2026-02-07T05:59:00,826 Created temporary directory: /tmp/pip-ephem-wheel-cache-sos_jlf_
2026-02-07T05:59:00,828 Created temporary directory: /tmp/pip-build-tracker-dmb0gnlh
2026-02-07T05:59:00,828 Initialized build tracking at /tmp/pip-build-tracker-dmb0gnlh
2026-02-07T05:59:00,829 Created build tracker: /tmp/pip-build-tracker-dmb0gnlh
2026-02-07T05:59:00,829 Entered build tracker: /tmp/pip-build-tracker-dmb0gnlh
2026-02-07T05:59:00,830 Created temporary directory: /tmp/pip-wheel-opamyo08
2026-02-07T05:59:00,833 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
2026-02-07T05:59:00,835 Created temporary directory: /tmp/pip-ephem-wheel-cache-9fu8radg
2026-02-07T05:59:00,857 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-02-07T05:59:00,860 2 location(s) to search for versions of scbamtools:
2026-02-07T05:59:00,860 * https://pypi.org/simple/scbamtools/
2026-02-07T05:59:00,860 * https://www.piwheels.org/simple/scbamtools/
2026-02-07T05:59:00,861 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/
2026-02-07T05:59:00,862 Getting page https://pypi.org/simple/scbamtools/
2026-02-07T05:59:00,863 Found index url https://pypi.org/simple
2026-02-07T05:59:01,077 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json
2026-02-07T05:59:01,081   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
2026-02-07T05:59:01,082   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
2026-02-07T05:59:01,083   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
2026-02-07T05:59:01,083   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
2026-02-07T05:59:01,084   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
2026-02-07T05:59:01,085   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
2026-02-07T05:59:01,086   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
2026-02-07T05:59:01,087   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
2026-02-07T05:59:01,088   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
2026-02-07T05:59:01,089   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
2026-02-07T05:59:01,090   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)
2026-02-07T05:59:01,091   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
2026-02-07T05:59:01,092 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/
2026-02-07T05:59:01,092 Getting page https://www.piwheels.org/simple/scbamtools/
2026-02-07T05:59:01,093 Found index url https://www.piwheels.org/simple
2026-02-07T05:59:01,249 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html
2026-02-07T05:59:01,260   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)
2026-02-07T05:59:01,260   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)
2026-02-07T05:59:01,261   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)
2026-02-07T05:59:01,261   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)
2026-02-07T05:59:01,262   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)
2026-02-07T05:59:01,262   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)
2026-02-07T05:59:01,263   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)
2026-02-07T05:59:01,263   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)
2026-02-07T05:59:01,264   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)
2026-02-07T05:59:01,265   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)
2026-02-07T05:59:01,265   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)
2026-02-07T05:59:01,266   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)
2026-02-07T05:59:01,267   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)
2026-02-07T05:59:01,267   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)
2026-02-07T05:59:01,267   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)
2026-02-07T05:59:01,268   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)
2026-02-07T05:59:01,268   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)
2026-02-07T05:59:01,269   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)
2026-02-07T05:59:01,270   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)
2026-02-07T05:59:01,270   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)
2026-02-07T05:59:01,271   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)
2026-02-07T05:59:01,271   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)
2026-02-07T05:59:01,272   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)
2026-02-07T05:59:01,272   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)
2026-02-07T05:59:01,273   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)
2026-02-07T05:59:01,274   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)
2026-02-07T05:59:01,274   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)
2026-02-07T05:59:01,275   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)
2026-02-07T05:59:01,275   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)
2026-02-07T05:59:01,276   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)
2026-02-07T05:59:01,276   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)
2026-02-07T05:59:01,277   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)
2026-02-07T05:59:01,277 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/
2026-02-07T05:59:01,278 Skipping link: not a file: https://pypi.org/simple/scbamtools/
2026-02-07T05:59:01,298 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates
2026-02-07T05:59:01,316 Collecting scbamtools==0.8.6
2026-02-07T05:59:01,318   Created temporary directory: /tmp/pip-unpack-gjm9kh03
2026-02-07T05:59:01,541   Downloading scbamtools-0.8.6.tar.gz (598 kB)
2026-02-07T05:59:01,875   Added scbamtools==0.8.6 from https://files.pythonhosted.org/packages/15/99/167036ec2645eb2793461a74cae353ea51708aa75af11e71db641e7fa0ac/scbamtools-0.8.6.tar.gz to build tracker '/tmp/pip-build-tracker-dmb0gnlh'
2026-02-07T05:59:01,883   Created temporary directory: /tmp/pip-build-env-xx5xfe2r
2026-02-07T05:59:01,888   Installing build dependencies: started
2026-02-07T05:59:01,889   Running command pip subprocess to install build dependencies
2026-02-07T05:59:03,031   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-02-07T05:59:03,623   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
2026-02-07T05:59:03,648   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-02-07T05:59:05,380   Collecting setuptools>=65.5.1
2026-02-07T05:59:05,401     Using cached setuptools-81.0.0-py3-none-any.whl (1.1 MB)
2026-02-07T05:59:05,665   Collecting wheel
2026-02-07T05:59:05,671     Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
2026-02-07T05:59:07,694   Collecting cython>=3.0.8
2026-02-07T05:59:08,514     Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB)
2026-02-07T05:59:09,941     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)
2026-02-07T05:59:09,948     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)
2026-02-07T05:59:09,955     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)
2026-02-07T05:59:09,962     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)
2026-02-07T05:59:09,970     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)
2026-02-07T05:59:10,825   Collecting numpy
2026-02-07T05:59:11,505     Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.1-cp311-cp311-linux_armv7l.whl (6.3 MB)
2026-02-07T05:59:11,882   Collecting packaging>=24.0
2026-02-07T05:59:11,888     Using cached packaging-26.0-py3-none-any.whl (74 kB)
2026-02-07T05:59:14,933   Installing collected packages: setuptools, packaging, numpy, cython, wheel
2026-02-07T05:59:27,264     Creating /tmp/pip-build-env-xx5xfe2r/overlay/local/bin
2026-02-07T05:59:27,266     changing mode of /tmp/pip-build-env-xx5xfe2r/overlay/local/bin/f2py to 755
2026-02-07T05:59:27,268     changing mode of /tmp/pip-build-env-xx5xfe2r/overlay/local/bin/numpy-config to 755
2026-02-07T05:59:31,076     changing mode of /tmp/pip-build-env-xx5xfe2r/overlay/local/bin/cygdb to 755
2026-02-07T05:59:31,078     changing mode of /tmp/pip-build-env-xx5xfe2r/overlay/local/bin/cython to 755
2026-02-07T05:59:31,080     changing mode of /tmp/pip-build-env-xx5xfe2r/overlay/local/bin/cythonize to 755
2026-02-07T05:59:31,206     changing mode of /tmp/pip-build-env-xx5xfe2r/overlay/local/bin/wheel to 755
2026-02-07T05:59:31,243   Successfully installed cython-3.2.4 numpy-2.4.1 packaging-26.0 setuptools-81.0.0 wheel-0.46.3
2026-02-07T05:59:31,716   Installing build dependencies: finished with status 'done'
2026-02-07T05:59:31,723   Getting requirements to build wheel: started
2026-02-07T05:59:31,724   Running command Getting requirements to build wheel
2026-02-07T05:59:35,918   warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier
2026-02-07T05:59:43,719   Compiling scbamtools/cython/kmers.pyx because it changed.
2026-02-07T05:59:43,719   Compiling scbamtools/cython/bctree.pyx because it changed.
2026-02-07T05:59:43,720   Compiling scbamtools/cython/fastquery.pyx because it changed.
2026-02-07T05:59:43,721   [1/3] Cythonizing scbamtools/cython/bctree.pyx
2026-02-07T05:59:43,721   [2/3] Cythonizing scbamtools/cython/fastquery.pyx
2026-02-07T05:59:43,722   [3/3] Cythonizing scbamtools/cython/kmers.pyx
2026-02-07T05:59:43,742   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-02-07T05:59:43,742   !!

2026-02-07T05:59:43,743           ********************************************************************************
2026-02-07T05:59:43,744           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-02-07T05:59:43,745           License :: OSI Approved :: MIT License

2026-02-07T05:59:43,746           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:43,746           ********************************************************************************

2026-02-07T05:59:43,747   !!
2026-02-07T05:59:43,748     self._finalize_license_expression()
2026-02-07T05:59:43,812   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2026-02-07T05:59:43,812   !!

2026-02-07T05:59:43,813           ********************************************************************************
2026-02-07T05:59:43,814           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).

2026-02-07T05:59:43,815           By 2027-Feb-18, you need to update your project and remove deprecated calls
2026-02-07T05:59:43,815           or your builds will no longer be supported.

2026-02-07T05:59:43,817           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:43,817           ********************************************************************************

2026-02-07T05:59:43,818   !!
2026-02-07T05:59:43,819     corresp(dist, value, root_dir)
2026-02-07T05:59:43,819   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2026-02-07T05:59:43,820     corresp(dist, value, root_dir)
2026-02-07T05:59:43,904   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-02-07T05:59:43,905   !!

2026-02-07T05:59:43,906           ********************************************************************************
2026-02-07T05:59:43,907           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-02-07T05:59:43,908           License :: OSI Approved :: MIT License

2026-02-07T05:59:43,909           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:43,909           ********************************************************************************

2026-02-07T05:59:43,911   !!
2026-02-07T05:59:43,911     dist._finalize_license_expression()
2026-02-07T05:59:43,921   running egg_info
2026-02-07T05:59:43,929   writing scbamtools.egg-info/PKG-INFO
2026-02-07T05:59:43,933   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2026-02-07T05:59:43,935   writing entry points to scbamtools.egg-info/entry_points.txt
2026-02-07T05:59:43,937   writing requirements to scbamtools.egg-info/requires.txt
2026-02-07T05:59:43,939   writing top-level names to scbamtools.egg-info/top_level.txt
2026-02-07T05:59:43,972   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,973   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,974   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,974   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,975   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,975   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,976   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,976   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,977   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,977   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,978   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,978   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,979   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,980   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,980   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:43,986   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2026-02-07T05:59:43,993   reading manifest template 'MANIFEST.in'
2026-02-07T05:59:43,997   adding license file 'LICENSE'
2026-02-07T05:59:44,001   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2026-02-07T05:59:44,836   Getting requirements to build wheel: finished with status 'done'
2026-02-07T05:59:44,840   Created temporary directory: /tmp/pip-modern-metadata-4rs_zbu5
2026-02-07T05:59:44,843   Preparing metadata (pyproject.toml): started
2026-02-07T05:59:44,844   Running command Preparing metadata (pyproject.toml)
2026-02-07T05:59:46,514   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2026-02-07T05:59:46,514   !!

2026-02-07T05:59:46,516           ********************************************************************************
2026-02-07T05:59:46,516           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).

2026-02-07T05:59:46,517           By 2027-Feb-18, you need to update your project and remove deprecated calls
2026-02-07T05:59:46,518           or your builds will no longer be supported.

2026-02-07T05:59:46,519           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:46,519           ********************************************************************************

2026-02-07T05:59:46,520   !!
2026-02-07T05:59:46,521     corresp(dist, value, root_dir)
2026-02-07T05:59:46,522   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2026-02-07T05:59:46,522     corresp(dist, value, root_dir)
2026-02-07T05:59:46,592   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-02-07T05:59:46,593   !!

2026-02-07T05:59:46,594           ********************************************************************************
2026-02-07T05:59:46,594           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-02-07T05:59:46,595           License :: OSI Approved :: MIT License

2026-02-07T05:59:46,597           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:46,597           ********************************************************************************

2026-02-07T05:59:46,598   !!
2026-02-07T05:59:46,599     dist._finalize_license_expression()
2026-02-07T05:59:46,600   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-02-07T05:59:46,600   !!

2026-02-07T05:59:46,601           ********************************************************************************
2026-02-07T05:59:46,602           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-02-07T05:59:46,603           License :: OSI Approved :: MIT License

2026-02-07T05:59:46,604           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:46,605           ********************************************************************************

2026-02-07T05:59:46,606   !!
2026-02-07T05:59:46,607     self._finalize_license_expression()
2026-02-07T05:59:46,607   running dist_info
2026-02-07T05:59:46,618   creating /tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info
2026-02-07T05:59:46,619   writing /tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/PKG-INFO
2026-02-07T05:59:46,624   writing dependency_links to /tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/dependency_links.txt
2026-02-07T05:59:46,626   writing entry points to /tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/entry_points.txt
2026-02-07T05:59:46,628   writing requirements to /tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/requires.txt
2026-02-07T05:59:46,629   writing top-level names to /tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/top_level.txt
2026-02-07T05:59:46,631   writing manifest file '/tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/SOURCES.txt'
2026-02-07T05:59:46,657   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,657   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,658   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,659   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,660   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,660   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,661   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,661   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,662   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,663   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,663   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,664   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,664   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,665   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,665   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:46,666   reading manifest file '/tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/SOURCES.txt'
2026-02-07T05:59:46,668   reading manifest template 'MANIFEST.in'
2026-02-07T05:59:46,672   adding license file 'LICENSE'
2026-02-07T05:59:46,675   writing manifest file '/tmp/pip-modern-metadata-4rs_zbu5/scbamtools.egg-info/SOURCES.txt'
2026-02-07T05:59:46,676   creating '/tmp/pip-modern-metadata-4rs_zbu5/scbamtools-0.8.6.dist-info'
2026-02-07T05:59:46,901   Preparing metadata (pyproject.toml): finished with status 'done'
2026-02-07T05:59:46,907   Source in /tmp/pip-wheel-opamyo08/scbamtools_d2c7ba897ca04ca283ad4417f73716e1 has version 0.8.6, which satisfies requirement scbamtools==0.8.6 from https://files.pythonhosted.org/packages/15/99/167036ec2645eb2793461a74cae353ea51708aa75af11e71db641e7fa0ac/scbamtools-0.8.6.tar.gz
2026-02-07T05:59:46,908   Removed scbamtools==0.8.6 from https://files.pythonhosted.org/packages/15/99/167036ec2645eb2793461a74cae353ea51708aa75af11e71db641e7fa0ac/scbamtools-0.8.6.tar.gz from build tracker '/tmp/pip-build-tracker-dmb0gnlh'
2026-02-07T05:59:46,913 Created temporary directory: /tmp/pip-unpack-vyh5jnx7
2026-02-07T05:59:46,914 Building wheels for collected packages: scbamtools
2026-02-07T05:59:46,919   Created temporary directory: /tmp/pip-wheel-xt_l2mgn
2026-02-07T05:59:46,919   Destination directory: /tmp/pip-wheel-xt_l2mgn
2026-02-07T05:59:46,921   Building wheel for scbamtools (pyproject.toml): started
2026-02-07T05:59:46,922   Running command Building wheel for scbamtools (pyproject.toml)
2026-02-07T05:59:48,510   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2026-02-07T05:59:48,510   !!

2026-02-07T05:59:48,511           ********************************************************************************
2026-02-07T05:59:48,512           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).

2026-02-07T05:59:48,513           By 2027-Feb-18, you need to update your project and remove deprecated calls
2026-02-07T05:59:48,513           or your builds will no longer be supported.

2026-02-07T05:59:48,514           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:48,514           ********************************************************************************

2026-02-07T05:59:48,515   !!
2026-02-07T05:59:48,516     corresp(dist, value, root_dir)
2026-02-07T05:59:48,516   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2026-02-07T05:59:48,517     corresp(dist, value, root_dir)
2026-02-07T05:59:48,581   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-02-07T05:59:48,582   !!

2026-02-07T05:59:48,583           ********************************************************************************
2026-02-07T05:59:48,583           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-02-07T05:59:48,584           License :: OSI Approved :: MIT License

2026-02-07T05:59:48,586           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:48,586           ********************************************************************************

2026-02-07T05:59:48,588   !!
2026-02-07T05:59:48,588     dist._finalize_license_expression()
2026-02-07T05:59:48,589   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-02-07T05:59:48,590   !!

2026-02-07T05:59:48,591           ********************************************************************************
2026-02-07T05:59:48,592           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-02-07T05:59:48,593           License :: OSI Approved :: MIT License

2026-02-07T05:59:48,594           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-02-07T05:59:48,594           ********************************************************************************

2026-02-07T05:59:48,596   !!
2026-02-07T05:59:48,596     self._finalize_license_expression()
2026-02-07T05:59:48,597   running bdist_wheel
2026-02-07T05:59:48,614   running build
2026-02-07T05:59:48,615   running build_py
2026-02-07T05:59:48,622   creating build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,625   copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,628   copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,631   copying scbamtools/pl.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,633   copying scbamtools/tk.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,635   copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,637   copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,639   copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,641   copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2026-02-07T05:59:48,645   creating build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,646   copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,648   copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,651   copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,653   copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,655   copying scbamtools/bin/pa_scanner.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,657   copying scbamtools/bin/cb_correct.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,660   copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2026-02-07T05:59:48,662   creating build/lib.linux-armv7l-cpython-311/scbamtools/config
2026-02-07T05:59:48,663   copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-311/scbamtools/config
2026-02-07T05:59:48,665   running egg_info
2026-02-07T05:59:48,677   writing scbamtools.egg-info/PKG-INFO
2026-02-07T05:59:48,680   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2026-02-07T05:59:48,681   writing entry points to scbamtools.egg-info/entry_points.txt
2026-02-07T05:59:48,683   writing requirements to scbamtools.egg-info/requires.txt
2026-02-07T05:59:48,684   writing top-level names to scbamtools.egg-info/top_level.txt
2026-02-07T05:59:48,692   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,692   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,693   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,693   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,694   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,695   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,695   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,696   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,696   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,697   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,698   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,698   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,699   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,699   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,700   dependency /tmp/pip-build-env-xx5xfe2r/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
2026-02-07T05:59:48,702   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2026-02-07T05:59:48,706   reading manifest template 'MANIFEST.in'
2026-02-07T05:59:48,709   adding license file 'LICENSE'
2026-02-07T05:59:48,714   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2026-02-07T05:59:48,716   /tmp/pip-build-env-xx5xfe2r/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'scbamtools.config.__pycache__' is absent from the `packages` configuration.
2026-02-07T05:59:48,717   !!

2026-02-07T05:59:48,719           ********************************************************************************
2026-02-07T05:59:48,720           ############################
2026-02-07T05:59:48,720           # Package would be ignored #
2026-02-07T05:59:48,721           ############################
2026-02-07T05:59:48,721           Python recognizes 'scbamtools.config.__pycache__' as an importable package[^1],
2026-02-07T05:59:48,722           but it is absent from setuptools' `packages` configuration.

2026-02-07T05:59:48,723           This leads to an ambiguous overall configuration. If you want to distribute this
2026-02-07T05:59:48,724           package, please make sure that 'scbamtools.config.__pycache__' is explicitly added
2026-02-07T05:59:48,724           to the `packages` configuration field.

2026-02-07T05:59:48,726           Alternatively, you can also rely on setuptools' discovery methods
2026-02-07T05:59:48,726           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-02-07T05:59:48,727           instead of `find_packages(...)`/`find:`).

2026-02-07T05:59:48,729           You can read more about "package discovery" on setuptools documentation page:

2026-02-07T05:59:48,744           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-02-07T05:59:48,749           If you don't want 'scbamtools.config.__pycache__' to be distributed and are
2026-02-07T05:59:48,750           already explicitly excluding 'scbamtools.config.__pycache__' via
2026-02-07T05:59:48,750           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-02-07T05:59:48,751           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-02-07T05:59:48,752           combination with a more fine grained `package-data` configuration.

2026-02-07T05:59:48,753           You can read more about "package data files" on setuptools documentation page:

2026-02-07T05:59:48,754           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-02-07T05:59:48,761           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-02-07T05:59:48,764                 even if it does not contain any `.py` files.
2026-02-07T05:59:48,766                 On the other hand, currently there is no concept of package data
2026-02-07T05:59:48,768                 directory, all directories are treated like packages.
2026-02-07T05:59:48,769           ********************************************************************************

2026-02-07T05:59:48,776   !!
2026-02-07T05:59:48,780     check.warn(importable)
2026-02-07T05:59:48,780   creating build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,784   copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,799   copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,802   copying scbamtools/cython/cigar.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,804   copying scbamtools/cython/fastquery.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,891   copying scbamtools/cython/fastquery.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,894   copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,915   copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,918   copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,920   copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-311/scbamtools/config
2026-02-07T05:59:48,922   creating build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2026-02-07T05:59:48,923   copying scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2026-02-07T05:59:48,925   copying scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2026-02-07T05:59:48,930   running build_ext
2026-02-07T05:59:48,937   building 'scbamtools.cython.kmers' extension
2026-02-07T05:59:48,938   creating build/temp.linux-armv7l-cpython-311/scbamtools/cython
2026-02-07T05:59:48,940   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-xx5xfe2r/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
2026-02-07T05:59:50,628   scbamtools/cython/kmers.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’:
2026-02-07T05:59:50,652   scbamtools/cython/kmers.c:27485:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2026-02-07T05:59:50,653   27485 |     if ((intval & PyLong_MASK) == intval) {
2026-02-07T05:59:50,653         |                                ^~
2026-02-07T05:59:50,676   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]
2026-02-07T05:59:50,677   27487 |         long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1));
2026-02-07T05:59:50,677         |                                                       ^~~~~~~~~~
2026-02-07T06:00:09,876   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
2026-02-07T06:00:10,015   building 'scbamtools.cython.bctree' extension
2026-02-07T06:00:10,015   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-xx5xfe2r/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
2026-02-07T06:00:10,787   scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’:
2026-02-07T06:00:10,805   scbamtools/cython/bctree.c:21046:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2026-02-07T06:00:10,806   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]) ))));
2026-02-07T06:00:10,807         |                  ^
2026-02-07T06:00:11,754   scbamtools/cython/bctree.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’:
2026-02-07T06:00:11,778   scbamtools/cython/bctree.c:27497:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2026-02-07T06:00:11,779   27497 |     if ((intval & PyLong_MASK) == intval) {
2026-02-07T06:00:11,779         |                                ^~
2026-02-07T06:00:11,802   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]
2026-02-07T06:00:11,803   27499 |         long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1));
2026-02-07T06:00:11,803         |                                                       ^~~~~~~~~~
2026-02-07T06:00:31,045   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
2026-02-07T06:00:31,197   building 'scbamtools.cython.fastquery' extension
2026-02-07T06:00:31,197   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-xx5xfe2r/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
2026-02-07T06:00:31,960   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_10query’:
2026-02-07T06:00:31,979   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]
2026-02-07T06:00:31,980   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)
2026-02-07T06:00:31,981         |                                                                                        ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:32,000   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 *’}
2026-02-07T06:00:32,001   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) {
2026-02-07T06:00:32,001         |                                                                                             ~~~~~~~~~~^~~~~~~~~~~~~
2026-02-07T06:00:32,017   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_12query_idx64’:
2026-02-07T06:00:32,036   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]
2026-02-07T06:00:32,037   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)
2026-02-07T06:00:32,038         |                                                                                        ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:32,057   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 *’}
2026-02-07T06:00:32,057   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) {
2026-02-07T06:00:32,058         |                                                                                             ~~~~~~~~~~^~~~~~~~~~~~~
2026-02-07T06:00:32,077   scbamtools/cython/fastquery.c: In function ‘__pyx_f_10scbamtools_6cython_9fastquery_make_variants_off_by_one’:
2026-02-07T06:00:32,097   scbamtools/cython/fastquery.c:24094:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2026-02-07T06:00:32,098   24094 |   for (__pyx_t_3 = __pyx_v_start; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
2026-02-07T06:00:32,099         |                                             ^
2026-02-07T06:00:32,114   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one’:
2026-02-07T06:00:32,135   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]
2026-02-07T06:00:32,136   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)
2026-02-07T06:00:32,137         |                                                                                           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:32,156   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 *’}
2026-02-07T06:00:32,157   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) {
2026-02-07T06:00:32,157         |                                                                                             ~~~~~~~~~~^~~~~~~~~~~~~
2026-02-07T06:00:32,178   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]
2026-02-07T06:00:32,179   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)
2026-02-07T06:00:32,180         |                                                                                          ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:32,199   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 *’}
2026-02-07T06:00:32,200   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) {
2026-02-07T06:00:32,201         |                                                                                             ~~~~~~~~~~^~~~~~~~~~~~~
2026-02-07T06:00:32,222   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_18query_idx64_variants_single’:
2026-02-07T06:00:32,244   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]
2026-02-07T06:00:32,245   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)
2026-02-07T06:00:32,245         |                                                                                       ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:32,265   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 *’}
2026-02-07T06:00:32,265   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) {
2026-02-07T06:00:32,266         |                                                                                             ~~~~~~~~~~^~~~~~~~~~~~~
2026-02-07T06:00:32,291   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_20query_idx64_variants’:
2026-02-07T06:00:32,313   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]
2026-02-07T06:00:32,314   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)
2026-02-07T06:00:32,315         |                                                                                          ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:32,334   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 *’}
2026-02-07T06:00:32,335   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) {
2026-02-07T06:00:32,335         |                                                                                             ~~~~~~~~~~^~~~~~~~~~~~~
2026-02-07T06:00:32,352   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp’:
2026-02-07T06:00:32,375   scbamtools/cython/fastquery.c:27171:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2026-02-07T06:00:32,376   27171 |   for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
2026-02-07T06:00:32,377         |                                 ^
2026-02-07T06:00:32,406   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]
2026-02-07T06:00:32,406   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)
2026-02-07T06:00:32,407         |                                                                                                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:32,426   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 *’}
2026-02-07T06:00:32,427   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) {
2026-02-07T06:00:32,427         |                                                                                             ~~~~~~~~~~^~~~~~~~~~~~~
2026-02-07T06:00:32,453   scbamtools/cython/fastquery.c:27663:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2026-02-07T06:00:32,454   27663 |   for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
2026-02-07T06:00:32,454         |                                 ^
2026-02-07T06:00:35,975   scbamtools/cython/fastquery.c: At top level:
2026-02-07T06:00:35,997   scbamtools/cython/fastquery.c:23205:18: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_make_shifts’ defined but not used [-Wunused-function]
2026-02-07T06:00:35,997   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) {
2026-02-07T06:00:35,998         |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:36,017   scbamtools/cython/fastquery.c:21833:17: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_seq_to_uint32_slice’ defined but not used [-Wunused-function]
2026-02-07T06:00:36,018   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) {
2026-02-07T06:00:36,019         |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:44,821   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp.constprop’:
2026-02-07T06:00:44,848   scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_thread_id’ may be used uninitialized [-Wmaybe-uninitialized]
2026-02-07T06:00:44,849   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)
2026-02-07T06:00:44,850         |                     ^~~
2026-02-07T06:00:44,870   scbamtools/cython/fastquery.c:26953:7: note: ‘__pyx_v_thread_id’ was declared here
2026-02-07T06:00:44,871   26953 |   int __pyx_v_thread_id;
2026-02-07T06:00:44,871         |       ^~~~~~~~~~~~~~~~~
2026-02-07T06:00:44,893   scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_idx_variants’ may be used uninitialized [-Wmaybe-uninitialized]
2026-02-07T06:00:44,894   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)
2026-02-07T06:00:44,895         |                     ^~~
2026-02-07T06:00:44,919   scbamtools/cython/fastquery.c:26951:13: note: ‘__pyx_v_idx_variants’ was declared here
2026-02-07T06:00:44,919   26951 |   uint64_t *__pyx_v_idx_variants;
2026-02-07T06:00:44,920         |             ^~~~~~~~~~~~~~~~~~~~
2026-02-07T06:00:53,792   scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one.constprop’:
2026-02-07T06:00:53,815   scbamtools/cython/fastquery.c:24725:12: warning: ‘__pyx_v_idx_s’ may be used uninitialized [-Wmaybe-uninitialized]
2026-02-07T06:00:53,815   24725 |         if (__pyx_t_10) {
2026-02-07T06:00:53,816         |            ^
2026-02-07T06:00:53,838   scbamtools/cython/fastquery.c:24339:12: note: ‘__pyx_v_idx_s’ was declared here
2026-02-07T06:00:53,838   24339 |   uint32_t __pyx_v_idx_s;
2026-02-07T06:00:53,839         |            ^~~~~~~~~~~~~
2026-02-07T06:00:57,997   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
2026-02-07T06:00:58,174   installing to build/bdist.linux-armv7l/wheel
2026-02-07T06:00:58,175   running install
2026-02-07T06:00:58,198   running install_lib
2026-02-07T06:00:58,205   creating build/bdist.linux-armv7l/wheel
2026-02-07T06:00:58,207   creating build/bdist.linux-armv7l/wheel/scbamtools
2026-02-07T06:00:58,209   copying build/lib.linux-armv7l-cpython-311/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,213   copying build/lib.linux-armv7l-cpython-311/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,216   creating build/bdist.linux-armv7l/wheel/scbamtools/bin
2026-02-07T06:00:58,218   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2026-02-07T06:00:58,221   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2026-02-07T06:00:58,223   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2026-02-07T06:00:58,226   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2026-02-07T06:00:58,229   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/pa_scanner.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2026-02-07T06:00:58,231   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/cb_correct.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2026-02-07T06:00:58,234   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2026-02-07T06:00:58,236   copying build/lib.linux-armv7l-cpython-311/scbamtools/pl.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,240   creating build/bdist.linux-armv7l/wheel/scbamtools/config
2026-02-07T06:00:58,242   creating build/bdist.linux-armv7l/wheel/scbamtools/config/__pycache__
2026-02-07T06:00:58,243   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__
2026-02-07T06:00:58,246   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__
2026-02-07T06:00:58,248   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/./scbamtools/config
2026-02-07T06:00:58,251   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/./scbamtools/config
2026-02-07T06:00:58,253   copying build/lib.linux-armv7l-cpython-311/scbamtools/tk.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,256   creating build/bdist.linux-armv7l/wheel/scbamtools/cython
2026-02-07T06:00:58,257   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,286   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,288   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,290   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,322   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,352   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,368   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,371   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,373   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,397   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,421   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/cigar.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2026-02-07T06:00:58,423   copying build/lib.linux-armv7l-cpython-311/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,425   copying build/lib.linux-armv7l-cpython-311/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,427   copying build/lib.linux-armv7l-cpython-311/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,430   copying build/lib.linux-armv7l-cpython-311/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2026-02-07T06:00:58,432   running install_egg_info
2026-02-07T06:00:58,439   Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/./scbamtools-0.8.6-py3.11.egg-info
2026-02-07T06:00:58,453   running install_scripts
2026-02-07T06:00:58,500   creating build/bdist.linux-armv7l/wheel/scbamtools-0.8.6.dist-info/WHEEL
2026-02-07T06:00:58,503   creating '/tmp/pip-wheel-xt_l2mgn/.tmp-ydbr7hn5/scbamtools-0.8.6-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-02-07T06:00:58,508   adding 'scbamtools/annotation.py'
2026-02-07T06:00:58,510   adding 'scbamtools/bctree.py'
2026-02-07T06:00:58,512   adding 'scbamtools/contrib.py'
2026-02-07T06:00:58,515   adding 'scbamtools/gene_model.py'
2026-02-07T06:00:58,517   adding 'scbamtools/pl.py'
2026-02-07T06:00:58,521   adding 'scbamtools/quant.py'
2026-02-07T06:00:58,523   adding 'scbamtools/tk.py'
2026-02-07T06:00:58,524   adding 'scbamtools/util.py'
2026-02-07T06:00:58,527   adding 'scbamtools/bin/BamTagHistogram.py'
2026-02-07T06:00:58,529   adding 'scbamtools/bin/ann.py'
2026-02-07T06:00:58,532   adding 'scbamtools/bin/cb_correct.py'
2026-02-07T06:00:58,534   adding 'scbamtools/bin/count.py'
2026-02-07T06:00:58,535   adding 'scbamtools/bin/pa_scanner.py'
2026-02-07T06:00:58,537   adding 'scbamtools/bin/trim.py'
2026-02-07T06:00:58,540   adding 'scbamtools/bin/uBAM.py'
2026-02-07T06:00:58,542   adding 'scbamtools/config/__init__.py'
2026-02-07T06:00:58,543   adding 'scbamtools/config/default.yaml'
2026-02-07T06:00:58,545   adding 'scbamtools/config/__pycache__/__init__.cpython-310.pyc'
2026-02-07T06:00:58,547   adding 'scbamtools/config/__pycache__/__init__.cpython-311.pyc'
2026-02-07T06:00:58,651   adding 'scbamtools/cython/bctree.c'
2026-02-07T06:00:58,878   adding 'scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so'
2026-02-07T06:00:58,886   adding 'scbamtools/cython/bctree.pyx'
2026-02-07T06:00:58,887   adding 'scbamtools/cython/cigar.pyx'
2026-02-07T06:00:59,013   adding 'scbamtools/cython/fastquery.c'
2026-02-07T06:00:59,279   adding 'scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so'
2026-02-07T06:00:59,290   adding 'scbamtools/cython/fastquery.pyx'
2026-02-07T06:00:59,394   adding 'scbamtools/cython/kmers.c'
2026-02-07T06:00:59,620   adding 'scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so'
2026-02-07T06:00:59,628   adding 'scbamtools/cython/kmers.pyx'
2026-02-07T06:00:59,629   adding 'scbamtools/cython/types.pxd'
2026-02-07T06:00:59,632   adding 'scbamtools-0.8.6.dist-info/licenses/LICENSE'
2026-02-07T06:00:59,633   adding 'scbamtools-0.8.6.dist-info/METADATA'
2026-02-07T06:00:59,634   adding 'scbamtools-0.8.6.dist-info/WHEEL'
2026-02-07T06:00:59,635   adding 'scbamtools-0.8.6.dist-info/entry_points.txt'
2026-02-07T06:00:59,636   adding 'scbamtools-0.8.6.dist-info/top_level.txt'
2026-02-07T06:00:59,637   adding 'scbamtools-0.8.6.dist-info/RECORD'
2026-02-07T06:00:59,658   removing build/bdist.linux-armv7l/wheel
2026-02-07T06:00:59,855   Building wheel for scbamtools (pyproject.toml): finished with status 'done'
2026-02-07T06:00:59,904   Created wheel for scbamtools: filename=scbamtools-0.8.6-cp311-cp311-linux_armv7l.whl size=1992174 sha256=e06d1f685481047d82616faced558ab95931ad4825326ad183cd4e3215948b53
2026-02-07T06:00:59,905   Stored in directory: /tmp/pip-ephem-wheel-cache-9fu8radg/wheels/1c/98/a7/e6919f4aef9dc5df572b26c266df43b1fd793b11b36169a660
2026-02-07T06:00:59,917 Successfully built scbamtools
2026-02-07T06:00:59,973 Removed build tracker: '/tmp/pip-build-tracker-dmb0gnlh'