2025-10-15T11:04:52,485 Created temporary directory: /tmp/pip-ephem-wheel-cache-cmkvdblm
2025-10-15T11:04:52,487 Created temporary directory: /tmp/pip-build-tracker-1nrtcyh2
2025-10-15T11:04:52,488 Initialized build tracking at /tmp/pip-build-tracker-1nrtcyh2
2025-10-15T11:04:52,488 Created build tracker: /tmp/pip-build-tracker-1nrtcyh2
2025-10-15T11:04:52,489 Entered build tracker: /tmp/pip-build-tracker-1nrtcyh2
2025-10-15T11:04:52,489 Created temporary directory: /tmp/pip-wheel-luyxwhla
2025-10-15T11:04:52,493 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
2025-10-15T11:04:52,495 Created temporary directory: /tmp/pip-ephem-wheel-cache-vka8e4lq
2025-10-15T11:04:52,519 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T11:04:52,523 2 location(s) to search for versions of scbamtools:
2025-10-15T11:04:52,523 * https://pypi.org/simple/scbamtools/
2025-10-15T11:04:52,523 * https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:04:52,524 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/
2025-10-15T11:04:52,524 Getting page https://pypi.org/simple/scbamtools/
2025-10-15T11:04:52,526 Found index url https://pypi.org/simple
2025-10-15T11:04:52,795 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json
2025-10-15T11:04:52,798   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
2025-10-15T11:04:52,799   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
2025-10-15T11:04:52,800   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
2025-10-15T11:04:52,801   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
2025-10-15T11:04:52,802   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
2025-10-15T11:04:52,803   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
2025-10-15T11:04:52,804   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
2025-10-15T11:04:52,804 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:04:52,805 Getting page https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:04:52,806 Found index url https://www.piwheels.org/simple
2025-10-15T11:04:52,974 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html
2025-10-15T11:04:52,980   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:04:52,981   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:04:52,982   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:04:52,982   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:04:52,983   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)
2025-10-15T11:04:52,983   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)
2025-10-15T11:04:52,984   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)
2025-10-15T11:04:52,984   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)
2025-10-15T11:04:52,985   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)
2025-10-15T11:04:52,985   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)
2025-10-15T11:04:52,986   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)
2025-10-15T11:04:52,987   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)
2025-10-15T11:04:52,987   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)
2025-10-15T11:04:52,988   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)
2025-10-15T11:04:52,989   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)
2025-10-15T11:04:52,989   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)
2025-10-15T11:04:52,990   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:04:52,990   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:04:52,991 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:04:52,991 Skipping link: not a file: https://pypi.org/simple/scbamtools/
2025-10-15T11:04:53,011 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates
2025-10-15T11:04:53,029 Collecting scbamtools==0.8.2
2025-10-15T11:04:53,031   Created temporary directory: /tmp/pip-unpack-vfnx9q_b
2025-10-15T11:04:53,243   Downloading scbamtools-0.8.2.tar.gz (392 kB)
2025-10-15T11:04:53,530   Added scbamtools==0.8.2 from https://files.pythonhosted.org/packages/f4/e3/382060f419dfa54214c760869e2272bf621f794cfabc13183ce0430f8539/scbamtools-0.8.2.tar.gz to build tracker '/tmp/pip-build-tracker-1nrtcyh2'
2025-10-15T11:04:53,537   Created temporary directory: /tmp/pip-build-env-g92uxo35
2025-10-15T11:04:53,542   Installing build dependencies: started
2025-10-15T11:04:53,543   Running command pip subprocess to install build dependencies
2025-10-15T11:04:54,689   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2025-10-15T11:04:55,281   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
2025-10-15T11:04:55,305   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T11:04:57,399   Collecting setuptools>=65.5.1
2025-10-15T11:04:57,485     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2025-10-15T11:04:57,753   Collecting wheel
2025-10-15T11:04:57,773     Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB)
2025-10-15T11:04:59,581   Collecting cython>=3.0.8
2025-10-15T11:04:59,604     Using cached cython-3.1.4-py3-none-any.whl (1.2 MB)
2025-10-15T11:05:00,638     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)
2025-10-15T11:05:00,646     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)
2025-10-15T11:05:00,653     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)
2025-10-15T11:05:00,659     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)
2025-10-15T11:05:00,666     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)
2025-10-15T11:05:01,259   Collecting numpy
2025-10-15T11:05:01,688     Using cached https://www.piwheels.org/simple/numpy/numpy-2.3.3-cp311-cp311-linux_armv7l.whl (6.1 MB)
2025-10-15T11:05:04,857   Installing collected packages: wheel, setuptools, numpy, cython
2025-10-15T11:05:05,099     Creating /tmp/pip-build-env-g92uxo35/overlay/local/bin
2025-10-15T11:05:05,101     changing mode of /tmp/pip-build-env-g92uxo35/overlay/local/bin/wheel to 755
2025-10-15T11:05:17,682     changing mode of /tmp/pip-build-env-g92uxo35/overlay/local/bin/f2py to 755
2025-10-15T11:05:17,684     changing mode of /tmp/pip-build-env-g92uxo35/overlay/local/bin/numpy-config to 755
2025-10-15T11:05:20,686     changing mode of /tmp/pip-build-env-g92uxo35/overlay/local/bin/cygdb to 755
2025-10-15T11:05:20,688     changing mode of /tmp/pip-build-env-g92uxo35/overlay/local/bin/cython to 755
2025-10-15T11:05:20,690     changing mode of /tmp/pip-build-env-g92uxo35/overlay/local/bin/cythonize to 755
2025-10-15T11:05:20,725   Successfully installed cython-3.1.4 numpy-2.3.3 setuptools-80.9.0 wheel-0.45.1
2025-10-15T11:05:21,164   Installing build dependencies: finished with status 'done'
2025-10-15T11:05:21,170   Getting requirements to build wheel: started
2025-10-15T11:05:21,171   Running command Getting requirements to build wheel
2025-10-15T11:05:26,312   warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier
2025-10-15T11:05:33,429   Compiling scbamtools/cython/kmers.pyx because it changed.
2025-10-15T11:05:33,430   Compiling scbamtools/cython/bctree.pyx because it changed.
2025-10-15T11:05:33,430   [1/2] Cythonizing scbamtools/cython/bctree.pyx
2025-10-15T11:05:33,431   [2/2] Cythonizing scbamtools/cython/kmers.pyx
2025-10-15T11:05:33,456   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:05:33,457   !!

2025-10-15T11:05:33,458           ********************************************************************************
2025-10-15T11:05:33,459           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:05:33,460           License :: OSI Approved :: MIT License

2025-10-15T11:05:33,461           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:33,462           ********************************************************************************

2025-10-15T11:05:33,463   !!
2025-10-15T11:05:33,464     self._finalize_license_expression()
2025-10-15T11:05:33,524   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-10-15T11:05:33,525   !!

2025-10-15T11:05:33,527           ********************************************************************************
2025-10-15T11:05:33,527           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).

2025-10-15T11:05:33,528           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-10-15T11:05:33,529           or your builds will no longer be supported.

2025-10-15T11:05:33,530           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:33,531           ********************************************************************************

2025-10-15T11:05:33,531   !!
2025-10-15T11:05:33,532     corresp(dist, value, root_dir)
2025-10-15T11:05:33,532   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2025-10-15T11:05:33,533     corresp(dist, value, root_dir)
2025-10-15T11:05:33,614   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:05:33,615   !!

2025-10-15T11:05:33,616           ********************************************************************************
2025-10-15T11:05:33,616           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:05:33,617           License :: OSI Approved :: MIT License

2025-10-15T11:05:33,618           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:33,619           ********************************************************************************

2025-10-15T11:05:33,620   !!
2025-10-15T11:05:33,620     dist._finalize_license_expression()
2025-10-15T11:05:33,628   running egg_info
2025-10-15T11:05:33,641   writing scbamtools.egg-info/PKG-INFO
2025-10-15T11:05:33,644   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2025-10-15T11:05:33,647   writing entry points to scbamtools.egg-info/entry_points.txt
2025-10-15T11:05:33,649   writing requirements to scbamtools.egg-info/requires.txt
2025-10-15T11:05:33,650   writing top-level names to scbamtools.egg-info/top_level.txt
2025-10-15T11:05:33,681   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,682   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,683   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,683   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,684   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,685   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,685   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,686   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,686   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,687   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:33,693   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:05:33,700   reading manifest template 'MANIFEST.in'
2025-10-15T11:05:33,704   adding license file 'LICENSE'
2025-10-15T11:05:33,708   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:05:34,407   Getting requirements to build wheel: finished with status 'done'
2025-10-15T11:05:34,411   Created temporary directory: /tmp/pip-modern-metadata-ewhwwb_w
2025-10-15T11:05:34,413   Preparing metadata (pyproject.toml): started
2025-10-15T11:05:34,414   Running command Preparing metadata (pyproject.toml)
2025-10-15T11:05:35,945   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-10-15T11:05:35,945   !!

2025-10-15T11:05:35,946           ********************************************************************************
2025-10-15T11:05:35,947           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).

2025-10-15T11:05:35,948           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-10-15T11:05:35,948           or your builds will no longer be supported.

2025-10-15T11:05:35,949           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:35,950           ********************************************************************************

2025-10-15T11:05:35,951   !!
2025-10-15T11:05:35,952     corresp(dist, value, root_dir)
2025-10-15T11:05:35,952   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2025-10-15T11:05:35,953     corresp(dist, value, root_dir)
2025-10-15T11:05:36,028   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:05:36,028   !!

2025-10-15T11:05:36,030           ********************************************************************************
2025-10-15T11:05:36,030           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:05:36,032           License :: OSI Approved :: MIT License

2025-10-15T11:05:36,033           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:36,034           ********************************************************************************

2025-10-15T11:05:36,035   !!
2025-10-15T11:05:36,036     dist._finalize_license_expression()
2025-10-15T11:05:36,036   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:05:36,037   !!

2025-10-15T11:05:36,038           ********************************************************************************
2025-10-15T11:05:36,039           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:05:36,040           License :: OSI Approved :: MIT License

2025-10-15T11:05:36,041           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:36,042           ********************************************************************************

2025-10-15T11:05:36,044   !!
2025-10-15T11:05:36,044     self._finalize_license_expression()
2025-10-15T11:05:36,045   running dist_info
2025-10-15T11:05:36,057   creating /tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info
2025-10-15T11:05:36,058   writing /tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/PKG-INFO
2025-10-15T11:05:36,062   writing dependency_links to /tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/dependency_links.txt
2025-10-15T11:05:36,064   writing entry points to /tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/entry_points.txt
2025-10-15T11:05:36,066   writing requirements to /tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/requires.txt
2025-10-15T11:05:36,067   writing top-level names to /tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/top_level.txt
2025-10-15T11:05:36,069   writing manifest file '/tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:05:36,099   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,100   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,100   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,101   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,101   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,102   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,103   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,103   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,104   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,105   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:36,108   reading manifest file '/tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:05:36,110   reading manifest template 'MANIFEST.in'
2025-10-15T11:05:36,113   adding license file 'LICENSE'
2025-10-15T11:05:36,117   writing manifest file '/tmp/pip-modern-metadata-ewhwwb_w/scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:05:36,118   creating '/tmp/pip-modern-metadata-ewhwwb_w/scbamtools-0.8.2.dist-info'
2025-10-15T11:05:36,328   Preparing metadata (pyproject.toml): finished with status 'done'
2025-10-15T11:05:36,333   Source in /tmp/pip-wheel-luyxwhla/scbamtools_8d0eb35a196a4986b93098273b1fe7cf has version 0.8.2, which satisfies requirement scbamtools==0.8.2 from https://files.pythonhosted.org/packages/f4/e3/382060f419dfa54214c760869e2272bf621f794cfabc13183ce0430f8539/scbamtools-0.8.2.tar.gz
2025-10-15T11:05:36,334   Removed scbamtools==0.8.2 from https://files.pythonhosted.org/packages/f4/e3/382060f419dfa54214c760869e2272bf621f794cfabc13183ce0430f8539/scbamtools-0.8.2.tar.gz from build tracker '/tmp/pip-build-tracker-1nrtcyh2'
2025-10-15T11:05:36,340 Created temporary directory: /tmp/pip-unpack-3dlg5xw9
2025-10-15T11:05:36,341 Building wheels for collected packages: scbamtools
2025-10-15T11:05:36,347   Created temporary directory: /tmp/pip-wheel-_uris1zx
2025-10-15T11:05:36,348   Destination directory: /tmp/pip-wheel-_uris1zx
2025-10-15T11:05:36,351   Building wheel for scbamtools (pyproject.toml): started
2025-10-15T11:05:36,352   Running command Building wheel for scbamtools (pyproject.toml)
2025-10-15T11:05:37,832   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-10-15T11:05:37,832   !!

2025-10-15T11:05:37,833           ********************************************************************************
2025-10-15T11:05:37,834           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).

2025-10-15T11:05:37,835           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-10-15T11:05:37,836           or your builds will no longer be supported.

2025-10-15T11:05:37,837           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:37,837           ********************************************************************************

2025-10-15T11:05:37,838   !!
2025-10-15T11:05:37,839     corresp(dist, value, root_dir)
2025-10-15T11:05:37,839   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2025-10-15T11:05:37,840     corresp(dist, value, root_dir)
2025-10-15T11:05:37,904   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:05:37,904   !!

2025-10-15T11:05:37,906           ********************************************************************************
2025-10-15T11:05:37,906           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:05:37,907           License :: OSI Approved :: MIT License

2025-10-15T11:05:37,909           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:37,909           ********************************************************************************

2025-10-15T11:05:37,911   !!
2025-10-15T11:05:37,911     dist._finalize_license_expression()
2025-10-15T11:05:37,912   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:05:37,912   !!

2025-10-15T11:05:37,914           ********************************************************************************
2025-10-15T11:05:37,914           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:05:37,915           License :: OSI Approved :: MIT License

2025-10-15T11:05:37,917           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:05:37,917           ********************************************************************************

2025-10-15T11:05:37,918   !!
2025-10-15T11:05:37,919     self._finalize_license_expression()
2025-10-15T11:05:37,920   running bdist_wheel
2025-10-15T11:05:37,937   running build
2025-10-15T11:05:37,938   running build_py
2025-10-15T11:05:37,945   creating build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:05:37,948   copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:05:37,951   copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:05:37,954   copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:05:37,956   copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:05:37,959   copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:05:37,961   copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:05:37,964   creating build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:05:37,965   copying scbamtools/bin/pa_scanner.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:05:37,967   copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:05:37,970   copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:05:37,972   copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:05:37,975   copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:05:37,977   copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:05:37,980   creating build/lib.linux-armv7l-cpython-311/scbamtools/config
2025-10-15T11:05:37,981   copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-311/scbamtools/config
2025-10-15T11:05:37,983   running egg_info
2025-10-15T11:05:37,999   writing scbamtools.egg-info/PKG-INFO
2025-10-15T11:05:38,002   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2025-10-15T11:05:38,004   writing entry points to scbamtools.egg-info/entry_points.txt
2025-10-15T11:05:38,005   writing requirements to scbamtools.egg-info/requires.txt
2025-10-15T11:05:38,006   writing top-level names to scbamtools.egg-info/top_level.txt
2025-10-15T11:05:38,014   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,015   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,015   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,016   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,016   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,017   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,018   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,018   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,019   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,020   dependency /tmp/pip-build-env-g92uxo35/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
2025-10-15T11:05:38,024   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:05:38,028   reading manifest template 'MANIFEST.in'
2025-10-15T11:05:38,031   adding license file 'LICENSE'
2025-10-15T11:05:38,035   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:05:38,038   /tmp/pip-build-env-g92uxo35/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'scbamtools.config.__pycache__' is absent from the `packages` configuration.
2025-10-15T11:05:38,038   !!

2025-10-15T11:05:38,039           ********************************************************************************
2025-10-15T11:05:38,040           ############################
2025-10-15T11:05:38,040           # Package would be ignored #
2025-10-15T11:05:38,041           ############################
2025-10-15T11:05:38,041           Python recognizes 'scbamtools.config.__pycache__' as an importable package[^1],
2025-10-15T11:05:38,042           but it is absent from setuptools' `packages` configuration.

2025-10-15T11:05:38,043           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-15T11:05:38,043           package, please make sure that 'scbamtools.config.__pycache__' is explicitly added
2025-10-15T11:05:38,044           to the `packages` configuration field.

2025-10-15T11:05:38,045           Alternatively, you can also rely on setuptools' discovery methods
2025-10-15T11:05:38,045           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-15T11:05:38,045           instead of `find_packages(...)`/`find:`).

2025-10-15T11:05:38,046           You can read more about "package discovery" on setuptools documentation page:

2025-10-15T11:05:38,047           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-15T11:05:38,048           If you don't want 'scbamtools.config.__pycache__' to be distributed and are
2025-10-15T11:05:38,049           already explicitly excluding 'scbamtools.config.__pycache__' via
2025-10-15T11:05:38,049           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-15T11:05:38,050           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-15T11:05:38,050           combination with a more fine grained `package-data` configuration.

2025-10-15T11:05:38,051           You can read more about "package data files" on setuptools documentation page:

2025-10-15T11:05:38,055           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-15T11:05:38,061           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-15T11:05:38,067                 even if it does not contain any `.py` files.
2025-10-15T11:05:38,068                 On the other hand, currently there is no concept of package data
2025-10-15T11:05:38,069                 directory, all directories are treated like packages.
2025-10-15T11:05:38,069           ********************************************************************************

2025-10-15T11:05:38,071   !!
2025-10-15T11:05:38,071     check.warn(importable)
2025-10-15T11:05:38,072   creating build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,073   copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,123   copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,126   copying scbamtools/cython/cigar.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,128   copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,181   copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,184   copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,186   copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-311/scbamtools/config
2025-10-15T11:05:38,188   creating build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2025-10-15T11:05:38,189   copying scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2025-10-15T11:05:38,192   copying scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2025-10-15T11:05:38,195   running build_ext
2025-10-15T11:05:38,202   building 'scbamtools.cython.kmers' extension
2025-10-15T11:05:38,203   creating build/temp.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:05:38,204   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-g92uxo35/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
2025-10-15T11:05:39,833   scbamtools/cython/kmers.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’:
2025-10-15T11:05:39,858   scbamtools/cython/kmers.c:27952:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2025-10-15T11:05:39,858   27952 |     if ((intval & PyLong_MASK) == intval) {
2025-10-15T11:05:39,859         |                                ^~
2025-10-15T11:05:39,883   scbamtools/cython/kmers.c:27954:67: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2025-10-15T11:05:39,884   27954 |         long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1));
2025-10-15T11:05:39,884         |                                                                   ^~~~~~~~~~
2025-10-15T11:05:59,289   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
2025-10-15T11:05:59,432   building 'scbamtools.cython.bctree' extension
2025-10-15T11:05:59,432   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-g92uxo35/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
2025-10-15T11:06:00,190   scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’:
2025-10-15T11:06:00,208   scbamtools/cython/bctree.c:21270:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2025-10-15T11:06:00,209   21270 |     __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]) ))));
2025-10-15T11:06:00,210         |                  ^
2025-10-15T11:06:01,096   scbamtools/cython/bctree.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’:
2025-10-15T11:06:01,120   scbamtools/cython/bctree.c:27964:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2025-10-15T11:06:01,121   27964 |     if ((intval & PyLong_MASK) == intval) {
2025-10-15T11:06:01,122         |                                ^~
2025-10-15T11:06:01,146   scbamtools/cython/bctree.c:27966:67: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare]
2025-10-15T11:06:01,147   27966 |         long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1));
2025-10-15T11:06:01,147         |                                                                   ^~~~~~~~~~
2025-10-15T11:06:20,631   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
2025-10-15T11:06:20,810   installing to build/bdist.linux-armv7l/wheel
2025-10-15T11:06:20,811   running install
2025-10-15T11:06:20,833   running install_lib
2025-10-15T11:06:20,840   creating build/bdist.linux-armv7l/wheel
2025-10-15T11:06:20,843   creating build/bdist.linux-armv7l/wheel/scbamtools
2025-10-15T11:06:20,844   copying build/lib.linux-armv7l-cpython-311/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:06:20,847   creating build/bdist.linux-armv7l/wheel/scbamtools/cython
2025-10-15T11:06:20,848   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,897   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/cigar.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,898   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,941   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,943   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,945   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,962   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,976   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:06:20,999   copying build/lib.linux-armv7l-cpython-311/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:06:21,001   copying build/lib.linux-armv7l-cpython-311/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:06:21,004   creating build/bdist.linux-armv7l/wheel/scbamtools/bin
2025-10-15T11:06:21,005   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/pa_scanner.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:06:21,007   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:06:21,010   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:06:21,012   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:06:21,015   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:06:21,017   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:06:21,020   creating build/bdist.linux-armv7l/wheel/scbamtools/config
2025-10-15T11:06:21,022   creating build/bdist.linux-armv7l/wheel/scbamtools/config/__pycache__
2025-10-15T11:06:21,023   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__
2025-10-15T11:06:21,025   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__
2025-10-15T11:06:21,027   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/./scbamtools/config
2025-10-15T11:06:21,029   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/./scbamtools/config
2025-10-15T11:06:21,031   copying build/lib.linux-armv7l-cpython-311/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:06:21,033   copying build/lib.linux-armv7l-cpython-311/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:06:21,036   copying build/lib.linux-armv7l-cpython-311/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:06:21,038   running install_egg_info
2025-10-15T11:06:21,045   Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/./scbamtools-0.8.2-py3.11.egg-info
2025-10-15T11:06:21,059   running install_scripts
2025-10-15T11:06:21,107   creating build/bdist.linux-armv7l/wheel/scbamtools-0.8.2.dist-info/WHEEL
2025-10-15T11:06:21,110   creating '/tmp/pip-wheel-_uris1zx/.tmp-diwqckpo/scbamtools-0.8.2-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-15T11:06:21,115   adding 'scbamtools/annotation.py'
2025-10-15T11:06:21,116   adding 'scbamtools/bctree.py'
2025-10-15T11:06:21,118   adding 'scbamtools/contrib.py'
2025-10-15T11:06:21,121   adding 'scbamtools/gene_model.py'
2025-10-15T11:06:21,125   adding 'scbamtools/quant.py'
2025-10-15T11:06:21,127   adding 'scbamtools/util.py'
2025-10-15T11:06:21,129   adding 'scbamtools/bin/BamTagHistogram.py'
2025-10-15T11:06:21,131   adding 'scbamtools/bin/ann.py'
2025-10-15T11:06:21,133   adding 'scbamtools/bin/count.py'
2025-10-15T11:06:21,134   adding 'scbamtools/bin/pa_scanner.py'
2025-10-15T11:06:21,136   adding 'scbamtools/bin/trim.py'
2025-10-15T11:06:21,138   adding 'scbamtools/bin/uBAM.py'
2025-10-15T11:06:21,140   adding 'scbamtools/config/__init__.py'
2025-10-15T11:06:21,141   adding 'scbamtools/config/default.yaml'
2025-10-15T11:06:21,143   adding 'scbamtools/config/__pycache__/__init__.cpython-310.pyc'
2025-10-15T11:06:21,145   adding 'scbamtools/config/__pycache__/__init__.cpython-311.pyc'
2025-10-15T11:06:21,255   adding 'scbamtools/cython/bctree.c'
2025-10-15T11:06:21,519   adding 'scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T11:06:21,527   adding 'scbamtools/cython/bctree.pyx'
2025-10-15T11:06:21,528   adding 'scbamtools/cython/cigar.pyx'
2025-10-15T11:06:21,630   adding 'scbamtools/cython/kmers.c'
2025-10-15T11:06:21,879   adding 'scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T11:06:21,887   adding 'scbamtools/cython/kmers.pyx'
2025-10-15T11:06:21,888   adding 'scbamtools/cython/types.pxd'
2025-10-15T11:06:21,891   adding 'scbamtools-0.8.2.dist-info/licenses/LICENSE'
2025-10-15T11:06:21,892   adding 'scbamtools-0.8.2.dist-info/METADATA'
2025-10-15T11:06:21,893   adding 'scbamtools-0.8.2.dist-info/WHEEL'
2025-10-15T11:06:21,894   adding 'scbamtools-0.8.2.dist-info/entry_points.txt'
2025-10-15T11:06:21,895   adding 'scbamtools-0.8.2.dist-info/top_level.txt'
2025-10-15T11:06:21,896   adding 'scbamtools-0.8.2.dist-info/RECORD'
2025-10-15T11:06:21,910   removing build/bdist.linux-armv7l/wheel
2025-10-15T11:06:22,117   Building wheel for scbamtools (pyproject.toml): finished with status 'done'
2025-10-15T11:06:22,156   Created wheel for scbamtools: filename=scbamtools-0.8.2-cp311-cp311-linux_armv7l.whl size=1262687 sha256=b4f10cfcbe618096f93e1c251428cff5983bd3752c3e358d36d2c27ce52df5ac
2025-10-15T11:06:22,157   Stored in directory: /tmp/pip-ephem-wheel-cache-vka8e4lq/wheels/09/c3/1f/880bcf5ff2685013dcef1fb8712762ccf5457a365d6c93ddb3
2025-10-15T11:06:22,178 Successfully built scbamtools
2025-10-15T11:06:22,231 Removed build tracker: '/tmp/pip-build-tracker-1nrtcyh2'