/d9/80/be7b6ed952e6f9c6d31b49f937ff6ce6c87183c6c8da3d7367703145bdc4/scbamtools-0.8.7.tar.gz to build tracker '/tmp/pip-build-tracker-z_l83ki9' 2026-02-08T22:19:21,090 Created temporary directory: /tmp/pip-build-env-ptgj512o 2026-02-08T22:19:21,095 Installing build dependencies: started 2026-02-08T22:19:21,096 Running command pip subprocess to install build dependencies 2026-02-08T22:19:22,289 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-08T22:19:22,925 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-08T22:19:22,951 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-08T22:19:24,682 Collecting setuptools>=65.5.1 2026-02-08T22:19:24,701 Using cached setuptools-82.0.0-py3-none-any.whl (1.0 MB) 2026-02-08T22:19:24,964 Collecting wheel 2026-02-08T22:19:24,970 Using cached wheel-0.46.3-py3-none-any.whl (30 kB) 2026-02-08T22:19:27,043 Collecting cython>=3.0.8 2026-02-08T22:19:27,052 Downloading https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-02-08T22:19:27,981 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.1/11.1 MB 11.6 MB/s eta 0:00:00 2026-02-08T22:19:29,257 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-08T22:19:29,265 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-08T22:19:29,272 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-08T22:19:29,279 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-08T22:19:29,287 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-08T22:19:30,155 Collecting numpy 2026-02-08T22:19:30,533 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.1-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-02-08T22:19:30,891 Collecting packaging>=24.0 2026-02-08T22:19:30,897 Using cached packaging-26.0-py3-none-any.whl (74 kB) 2026-02-08T22:19:33,981 Installing collected packages: setuptools, packaging, numpy, cython, wheel 2026-02-08T22:19:46,944 Creating /tmp/pip-build-env-ptgj512o/overlay/local/bin 2026-02-08T22:19:46,947 changing mode of /tmp/pip-build-env-ptgj512o/overlay/local/bin/f2py to 755 2026-02-08T22:19:46,949 changing mode of /tmp/pip-build-env-ptgj512o/overlay/local/bin/numpy-config to 755 2026-02-08T22:19:51,516 changing mode of /tmp/pip-build-env-ptgj512o/overlay/local/bin/cygdb to 755 2026-02-08T22:19:51,519 changing mode of /tmp/pip-build-env-ptgj512o/overlay/local/bin/cython to 755 2026-02-08T22:19:51,521 changing mode of /tmp/pip-build-env-ptgj512o/overlay/local/bin/cythonize to 755 2026-02-08T22:19:51,648 changing mode of /tmp/pip-build-env-ptgj512o/overlay/local/bin/wheel to 755 2026-02-08T22:19:51,690 Successfully installed cython-3.2.4 numpy-2.4.1 packaging-26.0 setuptools-82.0.0 wheel-0.46.3 2026-02-08T22:19:52,158 Installing build dependencies: finished with status 'done' 2026-02-08T22:19:52,165 Getting requirements to build wheel: started 2026-02-08T22:19:52,166 Running command Getting requirements to build wheel 2026-02-08T22:19:56,330 warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier 2026-02-08T22:20:04,549 Compiling scbamtools/cython/kmers.pyx because it changed. 2026-02-08T22:20:04,549 Compiling scbamtools/cython/bctree.pyx because it changed. 2026-02-08T22:20:04,550 Compiling scbamtools/cython/fastquery.pyx because it changed. 2026-02-08T22:20:04,550 [1/3] Cythonizing scbamtools/cython/bctree.pyx 2026-02-08T22:20:04,551 [2/3] Cythonizing scbamtools/cython/fastquery.pyx 2026-02-08T22:20:04,551 [3/3] Cythonizing scbamtools/cython/kmers.pyx 2026-02-08T22:20:04,570 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-08T22:20:04,571 !! 2026-02-08T22:20:04,572 ******************************************************************************** 2026-02-08T22:20:04,572 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-08T22:20:04,574 License :: OSI Approved :: MIT License 2026-02-08T22:20:04,574 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:04,575 ******************************************************************************** 2026-02-08T22:20:04,576 !! 2026-02-08T22:20:04,576 self._finalize_license_expression() 2026-02-08T22:20:04,639 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-08T22:20:04,640 !! 2026-02-08T22:20:04,641 ******************************************************************************** 2026-02-08T22:20:04,642 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-08T22:20:04,643 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-08T22:20:04,644 or your builds will no longer be supported. 2026-02-08T22:20:04,645 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:04,646 ******************************************************************************** 2026-02-08T22:20:04,647 !! 2026-02-08T22:20:04,648 corresp(dist, value, root_dir) 2026-02-08T22:20:04,649 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-02-08T22:20:04,649 corresp(dist, value, root_dir) 2026-02-08T22:20:04,730 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-08T22:20:04,731 !! 2026-02-08T22:20:04,733 ******************************************************************************** 2026-02-08T22:20:04,733 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-08T22:20:04,735 License :: OSI Approved :: MIT License 2026-02-08T22:20:04,736 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:04,737 ******************************************************************************** 2026-02-08T22:20:04,739 !! 2026-02-08T22:20:04,739 dist._finalize_license_expression() 2026-02-08T22:20:04,742 running egg_info 2026-02-08T22:20:04,749 writing scbamtools.egg-info/PKG-INFO 2026-02-08T22:20:04,752 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2026-02-08T22:20:04,754 writing entry points to scbamtools.egg-info/entry_points.txt 2026-02-08T22:20:04,756 writing requirements to scbamtools.egg-info/requires.txt 2026-02-08T22:20:04,757 writing top-level names to scbamtools.egg-info/top_level.txt 2026-02-08T22:20:04,790 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,790 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,791 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,791 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,792 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,792 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,793 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,794 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,794 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,795 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,796 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,797 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,800 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,801 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,802 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:04,803 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-08T22:20:04,812 reading manifest template 'MANIFEST.in' 2026-02-08T22:20:04,820 adding license file 'LICENSE' 2026-02-08T22:20:04,824 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-08T22:20:05,652 Getting requirements to build wheel: finished with status 'done' 2026-02-08T22:20:05,656 Created temporary directory: /tmp/pip-modern-metadata-ryeb_fff 2026-02-08T22:20:05,659 Preparing metadata (pyproject.toml): started 2026-02-08T22:20:05,660 Running command Preparing metadata (pyproject.toml) 2026-02-08T22:20:07,302 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-08T22:20:07,303 !! 2026-02-08T22:20:07,304 ******************************************************************************** 2026-02-08T22:20:07,304 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-08T22:20:07,305 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-08T22:20:07,306 or your builds will no longer be supported. 2026-02-08T22:20:07,307 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:07,307 ******************************************************************************** 2026-02-08T22:20:07,308 !! 2026-02-08T22:20:07,309 corresp(dist, value, root_dir) 2026-02-08T22:20:07,309 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-02-08T22:20:07,310 corresp(dist, value, root_dir) 2026-02-08T22:20:07,382 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-08T22:20:07,382 !! 2026-02-08T22:20:07,383 ******************************************************************************** 2026-02-08T22:20:07,384 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-08T22:20:07,385 License :: OSI Approved :: MIT License 2026-02-08T22:20:07,386 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:07,386 ******************************************************************************** 2026-02-08T22:20:07,387 !! 2026-02-08T22:20:07,388 dist._finalize_license_expression() 2026-02-08T22:20:07,389 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-08T22:20:07,389 !! 2026-02-08T22:20:07,390 ******************************************************************************** 2026-02-08T22:20:07,391 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-08T22:20:07,392 License :: OSI Approved :: MIT License 2026-02-08T22:20:07,393 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:07,394 ******************************************************************************** 2026-02-08T22:20:07,395 !! 2026-02-08T22:20:07,395 self._finalize_license_expression() 2026-02-08T22:20:07,398 running dist_info 2026-02-08T22:20:07,411 creating /tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info 2026-02-08T22:20:07,412 writing /tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/PKG-INFO 2026-02-08T22:20:07,416 writing dependency_links to /tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/dependency_links.txt 2026-02-08T22:20:07,417 writing entry points to /tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/entry_points.txt 2026-02-08T22:20:07,419 writing requirements to /tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/requires.txt 2026-02-08T22:20:07,420 writing top-level names to /tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/top_level.txt 2026-02-08T22:20:07,421 writing manifest file '/tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/SOURCES.txt' 2026-02-08T22:20:07,445 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,445 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,446 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,446 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,447 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,447 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,448 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,448 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,449 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,449 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,450 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,451 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,451 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,452 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,452 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:07,454 reading manifest file '/tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/SOURCES.txt' 2026-02-08T22:20:07,456 reading manifest template 'MANIFEST.in' 2026-02-08T22:20:07,459 adding license file 'LICENSE' 2026-02-08T22:20:07,463 writing manifest file '/tmp/pip-modern-metadata-ryeb_fff/scbamtools.egg-info/SOURCES.txt' 2026-02-08T22:20:07,464 creating '/tmp/pip-modern-metadata-ryeb_fff/scbamtools-0.8.7.dist-info' 2026-02-08T22:20:07,678 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-08T22:20:07,896 Source in /tmp/pip-wheel-9hine5qf/scbamtools_a79bdbc7c3294d43b11570ebc2755468 has version 0.8.7, which satisfies requirement scbamtools==0.8.7 from https://files.pythonhosted.org/packages/d9/80/be7b6ed952e6f9c6d31b49f937ff6ce6c87183c6c8da3d7367703145bdc4/scbamtools-0.8.7.tar.gz 2026-02-08T22:20:07,897 Removed scbamtools==0.8.7 from https://files.pythonhosted.org/packages/d9/80/be7b6ed952e6f9c6d31b49f937ff6ce6c87183c6c8da3d7367703145bdc4/scbamtools-0.8.7.tar.gz from build tracker '/tmp/pip-build-tracker-z_l83ki9' 2026-02-08T22:20:07,902 Created temporary directory: /tmp/pip-unpack-eah2whny 2026-02-08T22:20:07,902 Building wheels for collected packages: scbamtools 2026-02-08T22:20:07,906 Created temporary directory: /tmp/pip-wheel-6rzmqecy 2026-02-08T22:20:07,907 Destination directory: /tmp/pip-wheel-6rzmqecy 2026-02-08T22:20:07,909 Building wheel for scbamtools (pyproject.toml): started 2026-02-08T22:20:07,910 Running command Building wheel for scbamtools (pyproject.toml) 2026-02-08T22:20:09,483 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-08T22:20:09,483 !! 2026-02-08T22:20:09,485 ******************************************************************************** 2026-02-08T22:20:09,485 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-08T22:20:09,486 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-08T22:20:09,487 or your builds will no longer be supported. 2026-02-08T22:20:09,488 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:09,489 ******************************************************************************** 2026-02-08T22:20:09,490 !! 2026-02-08T22:20:09,490 corresp(dist, value, root_dir) 2026-02-08T22:20:09,491 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-02-08T22:20:09,491 corresp(dist, value, root_dir) 2026-02-08T22:20:09,553 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-08T22:20:09,554 !! 2026-02-08T22:20:09,555 ******************************************************************************** 2026-02-08T22:20:09,556 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-08T22:20:09,557 License :: OSI Approved :: MIT License 2026-02-08T22:20:09,558 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:09,559 ******************************************************************************** 2026-02-08T22:20:09,560 !! 2026-02-08T22:20:09,561 dist._finalize_license_expression() 2026-02-08T22:20:09,561 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-08T22:20:09,562 !! 2026-02-08T22:20:09,563 ******************************************************************************** 2026-02-08T22:20:09,563 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-08T22:20:09,564 License :: OSI Approved :: MIT License 2026-02-08T22:20:09,565 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-08T22:20:09,566 ******************************************************************************** 2026-02-08T22:20:09,567 !! 2026-02-08T22:20:09,567 self._finalize_license_expression() 2026-02-08T22:20:09,567 running bdist_wheel 2026-02-08T22:20:09,585 running build 2026-02-08T22:20:09,585 running build_py 2026-02-08T22:20:09,592 creating build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,595 copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,597 copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,600 copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,602 copying scbamtools/pl.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,604 copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,607 copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,609 copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,612 copying scbamtools/tk.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-08T22:20:09,615 creating build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,616 copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,619 copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,621 copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,623 copying scbamtools/bin/pa_scanner.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,625 copying scbamtools/bin/cb_correct.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,628 copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,630 copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-08T22:20:09,633 creating build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-02-08T22:20:09,635 copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-02-08T22:20:09,636 running egg_info 2026-02-08T22:20:09,649 writing scbamtools.egg-info/PKG-INFO 2026-02-08T22:20:09,652 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2026-02-08T22:20:09,654 writing entry points to scbamtools.egg-info/entry_points.txt 2026-02-08T22:20:09,656 writing requirements to scbamtools.egg-info/requires.txt 2026-02-08T22:20:09,657 writing top-level names to scbamtools.egg-info/top_level.txt 2026-02-08T22:20:09,665 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,666 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,667 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,667 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,668 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,669 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,669 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,670 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,670 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,671 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,671 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,672 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,672 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,673 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,673 dependency /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-08T22:20:09,679 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-08T22:20:09,684 reading manifest template 'MANIFEST.in' 2026-02-08T22:20:09,687 adding license file 'LICENSE' 2026-02-08T22:20:09,692 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-08T22:20:09,695 /tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'scbamtools.config.__pycache__' is absent from the `packages` configuration. 2026-02-08T22:20:09,695 !! 2026-02-08T22:20:09,697 ******************************************************************************** 2026-02-08T22:20:09,697 ############################ 2026-02-08T22:20:09,698 # Package would be ignored # 2026-02-08T22:20:09,698 ############################ 2026-02-08T22:20:09,699 Python recognizes 'scbamtools.config.__pycache__' as an importable package[^1], 2026-02-08T22:20:09,699 but it is absent from setuptools' `packages` configuration. 2026-02-08T22:20:09,700 This leads to an ambiguous overall configuration. If you want to distribute this 2026-02-08T22:20:09,701 package, please make sure that 'scbamtools.config.__pycache__' is explicitly added 2026-02-08T22:20:09,702 to the `packages` configuration field. 2026-02-08T22:20:09,703 Alternatively, you can also rely on setuptools' discovery methods 2026-02-08T22:20:09,703 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-02-08T22:20:09,704 instead of `find_packages(...)`/`find:`). 2026-02-08T22:20:09,704 You can read more about "package discovery" on setuptools documentation page: 2026-02-08T22:20:09,705 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-02-08T22:20:09,706 If you don't want 'scbamtools.config.__pycache__' to be distributed and are 2026-02-08T22:20:09,707 already explicitly excluding 'scbamtools.config.__pycache__' via 2026-02-08T22:20:09,707 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-02-08T22:20:09,707 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-02-08T22:20:09,708 combination with a more fine grained `package-data` configuration. 2026-02-08T22:20:09,709 You can read more about "package data files" on setuptools documentation page: 2026-02-08T22:20:09,710 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-02-08T22:20:09,712 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-02-08T22:20:09,712 even if it does not contain any `.py` files. 2026-02-08T22:20:09,712 On the other hand, currently there is no concept of package data 2026-02-08T22:20:09,713 directory, all directories are treated like packages. 2026-02-08T22:20:09,713 ******************************************************************************** 2026-02-08T22:20:09,714 !! 2026-02-08T22:20:09,715 check.warn(importable) 2026-02-08T22:20:09,715 creating build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,716 copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,735 copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,738 copying scbamtools/cython/cigar.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,740 copying scbamtools/cython/fastquery.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,768 copying scbamtools/cython/fastquery.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,771 copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,802 copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,804 copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,806 copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-02-08T22:20:09,808 creating build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-02-08T22:20:09,809 copying scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-02-08T22:20:09,811 copying scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-02-08T22:20:09,815 running build_ext 2026-02-08T22:20:09,822 building 'scbamtools.cython.kmers' extension 2026-02-08T22:20:09,823 creating build/temp.linux-armv7l-cpython-311/scbamtools/cython 2026-02-08T22:20:09,825 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c scbamtools/cython/kmers.c -o build/temp.linux-armv7l-cpython-311/scbamtools/cython/kmers.o 2026-02-08T22:20:11,517 scbamtools/cython/kmers.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’: 2026-02-08T22:20:11,541 scbamtools/cython/kmers.c:27485:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2026-02-08T22:20:11,542 27485 | if ((intval & PyLong_MASK) == intval) { 2026-02-08T22:20:11,542 | ^~ 2026-02-08T22:20:11,565 scbamtools/cython/kmers.c:27487:55: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2026-02-08T22:20:11,566 27487 | long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1)); 2026-02-08T22:20:11,566 | ^~~~~~~~~~ 2026-02-08T22:20:30,755 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/scbamtools/cython/kmers.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so 2026-02-08T22:20:30,928 building 'scbamtools.cython.bctree' extension 2026-02-08T22:20:30,930 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c scbamtools/cython/bctree.c -o build/temp.linux-armv7l-cpython-311/scbamtools/cython/bctree.o 2026-02-08T22:20:31,659 scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’: 2026-02-08T22:20:31,677 scbamtools/cython/bctree.c:21046:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:31,678 21046 | __pyx_v_node = (&(*((struct __pyx_t_10scbamtools_6cython_6bctree_bc_info_t const *) ( /* dim=0 */ (__pyx_v_buf.data + __pyx_t_2 * __pyx_v_buf.strides[0]) )))); 2026-02-08T22:20:31,678 | ^ 2026-02-08T22:20:32,632 scbamtools/cython/bctree.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’: 2026-02-08T22:20:32,656 scbamtools/cython/bctree.c:27497:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2026-02-08T22:20:32,657 27497 | if ((intval & PyLong_MASK) == intval) { 2026-02-08T22:20:32,657 | ^~ 2026-02-08T22:20:32,681 scbamtools/cython/bctree.c:27499:55: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2026-02-08T22:20:32,682 27499 | long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1)); 2026-02-08T22:20:32,682 | ^~~~~~~~~~ 2026-02-08T22:20:51,978 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/scbamtools/cython/bctree.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so 2026-02-08T22:20:52,153 building 'scbamtools.cython.fastquery' extension 2026-02-08T22:20:52,155 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-ptgj512o/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c scbamtools/cython/fastquery.c -o build/temp.linux-armv7l-cpython-311/scbamtools/cython/fastquery.o -fopenmp 2026-02-08T22:20:52,956 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_10query’: 2026-02-08T22:20:52,976 scbamtools/cython/fastquery.c:22650:89: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:52,976 22650 | __pyx_t_13 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ (__pyx_v_SL_view.data + __pyx_t_12 * __pyx_v_SL_view.strides[0]) )))), __pyx_v_nn); if (unlikely(__pyx_t_13 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 322, __pyx_L1_error) 2026-02-08T22:20:52,977 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:52,996 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-08T22:20:52,997 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-08T22:20:52,998 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-08T22:20:53,013 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_12query_idx64’: 2026-02-08T22:20:53,033 scbamtools/cython/fastquery.c:23111:89: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:53,034 23111 | __pyx_t_11 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ (__pyx_v_SL_view.data + __pyx_t_8 * __pyx_v_SL_view.strides[0]) )))), __pyx_v_nn); if (unlikely(__pyx_t_11 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 384, __pyx_L1_error) 2026-02-08T22:20:53,034 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:53,054 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-08T22:20:53,054 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-08T22:20:53,055 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-08T22:20:53,074 scbamtools/cython/fastquery.c: In function ‘__pyx_f_10scbamtools_6cython_9fastquery_make_variants_off_by_one’: 2026-02-08T22:20:53,095 scbamtools/cython/fastquery.c:24094:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-02-08T22:20:53,096 24094 | for (__pyx_t_3 = __pyx_v_start; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2026-02-08T22:20:53,096 | ^ 2026-02-08T22:20:53,112 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one’: 2026-02-08T22:20:53,133 scbamtools/cython/fastquery.c:24627:92: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:53,134 24627 | __pyx_t_16 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_sv, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_8)) )))), __pyx_v_nn); if (unlikely(__pyx_t_16 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 585, __pyx_L1_error) 2026-02-08T22:20:53,134 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:53,154 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-08T22:20:53,155 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-08T22:20:53,156 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-08T22:20:53,177 scbamtools/cython/fastquery.c:24723:91: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:53,178 24723 | __pyx_t_16 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_8)) )))), __pyx_v_nn); if (unlikely(__pyx_t_16 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 594, __pyx_L1_error) 2026-02-08T22:20:53,178 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:53,198 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-08T22:20:53,198 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-08T22:20:53,199 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-08T22:20:53,221 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_18query_idx64_variants_single’: 2026-02-08T22:20:53,243 scbamtools/cython/fastquery.c:25883:88: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:53,243 25883 | __pyx_t_6 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_5)) )))), __pyx_v_nn); if (unlikely(__pyx_t_6 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 800, __pyx_L1_error) 2026-02-08T22:20:53,244 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:53,263 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-08T22:20:53,264 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-08T22:20:53,264 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-08T22:20:53,289 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_20query_idx64_variants’: 2026-02-08T22:20:53,312 scbamtools/cython/fastquery.c:26559:91: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:53,313 26559 | __pyx_t_12 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_9)) )))), __pyx_v_nn); if (unlikely(__pyx_t_12 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 875, __pyx_L1_error) 2026-02-08T22:20:53,314 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:53,332 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-08T22:20:53,333 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-08T22:20:53,334 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-08T22:20:53,350 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp’: 2026-02-08T22:20:53,374 scbamtools/cython/fastquery.c:27171:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-08T22:20:53,374 27171 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2026-02-08T22:20:53,375 | ^ 2026-02-08T22:20:53,404 scbamtools/cython/fastquery.c:27377:119: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-08T22:20:53,405 27377 | __pyx_t_15 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_12)) )))), __pyx_v_nn); if (unlikely(__pyx_t_15 == ((uint8_t)-1) && __Pyx_ErrOccurredWithGIL())) __PYX_ERR(0, 963, __pyx_L14_error) 2026-02-08T22:20:53,405 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:53,425 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-08T22:20:53,425 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-08T22:20:53,426 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-08T22:20:53,452 scbamtools/cython/fastquery.c:27663:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-08T22:20:53,453 27663 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2026-02-08T22:20:53,453 | ^ 2026-02-08T22:20:56,974 scbamtools/cython/fastquery.c: At top level: 2026-02-08T22:20:57,002 scbamtools/cython/fastquery.c:23205:18: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_make_shifts’ defined but not used [-Wunused-function] 2026-02-08T22:20:57,003 23205 | static PyObject *__pyx_f_10scbamtools_6cython_9fastquery_make_shifts(uint64_t __pyx_v_idx, uint64_t *__pyx_v_shifts, struct __pyx_opt_args_10scbamtools_6cython_9fastquery_make_shifts *__pyx_optional_args) { 2026-02-08T22:20:57,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:20:57,017 scbamtools/cython/fastquery.c:21833:17: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_seq_to_uint32_slice’ defined but not used [-Wunused-function] 2026-02-08T22:20:57,018 21833 | static uint32_t __pyx_f_10scbamtools_6cython_9fastquery_seq_to_uint32_slice(PyObject *__pyx_v_seq, Py_ssize_t __pyx_v_start, Py_ssize_t __pyx_v_length) { 2026-02-08T22:20:57,018 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:21:05,807 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp.constprop’: 2026-02-08T22:21:05,831 scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_thread_id’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-08T22:21:05,831 27211 | #pragma omp parallel firstprivate(__pyx_v_idx_variants, __pyx_v_thread_id) private(__pyx_t_1, __pyx_t_10, __pyx_t_11, __pyx_t_12, __pyx_t_13, __pyx_t_14, __pyx_t_15, __pyx_t_16, __pyx_t_17, __pyx_t_18, __pyx_t_7) __Pyx_shared_in_cpython_freethreading(__pyx_parallel_freethreading_mutex) private(__pyx_filename, __pyx_lineno, __pyx_clineno) shared(__pyx_parallel_why, __pyx_parallel_exc_type, __pyx_parallel_exc_value, __pyx_parallel_exc_tb) 2026-02-08T22:21:05,832 | ^~~ 2026-02-08T22:21:05,856 scbamtools/cython/fastquery.c:26953:7: note: ‘__pyx_v_thread_id’ was declared here 2026-02-08T22:21:05,857 26953 | int __pyx_v_thread_id; 2026-02-08T22:21:05,857 | ^~~~~~~~~~~~~~~~~ 2026-02-08T22:21:05,879 scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_idx_variants’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-08T22:21:05,880 27211 | #pragma omp parallel firstprivate(__pyx_v_idx_variants, __pyx_v_thread_id) private(__pyx_t_1, __pyx_t_10, __pyx_t_11, __pyx_t_12, __pyx_t_13, __pyx_t_14, __pyx_t_15, __pyx_t_16, __pyx_t_17, __pyx_t_18, __pyx_t_7) __Pyx_shared_in_cpython_freethreading(__pyx_parallel_freethreading_mutex) private(__pyx_filename, __pyx_lineno, __pyx_clineno) shared(__pyx_parallel_why, __pyx_parallel_exc_type, __pyx_parallel_exc_value, __pyx_parallel_exc_tb) 2026-02-08T22:21:05,880 | ^~~ 2026-02-08T22:21:05,905 scbamtools/cython/fastquery.c:26951:13: note: ‘__pyx_v_idx_variants’ was declared here 2026-02-08T22:21:05,905 26951 | uint64_t *__pyx_v_idx_variants; 2026-02-08T22:21:05,906 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-08T22:21:14,751 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one.constprop’: 2026-02-08T22:21:14,774 scbamtools/cython/fastquery.c:24725:12: warning: ‘__pyx_v_idx_s’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-08T22:21:14,775 24725 | if (__pyx_t_10) { 2026-02-08T22:21:14,775 | ^ 2026-02-08T22:21:14,797 scbamtools/cython/fastquery.c:24339:12: note: ‘__pyx_v_idx_s’ was declared here 2026-02-08T22:21:14,798 24339 | uint32_t __pyx_v_idx_s; 2026-02-08T22:21:14,798 | ^~~~~~~~~~~~~ 2026-02-08T22:21:18,924 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/scbamtools/cython/fastquery.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so -fopenmp 2026-02-08T22:21:19,100 installing to build/bdist.linux-armv7l/wheel 2026-02-08T22:21:19,101 running install 2026-02-08T22:21:19,124 running install_lib 2026-02-08T22:21:19,131 creating build/bdist.linux-armv7l/wheel 2026-02-08T22:21:19,133 creating build/bdist.linux-armv7l/wheel/scbamtools 2026-02-08T22:21:19,135 creating build/bdist.linux-armv7l/wheel/scbamtools/cython 2026-02-08T22:21:19,137 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,169 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,207 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/cigar.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,209 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,211 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,250 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,295 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,313 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,316 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,319 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,321 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-08T22:21:19,342 copying build/lib.linux-armv7l-cpython-311/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,345 copying build/lib.linux-armv7l-cpython-311/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,347 copying build/lib.linux-armv7l-cpython-311/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,349 copying build/lib.linux-armv7l-cpython-311/scbamtools/pl.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,352 creating build/bdist.linux-armv7l/wheel/scbamtools/bin 2026-02-08T22:21:19,353 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-08T22:21:19,355 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-08T22:21:19,358 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-08T22:21:19,360 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/pa_scanner.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-08T22:21:19,362 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/cb_correct.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-08T22:21:19,364 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-08T22:21:19,366 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-08T22:21:19,369 copying build/lib.linux-armv7l-cpython-311/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,371 copying build/lib.linux-armv7l-cpython-311/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,373 copying build/lib.linux-armv7l-cpython-311/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,375 copying build/lib.linux-armv7l-cpython-311/scbamtools/tk.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-08T22:21:19,378 creating build/bdist.linux-armv7l/wheel/scbamtools/config 2026-02-08T22:21:19,379 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/./scbamtools/config 2026-02-08T22:21:19,381 creating build/bdist.linux-armv7l/wheel/scbamtools/config/__pycache__ 2026-02-08T22:21:19,382 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__ 2026-02-08T22:21:19,384 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__ 2026-02-08T22:21:19,386 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/./scbamtools/config 2026-02-08T22:21:19,388 running install_egg_info 2026-02-08T22:21:19,393 Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/./scbamtools-0.8.7-py3.11.egg-info 2026-02-08T22:21:19,407 running install_scripts 2026-02-08T22:21:19,453 creating build/bdist.linux-armv7l/wheel/scbamtools-0.8.7.dist-info/WHEEL 2026-02-08T22:21:19,456 creating '/tmp/pip-wheel-6rzmqecy/.tmp-v1utr4qf/scbamtools-0.8.7-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-08T22:21:19,460 adding 'scbamtools/annotation.py' 2026-02-08T22:21:19,462 adding 'scbamtools/bctree.py' 2026-02-08T22:21:19,463 adding 'scbamtools/contrib.py' 2026-02-08T22:21:19,467 adding 'scbamtools/gene_model.py' 2026-02-08T22:21:19,469 adding 'scbamtools/pl.py' 2026-02-08T22:21:19,472 adding 'scbamtools/quant.py' 2026-02-08T22:21:19,473 adding 'scbamtools/tk.py' 2026-02-08T22:21:19,475 adding 'scbamtools/util.py' 2026-02-08T22:21:19,477 adding 'scbamtools/bin/BamTagHistogram.py' 2026-02-08T22:21:19,479 adding 'scbamtools/bin/ann.py' 2026-02-08T22:21:19,482 adding 'scbamtools/bin/cb_correct.py' 2026-02-08T22:21:19,484 adding 'scbamtools/bin/count.py' 2026-02-08T22:21:19,485 adding 'scbamtools/bin/pa_scanner.py' 2026-02-08T22:21:19,487 adding 'scbamtools/bin/trim.py' 2026-02-08T22:21:19,489 adding 'scbamtools/bin/uBAM.py' 2026-02-08T22:21:19,491 adding 'scbamtools/config/__init__.py' 2026-02-08T22:21:19,492 adding 'scbamtools/config/default.yaml' 2026-02-08T22:21:19,494 adding 'scbamtools/config/__pycache__/__init__.cpython-310.pyc' 2026-02-08T22:21:19,495 adding 'scbamtools/config/__pycache__/__init__.cpython-311.pyc' 2026-02-08T22:21:19,633 adding 'scbamtools/cython/bctree.c' 2026-02-08T22:21:19,859 adding 'scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so' 2026-02-08T22:21:19,867 adding 'scbamtools/cython/bctree.pyx' 2026-02-08T22:21:19,868 adding 'scbamtools/cython/cigar.pyx' 2026-02-08T22:21:19,993 adding 'scbamtools/cython/fastquery.c' 2026-02-08T22:21:20,257 adding 'scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so' 2026-02-08T22:21:20,267 adding 'scbamtools/cython/fastquery.pyx' 2026-02-08T22:21:20,371 adding 'scbamtools/cython/kmers.c' 2026-02-08T22:21:20,595 adding 'scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so' 2026-02-08T22:21:20,603 adding 'scbamtools/cython/kmers.pyx' 2026-02-08T22:21:20,604 adding 'scbamtools/cython/types.pxd' 2026-02-08T22:21:20,607 adding 'scbamtools-0.8.7.dist-info/licenses/LICENSE' 2026-02-08T22:21:20,608 adding 'scbamtools-0.8.7.dist-info/METADATA' 2026-02-08T22:21:20,609 adding 'scbamtools-0.8.7.dist-info/WHEEL' 2026-02-08T22:21:20,610 adding 'scbamtools-0.8.7.dist-info/entry_points.txt' 2026-02-08T22:21:20,611 adding 'scbamtools-0.8.7.dist-info/top_level.txt' 2026-02-08T22:21:20,613 adding 'scbamtools-0.8.7.dist-info/RECORD' 2026-02-08T22:21:20,642 removing build/bdist.linux-armv7l/wheel 2026-02-08T22:21:20,837 Building wheel for scbamtools (pyproject.toml): finished with status 'done' 2026-02-08T22:21:20,889 Created wheel for scbamtools: filename=scbamtools-0.8.7-cp311-cp311-linux_armv7l.whl size=1992451 sha256=3bdbf53559ea976bd0e9c51f4498ab1aadc3eca1a83dfc0350255bc376186771 2026-02-08T22:21:20,890 Stored in directory: /tmp/pip-ephem-wheel-cache-ml88c83z/wheels/6d/ef/07/54b437e39ac7d7b53b064fdb2aae08281d01163bb05a67973c 2026-02-08T22:21:20,902 Successfully built scbamtools 2026-02-08T22:21:20,956 Removed build tracker: '/tmp/pip-build-tracker-z_l83ki9'