2026-01-13T15:11:18,615 Created temporary directory: /tmp/pip-ephem-wheel-cache-h8061gzv 2026-01-13T15:11:18,617 Created temporary directory: /tmp/pip-build-tracker-yh6ke4bl 2026-01-13T15:11:18,618 Initialized build tracking at /tmp/pip-build-tracker-yh6ke4bl 2026-01-13T15:11:18,618 Created build tracker: /tmp/pip-build-tracker-yh6ke4bl 2026-01-13T15:11:18,618 Entered build tracker: /tmp/pip-build-tracker-yh6ke4bl 2026-01-13T15:11:18,619 Created temporary directory: /tmp/pip-wheel-77sm9_ns 2026-01-13T15:11:18,622 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 2026-01-13T15:11:18,625 Created temporary directory: /tmp/pip-ephem-wheel-cache-m9dojhlq 2026-01-13T15:11:18,646 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-13T15:11:18,650 2 location(s) to search for versions of scbamtools: 2026-01-13T15:11:18,650 * https://pypi.org/simple/scbamtools/ 2026-01-13T15:11:18,650 * https://www.piwheels.org/simple/scbamtools/ 2026-01-13T15:11:18,650 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/ 2026-01-13T15:11:18,651 Getting page https://pypi.org/simple/scbamtools/ 2026-01-13T15:11:18,653 Found index url https://pypi.org/simple 2026-01-13T15:11:18,872 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json 2026-01-13T15:11:18,875 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 2026-01-13T15:11:18,876 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 2026-01-13T15:11:18,877 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 2026-01-13T15:11:18,878 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 2026-01-13T15:11:18,879 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 2026-01-13T15:11:18,880 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 2026-01-13T15:11:18,881 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 2026-01-13T15:11:18,882 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 2026-01-13T15:11:18,883 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/ 2026-01-13T15:11:18,884 Getting page https://www.piwheels.org/simple/scbamtools/ 2026-01-13T15:11:18,885 Found index url https://www.piwheels.org/simple 2026-01-13T15:11:19,046 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html 2026-01-13T15:11:19,054 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) 2026-01-13T15:11:19,055 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) 2026-01-13T15:11:19,056 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) 2026-01-13T15:11:19,057 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) 2026-01-13T15:11:19,057 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) 2026-01-13T15:11:19,058 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) 2026-01-13T15:11:19,059 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) 2026-01-13T15:11:19,059 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) 2026-01-13T15:11:19,060 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) 2026-01-13T15:11:19,061 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) 2026-01-13T15:11:19,061 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) 2026-01-13T15:11:19,062 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) 2026-01-13T15:11:19,063 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) 2026-01-13T15:11:19,063 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) 2026-01-13T15:11:19,064 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) 2026-01-13T15:11:19,065 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) 2026-01-13T15:11:19,065 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) 2026-01-13T15:11:19,066 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) 2026-01-13T15:11:19,066 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) 2026-01-13T15:11:19,067 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) 2026-01-13T15:11:19,068 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) 2026-01-13T15:11:19,068 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) 2026-01-13T15:11:19,069 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) 2026-01-13T15:11:19,070 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) 2026-01-13T15:11:19,070 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) 2026-01-13T15:11:19,071 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) 2026-01-13T15:11:19,072 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/ 2026-01-13T15:11:19,073 Skipping link: not a file: https://pypi.org/simple/scbamtools/ 2026-01-13T15:11:19,101 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates 2026-01-13T15:11:19,128 Collecting scbamtools==0.8.5 2026-01-13T15:11:19,131 Created temporary directory: /tmp/pip-unpack-nd7617ac 2026-01-13T15:11:19,277 Downloading scbamtools-0.8.5.tar.gz (618 kB) 2026-01-13T15:11:19,692 Added scbamtools==0.8.5 from https://files.pythonhosted.org/packages/f7/c0/d98768b070c431f1c02c5d08bd1e9b5bf59e6b8e0513ef157ff6aa604673/scbamtools-0.8.5.tar.gz to build tracker '/tmp/pip-build-tracker-yh6ke4bl' 2026-01-13T15:11:19,699 Created temporary directory: /tmp/pip-build-env-vrswjdzz 2026-01-13T15:11:19,704 Installing build dependencies: started 2026-01-13T15:11:19,705 Running command pip subprocess to install build dependencies 2026-01-13T15:11:20,838 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-01-13T15:11:21,492 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 2026-01-13T15:11:21,516 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-13T15:11:23,222 Collecting setuptools>=65.5.1 2026-01-13T15:11:23,310 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2026-01-13T15:11:23,573 Collecting wheel 2026-01-13T15:11:23,589 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2026-01-13T15:11:25,600 Collecting cython>=3.0.8 2026-01-13T15:11:26,530 Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-01-13T15:11:27,924 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) 2026-01-13T15:11:27,931 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) 2026-01-13T15:11:27,938 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) 2026-01-13T15:11:27,945 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) 2026-01-13T15:11:27,951 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) 2026-01-13T15:11:28,788 Collecting numpy 2026-01-13T15:11:29,258 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.1-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-01-13T15:11:32,544 Installing collected packages: wheel, setuptools, numpy, cython 2026-01-13T15:11:32,793 Creating /tmp/pip-build-env-vrswjdzz/overlay/local/bin 2026-01-13T15:11:32,795 changing mode of /tmp/pip-build-env-vrswjdzz/overlay/local/bin/wheel to 755 2026-01-13T15:11:45,212 changing mode of /tmp/pip-build-env-vrswjdzz/overlay/local/bin/f2py to 755 2026-01-13T15:11:45,214 changing mode of /tmp/pip-build-env-vrswjdzz/overlay/local/bin/numpy-config to 755 2026-01-13T15:11:48,923 changing mode of /tmp/pip-build-env-vrswjdzz/overlay/local/bin/cygdb to 755 2026-01-13T15:11:48,925 changing mode of /tmp/pip-build-env-vrswjdzz/overlay/local/bin/cython to 755 2026-01-13T15:11:48,927 changing mode of /tmp/pip-build-env-vrswjdzz/overlay/local/bin/cythonize to 755 2026-01-13T15:11:48,962 Successfully installed cython-3.2.4 numpy-2.4.1 setuptools-80.9.0 wheel-0.45.1 2026-01-13T15:11:49,424 Installing build dependencies: finished with status 'done' 2026-01-13T15:11:49,430 Getting requirements to build wheel: started 2026-01-13T15:11:49,432 Running command Getting requirements to build wheel 2026-01-13T15:11:53,759 warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier 2026-01-13T15:12:01,539 Compiling scbamtools/cython/kmers.pyx because it changed. 2026-01-13T15:12:01,540 Compiling scbamtools/cython/bctree.pyx because it changed. 2026-01-13T15:12:01,541 Compiling scbamtools/cython/fastquery.pyx because it changed. 2026-01-13T15:12:01,541 [1/3] Cythonizing scbamtools/cython/bctree.pyx 2026-01-13T15:12:01,542 [2/3] Cythonizing scbamtools/cython/fastquery.pyx 2026-01-13T15:12:01,542 [3/3] Cythonizing scbamtools/cython/kmers.pyx 2026-01-13T15:12:01,564 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T15:12:01,564 !! 2026-01-13T15:12:01,565 ******************************************************************************** 2026-01-13T15:12:01,566 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T15:12:01,567 License :: OSI Approved :: MIT License 2026-01-13T15:12:01,568 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:01,569 ******************************************************************************** 2026-01-13T15:12:01,570 !! 2026-01-13T15:12:01,570 self._finalize_license_expression() 2026-01-13T15:12:01,626 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-01-13T15:12:01,626 !! 2026-01-13T15:12:01,628 ******************************************************************************** 2026-01-13T15:12:01,628 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). 2026-01-13T15:12:01,629 By 2026-Feb-18, you need to update your project and remove deprecated calls 2026-01-13T15:12:01,630 or your builds will no longer be supported. 2026-01-13T15:12:01,631 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:01,632 ******************************************************************************** 2026-01-13T15:12:01,633 !! 2026-01-13T15:12:01,633 corresp(dist, value, root_dir) 2026-01-13T15:12:01,634 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-13T15:12:01,634 corresp(dist, value, root_dir) 2026-01-13T15:12:01,710 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T15:12:01,711 !! 2026-01-13T15:12:01,712 ******************************************************************************** 2026-01-13T15:12:01,713 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T15:12:01,714 License :: OSI Approved :: MIT License 2026-01-13T15:12:01,715 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:01,715 ******************************************************************************** 2026-01-13T15:12:01,716 !! 2026-01-13T15:12:01,716 dist._finalize_license_expression() 2026-01-13T15:12:01,720 running egg_info 2026-01-13T15:12:01,728 writing scbamtools.egg-info/PKG-INFO 2026-01-13T15:12:01,731 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2026-01-13T15:12:01,733 writing entry points to scbamtools.egg-info/entry_points.txt 2026-01-13T15:12:01,735 writing requirements to scbamtools.egg-info/requires.txt 2026-01-13T15:12:01,736 writing top-level names to scbamtools.egg-info/top_level.txt 2026-01-13T15:12:01,766 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,767 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,767 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,768 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,768 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,769 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,769 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,770 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,771 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,771 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,772 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,772 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,773 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,773 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,774 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:01,777 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-01-13T15:12:01,784 reading manifest template 'MANIFEST.in' 2026-01-13T15:12:01,787 adding license file 'LICENSE' 2026-01-13T15:12:01,791 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-01-13T15:12:02,635 Getting requirements to build wheel: finished with status 'done' 2026-01-13T15:12:02,639 Created temporary directory: /tmp/pip-modern-metadata-ruffee1g 2026-01-13T15:12:02,641 Preparing metadata (pyproject.toml): started 2026-01-13T15:12:02,642 Running command Preparing metadata (pyproject.toml) 2026-01-13T15:12:04,366 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-01-13T15:12:04,366 !! 2026-01-13T15:12:04,367 ******************************************************************************** 2026-01-13T15:12:04,368 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). 2026-01-13T15:12:04,369 By 2026-Feb-18, you need to update your project and remove deprecated calls 2026-01-13T15:12:04,369 or your builds will no longer be supported. 2026-01-13T15:12:04,370 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:04,371 ******************************************************************************** 2026-01-13T15:12:04,372 !! 2026-01-13T15:12:04,372 corresp(dist, value, root_dir) 2026-01-13T15:12:04,373 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-13T15:12:04,374 corresp(dist, value, root_dir) 2026-01-13T15:12:04,444 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T15:12:04,445 !! 2026-01-13T15:12:04,446 ******************************************************************************** 2026-01-13T15:12:04,447 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T15:12:04,448 License :: OSI Approved :: MIT License 2026-01-13T15:12:04,450 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:04,450 ******************************************************************************** 2026-01-13T15:12:04,452 !! 2026-01-13T15:12:04,452 dist._finalize_license_expression() 2026-01-13T15:12:04,453 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T15:12:04,454 !! 2026-01-13T15:12:04,455 ******************************************************************************** 2026-01-13T15:12:04,455 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T15:12:04,456 License :: OSI Approved :: MIT License 2026-01-13T15:12:04,458 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:04,458 ******************************************************************************** 2026-01-13T15:12:04,460 !! 2026-01-13T15:12:04,460 self._finalize_license_expression() 2026-01-13T15:12:04,461 running dist_info 2026-01-13T15:12:04,473 creating /tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info 2026-01-13T15:12:04,474 writing /tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/PKG-INFO 2026-01-13T15:12:04,478 writing dependency_links to /tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/dependency_links.txt 2026-01-13T15:12:04,480 writing entry points to /tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/entry_points.txt 2026-01-13T15:12:04,481 writing requirements to /tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/requires.txt 2026-01-13T15:12:04,482 writing top-level names to /tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/top_level.txt 2026-01-13T15:12:04,483 writing manifest file '/tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/SOURCES.txt' 2026-01-13T15:12:04,510 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,510 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,511 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,511 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,512 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,512 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,512 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,513 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,514 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,514 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,515 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,515 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,516 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,516 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,517 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:04,520 reading manifest file '/tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/SOURCES.txt' 2026-01-13T15:12:04,523 reading manifest template 'MANIFEST.in' 2026-01-13T15:12:04,525 adding license file 'LICENSE' 2026-01-13T15:12:04,529 writing manifest file '/tmp/pip-modern-metadata-ruffee1g/scbamtools.egg-info/SOURCES.txt' 2026-01-13T15:12:04,530 creating '/tmp/pip-modern-metadata-ruffee1g/scbamtools-0.8.5.dist-info' 2026-01-13T15:12:04,743 Preparing metadata (pyproject.toml): finished with status 'done' 2026-01-13T15:12:04,747 Source in /tmp/pip-wheel-77sm9_ns/scbamtools_6de4f8c1fc474d34a4f1eee25edd492e has version 0.8.5, which satisfies requirement scbamtools==0.8.5 from https://files.pythonhosted.org/packages/f7/c0/d98768b070c431f1c02c5d08bd1e9b5bf59e6b8e0513ef157ff6aa604673/scbamtools-0.8.5.tar.gz 2026-01-13T15:12:04,748 Removed scbamtools==0.8.5 from https://files.pythonhosted.org/packages/f7/c0/d98768b070c431f1c02c5d08bd1e9b5bf59e6b8e0513ef157ff6aa604673/scbamtools-0.8.5.tar.gz from build tracker '/tmp/pip-build-tracker-yh6ke4bl' 2026-01-13T15:12:04,753 Created temporary directory: /tmp/pip-unpack-nu6kvn94 2026-01-13T15:12:04,754 Building wheels for collected packages: scbamtools 2026-01-13T15:12:04,758 Created temporary directory: /tmp/pip-wheel-dphcdebv 2026-01-13T15:12:04,759 Destination directory: /tmp/pip-wheel-dphcdebv 2026-01-13T15:12:04,761 Building wheel for scbamtools (pyproject.toml): started 2026-01-13T15:12:04,763 Running command Building wheel for scbamtools (pyproject.toml) 2026-01-13T15:12:06,431 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-01-13T15:12:06,431 !! 2026-01-13T15:12:06,432 ******************************************************************************** 2026-01-13T15:12:06,432 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). 2026-01-13T15:12:06,433 By 2026-Feb-18, you need to update your project and remove deprecated calls 2026-01-13T15:12:06,434 or your builds will no longer be supported. 2026-01-13T15:12:06,435 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:06,436 ******************************************************************************** 2026-01-13T15:12:06,436 !! 2026-01-13T15:12:06,437 corresp(dist, value, root_dir) 2026-01-13T15:12:06,438 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-01-13T15:12:06,438 corresp(dist, value, root_dir) 2026-01-13T15:12:06,502 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T15:12:06,503 !! 2026-01-13T15:12:06,504 ******************************************************************************** 2026-01-13T15:12:06,505 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T15:12:06,506 License :: OSI Approved :: MIT License 2026-01-13T15:12:06,507 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:06,507 ******************************************************************************** 2026-01-13T15:12:06,509 !! 2026-01-13T15:12:06,509 dist._finalize_license_expression() 2026-01-13T15:12:06,510 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T15:12:06,511 !! 2026-01-13T15:12:06,512 ******************************************************************************** 2026-01-13T15:12:06,512 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T15:12:06,513 License :: OSI Approved :: MIT License 2026-01-13T15:12:06,514 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T15:12:06,515 ******************************************************************************** 2026-01-13T15:12:06,515 !! 2026-01-13T15:12:06,516 self._finalize_license_expression() 2026-01-13T15:12:06,516 running bdist_wheel 2026-01-13T15:12:06,536 running build 2026-01-13T15:12:06,537 running build_py 2026-01-13T15:12:06,545 creating build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,547 copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,549 copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,551 copying scbamtools/pl.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,553 copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,555 copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,558 copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,561 copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-01-13T15:12:06,564 creating build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,565 copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,568 copying scbamtools/bin/pa_scanner.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,570 copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,572 copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,574 copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,577 copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,579 copying scbamtools/bin/cb_correct.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-01-13T15:12:06,582 creating build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-01-13T15:12:06,583 copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-01-13T15:12:06,585 running egg_info 2026-01-13T15:12:06,598 writing scbamtools.egg-info/PKG-INFO 2026-01-13T15:12:06,601 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2026-01-13T15:12:06,602 writing entry points to scbamtools.egg-info/entry_points.txt 2026-01-13T15:12:06,604 writing requirements to scbamtools.egg-info/requires.txt 2026-01-13T15:12:06,605 writing top-level names to scbamtools.egg-info/top_level.txt 2026-01-13T15:12:06,613 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,613 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,614 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,614 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,615 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,615 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,617 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,617 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,618 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,618 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,618 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,619 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,619 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,620 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,621 dependency /tmp/pip-build-env-vrswjdzz/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 2026-01-13T15:12:06,624 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-01-13T15:12:06,628 reading manifest template 'MANIFEST.in' 2026-01-13T15:12:06,631 adding license file 'LICENSE' 2026-01-13T15:12:06,635 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-01-13T15:12:06,638 /tmp/pip-build-env-vrswjdzz/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'scbamtools.config.__pycache__' is absent from the `packages` configuration. 2026-01-13T15:12:06,638 !! 2026-01-13T15:12:06,640 ******************************************************************************** 2026-01-13T15:12:06,640 ############################ 2026-01-13T15:12:06,641 # Package would be ignored # 2026-01-13T15:12:06,641 ############################ 2026-01-13T15:12:06,642 Python recognizes 'scbamtools.config.__pycache__' as an importable package[^1], 2026-01-13T15:12:06,642 but it is absent from setuptools' `packages` configuration. 2026-01-13T15:12:06,643 This leads to an ambiguous overall configuration. If you want to distribute this 2026-01-13T15:12:06,644 package, please make sure that 'scbamtools.config.__pycache__' is explicitly added 2026-01-13T15:12:06,644 to the `packages` configuration field. 2026-01-13T15:12:06,645 Alternatively, you can also rely on setuptools' discovery methods 2026-01-13T15:12:06,646 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-01-13T15:12:06,646 instead of `find_packages(...)`/`find:`). 2026-01-13T15:12:06,648 You can read more about "package discovery" on setuptools documentation page: 2026-01-13T15:12:06,649 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-01-13T15:12:06,651 If you don't want 'scbamtools.config.__pycache__' to be distributed and are 2026-01-13T15:12:06,651 already explicitly excluding 'scbamtools.config.__pycache__' via 2026-01-13T15:12:06,652 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-01-13T15:12:06,652 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-01-13T15:12:06,652 combination with a more fine grained `package-data` configuration. 2026-01-13T15:12:06,653 You can read more about "package data files" on setuptools documentation page: 2026-01-13T15:12:06,654 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-01-13T15:12:06,656 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-01-13T15:12:06,656 even if it does not contain any `.py` files. 2026-01-13T15:12:06,657 On the other hand, currently there is no concept of package data 2026-01-13T15:12:06,658 directory, all directories are treated like packages. 2026-01-13T15:12:06,658 ******************************************************************************** 2026-01-13T15:12:06,659 !! 2026-01-13T15:12:06,660 check.warn(importable) 2026-01-13T15:12:06,661 creating build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,661 copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,679 copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,682 copying scbamtools/cython/cigar.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,684 copying scbamtools/cython/fastquery.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,728 copying scbamtools/cython/fastquery.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,731 copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,758 copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,761 copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,763 copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-01-13T15:12:06,765 creating build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-01-13T15:12:06,767 copying scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-01-13T15:12:06,770 copying scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-01-13T15:12:06,774 running build_ext 2026-01-13T15:12:06,781 building 'scbamtools.cython.kmers' extension 2026-01-13T15:12:06,783 creating build/temp.linux-armv7l-cpython-311/scbamtools/cython 2026-01-13T15:12:06,785 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-vrswjdzz/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 2026-01-13T15:12:08,471 scbamtools/cython/kmers.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’: 2026-01-13T15:12:08,495 scbamtools/cython/kmers.c:27485:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2026-01-13T15:12:08,496 27485 | if ((intval & PyLong_MASK) == intval) { 2026-01-13T15:12:08,497 | ^~ 2026-01-13T15:12:08,519 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] 2026-01-13T15:12:08,520 27487 | long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1)); 2026-01-13T15:12:08,521 | ^~~~~~~~~~ 2026-01-13T15:12:27,740 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 2026-01-13T15:12:27,883 building 'scbamtools.cython.bctree' extension 2026-01-13T15:12:27,884 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-vrswjdzz/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 2026-01-13T15:12:28,615 scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’: 2026-01-13T15:12:28,633 scbamtools/cython/bctree.c:21046:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-01-13T15:12:28,633 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]) )))); 2026-01-13T15:12:28,634 | ^ 2026-01-13T15:12:29,585 scbamtools/cython/bctree.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’: 2026-01-13T15:12:29,610 scbamtools/cython/bctree.c:27497:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2026-01-13T15:12:29,611 27497 | if ((intval & PyLong_MASK) == intval) { 2026-01-13T15:12:29,612 | ^~ 2026-01-13T15:12:29,636 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] 2026-01-13T15:12:29,636 27499 | long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1)); 2026-01-13T15:12:29,637 | ^~~~~~~~~~ 2026-01-13T15:12:49,037 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 2026-01-13T15:12:49,172 building 'scbamtools.cython.fastquery' extension 2026-01-13T15:12:49,172 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-vrswjdzz/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 2026-01-13T15:12:49,937 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_10query’: 2026-01-13T15:12:49,957 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] 2026-01-13T15:12:49,958 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) 2026-01-13T15:12:49,958 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:49,979 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 *’} 2026-01-13T15:12:49,980 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) { 2026-01-13T15:12:49,980 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-01-13T15:12:49,996 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_12query_idx64’: 2026-01-13T15:12:50,016 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] 2026-01-13T15:12:50,017 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) 2026-01-13T15:12:50,018 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:50,039 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 *’} 2026-01-13T15:12:50,040 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) { 2026-01-13T15:12:50,040 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-01-13T15:12:50,061 scbamtools/cython/fastquery.c: In function ‘__pyx_f_10scbamtools_6cython_9fastquery_make_variants_off_by_one’: 2026-01-13T15:12:50,082 scbamtools/cython/fastquery.c:24094:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-01-13T15:12:50,083 24094 | for (__pyx_t_3 = __pyx_v_start; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2026-01-13T15:12:50,084 | ^ 2026-01-13T15:12:50,101 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one’: 2026-01-13T15:12:50,122 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] 2026-01-13T15:12:50,123 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) 2026-01-13T15:12:50,124 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:50,144 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 *’} 2026-01-13T15:12:50,144 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) { 2026-01-13T15:12:50,145 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-01-13T15:12:50,168 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] 2026-01-13T15:12:50,169 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) 2026-01-13T15:12:50,169 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:50,189 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 *’} 2026-01-13T15:12:50,189 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) { 2026-01-13T15:12:50,190 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-01-13T15:12:50,212 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_18query_idx64_variants_single’: 2026-01-13T15:12:50,235 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] 2026-01-13T15:12:50,235 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) 2026-01-13T15:12:50,236 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:50,256 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 *’} 2026-01-13T15:12:50,256 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) { 2026-01-13T15:12:50,257 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-01-13T15:12:50,282 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_20query_idx64_variants’: 2026-01-13T15:12:50,306 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] 2026-01-13T15:12:50,306 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) 2026-01-13T15:12:50,307 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:50,327 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 *’} 2026-01-13T15:12:50,328 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) { 2026-01-13T15:12:50,329 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-01-13T15:12:50,345 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp’: 2026-01-13T15:12:50,369 scbamtools/cython/fastquery.c:27171:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-01-13T15:12:50,370 27171 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2026-01-13T15:12:50,371 | ^ 2026-01-13T15:12:50,400 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] 2026-01-13T15:12:50,401 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) 2026-01-13T15:12:50,401 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:50,421 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 *’} 2026-01-13T15:12:50,422 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) { 2026-01-13T15:12:50,423 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-01-13T15:12:50,449 scbamtools/cython/fastquery.c:27663:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-01-13T15:12:50,450 27663 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2026-01-13T15:12:50,450 | ^ 2026-01-13T15:12:53,983 scbamtools/cython/fastquery.c: At top level: 2026-01-13T15:12:54,006 scbamtools/cython/fastquery.c:23205:18: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_make_shifts’ defined but not used [-Wunused-function] 2026-01-13T15:12:54,007 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) { 2026-01-13T15:12:54,007 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:12:54,028 scbamtools/cython/fastquery.c:21833:17: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_seq_to_uint32_slice’ defined but not used [-Wunused-function] 2026-01-13T15:12:54,028 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) { 2026-01-13T15:12:54,029 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:13:02,835 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp.constprop’: 2026-01-13T15:13:02,859 scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_thread_id’ may be used uninitialized [-Wmaybe-uninitialized] 2026-01-13T15:13:02,860 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) 2026-01-13T15:13:02,860 | ^~~ 2026-01-13T15:13:02,886 scbamtools/cython/fastquery.c:26953:7: note: ‘__pyx_v_thread_id’ was declared here 2026-01-13T15:13:02,886 26953 | int __pyx_v_thread_id; 2026-01-13T15:13:02,887 | ^~~~~~~~~~~~~~~~~ 2026-01-13T15:13:02,910 scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_idx_variants’ may be used uninitialized [-Wmaybe-uninitialized] 2026-01-13T15:13:02,911 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) 2026-01-13T15:13:02,911 | ^~~ 2026-01-13T15:13:02,936 scbamtools/cython/fastquery.c:26951:13: note: ‘__pyx_v_idx_variants’ was declared here 2026-01-13T15:13:02,937 26951 | uint64_t *__pyx_v_idx_variants; 2026-01-13T15:13:02,938 | ^~~~~~~~~~~~~~~~~~~~ 2026-01-13T15:13:11,823 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one.constprop’: 2026-01-13T15:13:11,848 scbamtools/cython/fastquery.c:24725:12: warning: ‘__pyx_v_idx_s’ may be used uninitialized [-Wmaybe-uninitialized] 2026-01-13T15:13:11,848 24725 | if (__pyx_t_10) { 2026-01-13T15:13:11,849 | ^ 2026-01-13T15:13:11,872 scbamtools/cython/fastquery.c:24339:12: note: ‘__pyx_v_idx_s’ was declared here 2026-01-13T15:13:11,873 24339 | uint32_t __pyx_v_idx_s; 2026-01-13T15:13:11,874 | ^~~~~~~~~~~~~ 2026-01-13T15:13:16,025 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 2026-01-13T15:13:16,201 installing to build/bdist.linux-armv7l/wheel 2026-01-13T15:13:16,202 running install 2026-01-13T15:13:16,225 running install_lib 2026-01-13T15:13:16,232 creating build/bdist.linux-armv7l/wheel 2026-01-13T15:13:16,234 creating build/bdist.linux-armv7l/wheel/scbamtools 2026-01-13T15:13:16,236 copying build/lib.linux-armv7l-cpython-311/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-01-13T15:13:16,238 creating build/bdist.linux-armv7l/wheel/scbamtools/config 2026-01-13T15:13:16,239 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/./scbamtools/config 2026-01-13T15:13:16,241 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/./scbamtools/config 2026-01-13T15:13:16,244 creating build/bdist.linux-armv7l/wheel/scbamtools/config/__pycache__ 2026-01-13T15:13:16,245 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__ 2026-01-13T15:13:16,247 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__ 2026-01-13T15:13:16,249 creating build/bdist.linux-armv7l/wheel/scbamtools/bin 2026-01-13T15:13:16,251 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-01-13T15:13:16,254 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/pa_scanner.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-01-13T15:13:16,256 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-01-13T15:13:16,258 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-01-13T15:13:16,260 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-01-13T15:13:16,262 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-01-13T15:13:16,265 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/cb_correct.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-01-13T15:13:16,267 copying build/lib.linux-armv7l-cpython-311/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-01-13T15:13:16,269 copying build/lib.linux-armv7l-cpython-311/scbamtools/pl.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-01-13T15:13:16,271 copying build/lib.linux-armv7l-cpython-311/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-01-13T15:13:16,274 copying build/lib.linux-armv7l-cpython-311/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-01-13T15:13:16,276 copying build/lib.linux-armv7l-cpython-311/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-01-13T15:13:16,280 creating build/bdist.linux-armv7l/wheel/scbamtools/cython 2026-01-13T15:13:16,281 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,299 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,302 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,324 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,344 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,347 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/cigar.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,348 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,351 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,371 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,372 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,398 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-01-13T15:13:16,413 copying build/lib.linux-armv7l-cpython-311/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-01-13T15:13:16,415 running install_egg_info 2026-01-13T15:13:16,422 Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/./scbamtools-0.8.5-py3.11.egg-info 2026-01-13T15:13:16,435 running install_scripts 2026-01-13T15:13:16,487 creating build/bdist.linux-armv7l/wheel/scbamtools-0.8.5.dist-info/WHEEL 2026-01-13T15:13:16,491 creating '/tmp/pip-wheel-dphcdebv/.tmp-fh_bi8sc/scbamtools-0.8.5-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-01-13T15:13:16,496 adding 'scbamtools/annotation.py' 2026-01-13T15:13:16,498 adding 'scbamtools/bctree.py' 2026-01-13T15:13:16,499 adding 'scbamtools/contrib.py' 2026-01-13T15:13:16,502 adding 'scbamtools/gene_model.py' 2026-01-13T15:13:16,504 adding 'scbamtools/pl.py' 2026-01-13T15:13:16,507 adding 'scbamtools/quant.py' 2026-01-13T15:13:16,509 adding 'scbamtools/util.py' 2026-01-13T15:13:16,511 adding 'scbamtools/bin/BamTagHistogram.py' 2026-01-13T15:13:16,513 adding 'scbamtools/bin/ann.py' 2026-01-13T15:13:16,515 adding 'scbamtools/bin/cb_correct.py' 2026-01-13T15:13:16,518 adding 'scbamtools/bin/count.py' 2026-01-13T15:13:16,519 adding 'scbamtools/bin/pa_scanner.py' 2026-01-13T15:13:16,520 adding 'scbamtools/bin/trim.py' 2026-01-13T15:13:16,522 adding 'scbamtools/bin/uBAM.py' 2026-01-13T15:13:16,524 adding 'scbamtools/config/__init__.py' 2026-01-13T15:13:16,525 adding 'scbamtools/config/default.yaml' 2026-01-13T15:13:16,527 adding 'scbamtools/config/__pycache__/__init__.cpython-310.pyc' 2026-01-13T15:13:16,529 adding 'scbamtools/config/__pycache__/__init__.cpython-311.pyc' 2026-01-13T15:13:16,633 adding 'scbamtools/cython/bctree.c' 2026-01-13T15:13:16,859 adding 'scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so' 2026-01-13T15:13:16,866 adding 'scbamtools/cython/bctree.pyx' 2026-01-13T15:13:16,868 adding 'scbamtools/cython/cigar.pyx' 2026-01-13T15:13:16,993 adding 'scbamtools/cython/fastquery.c' 2026-01-13T15:13:17,257 adding 'scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so' 2026-01-13T15:13:17,268 adding 'scbamtools/cython/fastquery.pyx' 2026-01-13T15:13:17,371 adding 'scbamtools/cython/kmers.c' 2026-01-13T15:13:17,596 adding 'scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so' 2026-01-13T15:13:17,604 adding 'scbamtools/cython/kmers.pyx' 2026-01-13T15:13:17,606 adding 'scbamtools/cython/types.pxd' 2026-01-13T15:13:17,609 adding 'scbamtools-0.8.5.dist-info/licenses/LICENSE' 2026-01-13T15:13:17,610 adding 'scbamtools-0.8.5.dist-info/METADATA' 2026-01-13T15:13:17,611 adding 'scbamtools-0.8.5.dist-info/WHEEL' 2026-01-13T15:13:17,612 adding 'scbamtools-0.8.5.dist-info/entry_points.txt' 2026-01-13T15:13:17,614 adding 'scbamtools-0.8.5.dist-info/top_level.txt' 2026-01-13T15:13:17,615 adding 'scbamtools-0.8.5.dist-info/RECORD' 2026-01-13T15:13:17,860 removing build/bdist.linux-armv7l/wheel 2026-01-13T15:13:18,057 Building wheel for scbamtools (pyproject.toml): finished with status 'done' 2026-01-13T15:13:18,103 Created wheel for scbamtools: filename=scbamtools-0.8.5-cp311-cp311-linux_armv7l.whl size=1990830 sha256=7fbc4b6e883667481fe381c8b7a08074a1cd79eacf7fafc9a0ccbab4777bcfb6 2026-01-13T15:13:18,104 Stored in directory: /tmp/pip-ephem-wheel-cache-m9dojhlq/wheels/a3/21/a9/2f83c3a5910710c6c900567ce83014212de9c2e9396dde026d 2026-01-13T15:13:18,116 Successfully built scbamtools 2026-01-13T15:13:18,257 Removed build tracker: '/tmp/pip-build-tracker-yh6ke4bl'