2025-10-15T11:27:15,884 Created temporary directory: /tmp/pip-ephem-wheel-cache-p8wd48lj
2025-10-15T11:27:15,886 Created temporary directory: /tmp/pip-build-tracker-dz40uqlk
2025-10-15T11:27:15,886 Initialized build tracking at /tmp/pip-build-tracker-dz40uqlk
2025-10-15T11:27:15,887 Created build tracker: /tmp/pip-build-tracker-dz40uqlk
2025-10-15T11:27:15,887 Entered build tracker: /tmp/pip-build-tracker-dz40uqlk
2025-10-15T11:27:15,888 Created temporary directory: /tmp/pip-wheel-981ebcpw
2025-10-15T11:27:15,891 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
2025-10-15T11:27:15,893 Created temporary directory: /tmp/pip-ephem-wheel-cache-lejhg_9q
2025-10-15T11:27:15,918 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T11:27:15,922 2 location(s) to search for versions of scbamtools:
2025-10-15T11:27:15,922 * https://pypi.org/simple/scbamtools/
2025-10-15T11:27:15,922 * https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:27:15,922 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/
2025-10-15T11:27:15,923 Getting page https://pypi.org/simple/scbamtools/
2025-10-15T11:27:15,925 Found index url https://pypi.org/simple
2025-10-15T11:27:16,134 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json
2025-10-15T11:27:16,137   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
2025-10-15T11:27:16,138   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
2025-10-15T11:27:16,139   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
2025-10-15T11:27:16,140   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
2025-10-15T11:27:16,141   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
2025-10-15T11:27:16,142   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
2025-10-15T11:27:16,143   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
2025-10-15T11:27:16,144 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:27:16,145 Getting page https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:27:16,146 Found index url https://www.piwheels.org/simple
2025-10-15T11:27:16,337 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html
2025-10-15T11:27:16,344   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)
2025-10-15T11:27:16,345   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)
2025-10-15T11:27:16,345   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)
2025-10-15T11:27:16,346   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)
2025-10-15T11:27:16,346   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:27:16,347   Skipping link: No binaries permitted for scbamtools: https://www.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)
2025-10-15T11:27:16,347   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)
2025-10-15T11:27:16,348   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)
2025-10-15T11:27:16,348   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)
2025-10-15T11:27:16,349   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)
2025-10-15T11:27:16,350   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)
2025-10-15T11:27:16,350   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)
2025-10-15T11:27:16,351   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)
2025-10-15T11:27:16,352   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)
2025-10-15T11:27:16,352   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)
2025-10-15T11:27:16,353   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)
2025-10-15T11:27:16,354   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)
2025-10-15T11:27:16,354   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)
2025-10-15T11:27:16,354   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)
2025-10-15T11:27:16,355   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)
2025-10-15T11:27:16,356 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/
2025-10-15T11:27:16,356 Skipping link: not a file: https://pypi.org/simple/scbamtools/
2025-10-15T11:27:16,375 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates
2025-10-15T11:27:16,393 Collecting scbamtools==0.8.3
2025-10-15T11:27:16,396   Created temporary directory: /tmp/pip-unpack-ciyctdn9
2025-10-15T11:27:16,604   Downloading scbamtools-0.8.3.tar.gz (393 kB)
2025-10-15T11:27:16,867   Added scbamtools==0.8.3 from https://files.pythonhosted.org/packages/58/a8/a17afb0e466cf567d8c13497d0f025c286b28da8ade10f7bb4697652cdec/scbamtools-0.8.3.tar.gz to build tracker '/tmp/pip-build-tracker-dz40uqlk'
2025-10-15T11:27:16,874   Created temporary directory: /tmp/pip-build-env-y40ddyt_
2025-10-15T11:27:16,878   Installing build dependencies: started
2025-10-15T11:27:16,879   Running command pip subprocess to install build dependencies
2025-10-15T11:27:18,027   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2025-10-15T11:27:18,649   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
2025-10-15T11:27:18,678   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T11:27:20,405   Collecting setuptools>=65.5.1
2025-10-15T11:27:20,505     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2025-10-15T11:27:20,788   Collecting wheel
2025-10-15T11:27:20,805     Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB)
2025-10-15T11:27:22,610   Collecting cython>=3.0.8
2025-10-15T11:27:22,632     Using cached cython-3.1.4-py3-none-any.whl (1.2 MB)
2025-10-15T11:27:23,640     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)
2025-10-15T11:27:23,648     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)
2025-10-15T11:27:23,654     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)
2025-10-15T11:27:23,661     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)
2025-10-15T11:27:23,668     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)
2025-10-15T11:27:24,259   Collecting numpy
2025-10-15T11:27:25,059     Using cached https://www.piwheels.org/simple/numpy/numpy-2.3.3-cp311-cp311-linux_armv7l.whl (6.1 MB)
2025-10-15T11:27:28,284   Installing collected packages: wheel, setuptools, numpy, cython
2025-10-15T11:27:28,531     Creating /tmp/pip-build-env-y40ddyt_/overlay/local/bin
2025-10-15T11:27:28,533     changing mode of /tmp/pip-build-env-y40ddyt_/overlay/local/bin/wheel to 755
2025-10-15T11:27:41,195     changing mode of /tmp/pip-build-env-y40ddyt_/overlay/local/bin/f2py to 755
2025-10-15T11:27:41,197     changing mode of /tmp/pip-build-env-y40ddyt_/overlay/local/bin/numpy-config to 755
2025-10-15T11:27:44,129     changing mode of /tmp/pip-build-env-y40ddyt_/overlay/local/bin/cygdb to 755
2025-10-15T11:27:44,131     changing mode of /tmp/pip-build-env-y40ddyt_/overlay/local/bin/cython to 755
2025-10-15T11:27:44,133     changing mode of /tmp/pip-build-env-y40ddyt_/overlay/local/bin/cythonize to 755
2025-10-15T11:27:44,170   Successfully installed cython-3.1.4 numpy-2.3.3 setuptools-80.9.0 wheel-0.45.1
2025-10-15T11:27:44,605   Installing build dependencies: finished with status 'done'
2025-10-15T11:27:44,611   Getting requirements to build wheel: started
2025-10-15T11:27:44,613   Running command Getting requirements to build wheel
2025-10-15T11:27:49,739   warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier
2025-10-15T11:27:56,913   Compiling scbamtools/cython/kmers.pyx because it changed.
2025-10-15T11:27:56,914   Compiling scbamtools/cython/bctree.pyx because it changed.
2025-10-15T11:27:56,914   [1/2] Cythonizing scbamtools/cython/bctree.pyx
2025-10-15T11:27:56,915   [2/2] Cythonizing scbamtools/cython/kmers.pyx
2025-10-15T11:27:56,937   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:27:56,938   !!

2025-10-15T11:27:56,939           ********************************************************************************
2025-10-15T11:27:56,939           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:27:56,940           License :: OSI Approved :: MIT License

2025-10-15T11:27:56,941           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:27:56,942           ********************************************************************************

2025-10-15T11:27:56,944   !!
2025-10-15T11:27:56,944     self._finalize_license_expression()
2025-10-15T11:27:57,006   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-10-15T11:27:57,006   !!

2025-10-15T11:27:57,008           ********************************************************************************
2025-10-15T11:27:57,008           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).

2025-10-15T11:27:57,009           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-10-15T11:27:57,009           or your builds will no longer be supported.

2025-10-15T11:27:57,010           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:27:57,011           ********************************************************************************

2025-10-15T11:27:57,012   !!
2025-10-15T11:27:57,012     corresp(dist, value, root_dir)
2025-10-15T11:27:57,013   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2025-10-15T11:27:57,013     corresp(dist, value, root_dir)
2025-10-15T11:27:57,091   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:27:57,091   !!

2025-10-15T11:27:57,092           ********************************************************************************
2025-10-15T11:27:57,093           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:27:57,094           License :: OSI Approved :: MIT License

2025-10-15T11:27:57,095           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:27:57,096           ********************************************************************************

2025-10-15T11:27:57,097   !!
2025-10-15T11:27:57,097     dist._finalize_license_expression()
2025-10-15T11:27:57,101   running egg_info
2025-10-15T11:27:57,114   writing scbamtools.egg-info/PKG-INFO
2025-10-15T11:27:57,117   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2025-10-15T11:27:57,120   writing entry points to scbamtools.egg-info/entry_points.txt
2025-10-15T11:27:57,121   writing requirements to scbamtools.egg-info/requires.txt
2025-10-15T11:27:57,123   writing top-level names to scbamtools.egg-info/top_level.txt
2025-10-15T11:27:57,156   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,156   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,157   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,157   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,158   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,159   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,159   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,160   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,161   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,162   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:57,166   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:27:57,173   reading manifest template 'MANIFEST.in'
2025-10-15T11:27:57,176   adding license file 'LICENSE'
2025-10-15T11:27:57,180   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:27:57,871   Getting requirements to build wheel: finished with status 'done'
2025-10-15T11:27:57,875   Created temporary directory: /tmp/pip-modern-metadata-9d5yv57e
2025-10-15T11:27:57,877   Preparing metadata (pyproject.toml): started
2025-10-15T11:27:57,878   Running command Preparing metadata (pyproject.toml)
2025-10-15T11:27:59,415   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-10-15T11:27:59,415   !!

2025-10-15T11:27:59,416           ********************************************************************************
2025-10-15T11:27:59,417           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).

2025-10-15T11:27:59,418           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-10-15T11:27:59,419           or your builds will no longer be supported.

2025-10-15T11:27:59,420           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:27:59,420           ********************************************************************************

2025-10-15T11:27:59,422   !!
2025-10-15T11:27:59,422     corresp(dist, value, root_dir)
2025-10-15T11:27:59,423   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2025-10-15T11:27:59,424     corresp(dist, value, root_dir)
2025-10-15T11:27:59,493   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:27:59,494   !!

2025-10-15T11:27:59,495           ********************************************************************************
2025-10-15T11:27:59,495           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:27:59,496           License :: OSI Approved :: MIT License

2025-10-15T11:27:59,497           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:27:59,498           ********************************************************************************

2025-10-15T11:27:59,499   !!
2025-10-15T11:27:59,500     dist._finalize_license_expression()
2025-10-15T11:27:59,500   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:27:59,501   !!

2025-10-15T11:27:59,502           ********************************************************************************
2025-10-15T11:27:59,503           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:27:59,505           License :: OSI Approved :: MIT License

2025-10-15T11:27:59,506           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:27:59,506           ********************************************************************************

2025-10-15T11:27:59,507   !!
2025-10-15T11:27:59,507     self._finalize_license_expression()
2025-10-15T11:27:59,508   running dist_info
2025-10-15T11:27:59,521   creating /tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info
2025-10-15T11:27:59,522   writing /tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/PKG-INFO
2025-10-15T11:27:59,526   writing dependency_links to /tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/dependency_links.txt
2025-10-15T11:27:59,528   writing entry points to /tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/entry_points.txt
2025-10-15T11:27:59,529   writing requirements to /tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/requires.txt
2025-10-15T11:27:59,530   writing top-level names to /tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/top_level.txt
2025-10-15T11:27:59,532   writing manifest file '/tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:27:59,560   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,561   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,561   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,562   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,563   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,563   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,564   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,564   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,565   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,565   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:27:59,569   reading manifest file '/tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:27:59,571   reading manifest template 'MANIFEST.in'
2025-10-15T11:27:59,574   adding license file 'LICENSE'
2025-10-15T11:27:59,577   writing manifest file '/tmp/pip-modern-metadata-9d5yv57e/scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:27:59,578   creating '/tmp/pip-modern-metadata-9d5yv57e/scbamtools-0.8.3.dist-info'
2025-10-15T11:27:59,784   Preparing metadata (pyproject.toml): finished with status 'done'
2025-10-15T11:27:59,789   Source in /tmp/pip-wheel-981ebcpw/scbamtools_0fbae44466eb4fe99dc6ff6380462a66 has version 0.8.3, which satisfies requirement scbamtools==0.8.3 from https://files.pythonhosted.org/packages/58/a8/a17afb0e466cf567d8c13497d0f025c286b28da8ade10f7bb4697652cdec/scbamtools-0.8.3.tar.gz
2025-10-15T11:27:59,790   Removed scbamtools==0.8.3 from https://files.pythonhosted.org/packages/58/a8/a17afb0e466cf567d8c13497d0f025c286b28da8ade10f7bb4697652cdec/scbamtools-0.8.3.tar.gz from build tracker '/tmp/pip-build-tracker-dz40uqlk'
2025-10-15T11:27:59,795 Created temporary directory: /tmp/pip-unpack-e75m40ek
2025-10-15T11:27:59,796 Building wheels for collected packages: scbamtools
2025-10-15T11:27:59,801   Created temporary directory: /tmp/pip-wheel-6ot839ph
2025-10-15T11:27:59,801   Destination directory: /tmp/pip-wheel-6ot839ph
2025-10-15T11:27:59,803   Building wheel for scbamtools (pyproject.toml): started
2025-10-15T11:27:59,804   Running command Building wheel for scbamtools (pyproject.toml)
2025-10-15T11:28:01,267   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
2025-10-15T11:28:01,268   !!

2025-10-15T11:28:01,269           ********************************************************************************
2025-10-15T11:28:01,269           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).

2025-10-15T11:28:01,270           By 2026-Feb-18, you need to update your project and remove deprecated calls
2025-10-15T11:28:01,271           or your builds will no longer be supported.

2025-10-15T11:28:01,272           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:28:01,272           ********************************************************************************

2025-10-15T11:28:01,273   !!
2025-10-15T11:28:01,274     corresp(dist, value, root_dir)
2025-10-15T11:28:01,274   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2025-10-15T11:28:01,275     corresp(dist, value, root_dir)
2025-10-15T11:28:01,341   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:28:01,341   !!

2025-10-15T11:28:01,343           ********************************************************************************
2025-10-15T11:28:01,343           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:28:01,344           License :: OSI Approved :: MIT License

2025-10-15T11:28:01,345           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:28:01,346           ********************************************************************************

2025-10-15T11:28:01,347   !!
2025-10-15T11:28:01,351     dist._finalize_license_expression()
2025-10-15T11:28:01,351   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T11:28:01,352   !!

2025-10-15T11:28:01,353           ********************************************************************************
2025-10-15T11:28:01,353           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T11:28:01,355           License :: OSI Approved :: MIT License

2025-10-15T11:28:01,356           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T11:28:01,356           ********************************************************************************

2025-10-15T11:28:01,358   !!
2025-10-15T11:28:01,358     self._finalize_license_expression()
2025-10-15T11:28:01,359   running bdist_wheel
2025-10-15T11:28:01,376   running build
2025-10-15T11:28:01,377   running build_py
2025-10-15T11:28:01,384   creating build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:28:01,386   copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:28:01,388   copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:28:01,391   copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:28:01,393   copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:28:01,395   copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:28:01,397   copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-311/scbamtools
2025-10-15T11:28:01,401   creating build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:28:01,402   copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:28:01,404   copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:28:01,406   copying scbamtools/bin/pa_scanner.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:28:01,408   copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:28:01,410   copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:28:01,412   copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin
2025-10-15T11:28:01,415   creating build/lib.linux-armv7l-cpython-311/scbamtools/config
2025-10-15T11:28:01,416   copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-311/scbamtools/config
2025-10-15T11:28:01,417   running egg_info
2025-10-15T11:28:01,433   writing scbamtools.egg-info/PKG-INFO
2025-10-15T11:28:01,436   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2025-10-15T11:28:01,438   writing entry points to scbamtools.egg-info/entry_points.txt
2025-10-15T11:28:01,439   writing requirements to scbamtools.egg-info/requires.txt
2025-10-15T11:28:01,440   writing top-level names to scbamtools.egg-info/top_level.txt
2025-10-15T11:28:01,447   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,448   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,449   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,449   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,450   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,450   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,451   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,452   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,452   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,453   dependency /tmp/pip-build-env-y40ddyt_/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
2025-10-15T11:28:01,456   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:28:01,460   reading manifest template 'MANIFEST.in'
2025-10-15T11:28:01,463   adding license file 'LICENSE'
2025-10-15T11:28:01,467   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2025-10-15T11:28:01,469   /tmp/pip-build-env-y40ddyt_/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'scbamtools.config.__pycache__' is absent from the `packages` configuration.
2025-10-15T11:28:01,470   !!

2025-10-15T11:28:01,471           ********************************************************************************
2025-10-15T11:28:01,471           ############################
2025-10-15T11:28:01,472           # Package would be ignored #
2025-10-15T11:28:01,472           ############################
2025-10-15T11:28:01,473           Python recognizes 'scbamtools.config.__pycache__' as an importable package[^1],
2025-10-15T11:28:01,473           but it is absent from setuptools' `packages` configuration.

2025-10-15T11:28:01,474           This leads to an ambiguous overall configuration. If you want to distribute this
2025-10-15T11:28:01,474           package, please make sure that 'scbamtools.config.__pycache__' is explicitly added
2025-10-15T11:28:01,475           to the `packages` configuration field.

2025-10-15T11:28:01,476           Alternatively, you can also rely on setuptools' discovery methods
2025-10-15T11:28:01,476           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2025-10-15T11:28:01,477           instead of `find_packages(...)`/`find:`).

2025-10-15T11:28:01,478           You can read more about "package discovery" on setuptools documentation page:

2025-10-15T11:28:01,479           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2025-10-15T11:28:01,481           If you don't want 'scbamtools.config.__pycache__' to be distributed and are
2025-10-15T11:28:01,481           already explicitly excluding 'scbamtools.config.__pycache__' via
2025-10-15T11:28:01,482           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2025-10-15T11:28:01,482           you can try to use `exclude_package_data`, or `include-package-data=False` in
2025-10-15T11:28:01,483           combination with a more fine grained `package-data` configuration.

2025-10-15T11:28:01,487           You can read more about "package data files" on setuptools documentation page:

2025-10-15T11:28:01,497           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2025-10-15T11:28:01,499           [^1]: For Python, any directory (with suitable naming) can be imported,
2025-10-15T11:28:01,500                 even if it does not contain any `.py` files.
2025-10-15T11:28:01,500                 On the other hand, currently there is no concept of package data
2025-10-15T11:28:01,501                 directory, all directories are treated like packages.
2025-10-15T11:28:01,501           ********************************************************************************

2025-10-15T11:28:01,502   !!
2025-10-15T11:28:01,503     check.warn(importable)
2025-10-15T11:28:01,503   creating build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,504   copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,504   copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,505   copying scbamtools/cython/cigar.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,505   copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,527   copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,530   copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,532   copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-311/scbamtools/config
2025-10-15T11:28:01,534   creating build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2025-10-15T11:28:01,535   copying scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2025-10-15T11:28:01,537   copying scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__
2025-10-15T11:28:01,541   running build_ext
2025-10-15T11:28:01,547   building 'scbamtools.cython.kmers' extension
2025-10-15T11:28:01,548   creating build/temp.linux-armv7l-cpython-311/scbamtools/cython
2025-10-15T11:28:01,550   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-y40ddyt_/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
2025-10-15T11:28:03,193   scbamtools/cython/kmers.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’:
2025-10-15T11:28:03,218   scbamtools/cython/kmers.c:27952:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2025-10-15T11:28:03,218   27952 |     if ((intval & PyLong_MASK) == intval) {
2025-10-15T11:28:03,219         |                                ^~
2025-10-15T11:28:03,243   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]
2025-10-15T11:28:03,244   27954 |         long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1));
2025-10-15T11:28:03,244         |                                                                   ^~~~~~~~~~
2025-10-15T11:28:22,597   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
2025-10-15T11:28:22,734   building 'scbamtools.cython.bctree' extension
2025-10-15T11:28:22,734   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-y40ddyt_/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
2025-10-15T11:28:23,469   scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’:
2025-10-15T11:28:23,488   scbamtools/cython/bctree.c:21270:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2025-10-15T11:28:23,488   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]) ))));
2025-10-15T11:28:23,489         |                  ^
2025-10-15T11:28:24,378   scbamtools/cython/bctree.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’:
2025-10-15T11:28:24,402   scbamtools/cython/bctree.c:27964:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare]
2025-10-15T11:28:24,403   27964 |     if ((intval & PyLong_MASK) == intval) {
2025-10-15T11:28:24,404         |                                ^~
2025-10-15T11:28:24,428   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]
2025-10-15T11:28:24,429   27966 |         long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1));
2025-10-15T11:28:24,429         |                                                                   ^~~~~~~~~~
2025-10-15T11:28:43,906   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
2025-10-15T11:28:44,055   installing to build/bdist.linux-armv7l/wheel
2025-10-15T11:28:44,055   running install
2025-10-15T11:28:44,078   running install_lib
2025-10-15T11:28:44,085   creating build/bdist.linux-armv7l/wheel
2025-10-15T11:28:44,087   creating build/bdist.linux-armv7l/wheel/scbamtools
2025-10-15T11:28:44,089   copying build/lib.linux-armv7l-cpython-311/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:28:44,091   copying build/lib.linux-armv7l-cpython-311/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:28:44,094   creating build/bdist.linux-armv7l/wheel/scbamtools/bin
2025-10-15T11:28:44,095   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:28:44,097   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:28:44,099   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/pa_scanner.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:28:44,101   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:28:44,103   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:28:44,106   copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin
2025-10-15T11:28:44,108   copying build/lib.linux-armv7l-cpython-311/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:28:44,110   copying build/lib.linux-armv7l-cpython-311/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:28:44,112   creating build/bdist.linux-armv7l/wheel/scbamtools/config
2025-10-15T11:28:44,113   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/./scbamtools/config
2025-10-15T11:28:44,115   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/./scbamtools/config
2025-10-15T11:28:44,118   creating build/bdist.linux-armv7l/wheel/scbamtools/config/__pycache__
2025-10-15T11:28:44,119   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__
2025-10-15T11:28:44,121   copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__
2025-10-15T11:28:44,122   copying build/lib.linux-armv7l-cpython-311/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:28:44,125   copying build/lib.linux-armv7l-cpython-311/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/./scbamtools
2025-10-15T11:28:44,128   creating build/bdist.linux-armv7l/wheel/scbamtools/cython
2025-10-15T11:28:44,129   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,132   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/cigar.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,133   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,136   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,157   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,179   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,181   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,201   copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython
2025-10-15T11:28:44,218   running install_egg_info
2025-10-15T11:28:44,225   Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/./scbamtools-0.8.3-py3.11.egg-info
2025-10-15T11:28:44,238   running install_scripts
2025-10-15T11:28:44,284   creating build/bdist.linux-armv7l/wheel/scbamtools-0.8.3.dist-info/WHEEL
2025-10-15T11:28:44,287   creating '/tmp/pip-wheel-6ot839ph/.tmp-p13pt7vq/scbamtools-0.8.3-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-15T11:28:44,292   adding 'scbamtools/annotation.py'
2025-10-15T11:28:44,294   adding 'scbamtools/bctree.py'
2025-10-15T11:28:44,295   adding 'scbamtools/contrib.py'
2025-10-15T11:28:44,298   adding 'scbamtools/gene_model.py'
2025-10-15T11:28:44,302   adding 'scbamtools/quant.py'
2025-10-15T11:28:44,304   adding 'scbamtools/util.py'
2025-10-15T11:28:44,306   adding 'scbamtools/bin/BamTagHistogram.py'
2025-10-15T11:28:44,308   adding 'scbamtools/bin/ann.py'
2025-10-15T11:28:44,310   adding 'scbamtools/bin/count.py'
2025-10-15T11:28:44,311   adding 'scbamtools/bin/pa_scanner.py'
2025-10-15T11:28:44,313   adding 'scbamtools/bin/trim.py'
2025-10-15T11:28:44,315   adding 'scbamtools/bin/uBAM.py'
2025-10-15T11:28:44,317   adding 'scbamtools/config/__init__.py'
2025-10-15T11:28:44,318   adding 'scbamtools/config/default.yaml'
2025-10-15T11:28:44,320   adding 'scbamtools/config/__pycache__/__init__.cpython-310.pyc'
2025-10-15T11:28:44,321   adding 'scbamtools/config/__pycache__/__init__.cpython-311.pyc'
2025-10-15T11:28:44,423   adding 'scbamtools/cython/bctree.c'
2025-10-15T11:28:44,652   adding 'scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T11:28:44,660   adding 'scbamtools/cython/bctree.pyx'
2025-10-15T11:28:44,661   adding 'scbamtools/cython/cigar.pyx'
2025-10-15T11:28:44,762   adding 'scbamtools/cython/kmers.c'
2025-10-15T11:28:44,991   adding 'scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T11:28:44,998   adding 'scbamtools/cython/kmers.pyx'
2025-10-15T11:28:44,999   adding 'scbamtools/cython/types.pxd'
2025-10-15T11:28:45,002   adding 'scbamtools-0.8.3.dist-info/licenses/LICENSE'
2025-10-15T11:28:45,003   adding 'scbamtools-0.8.3.dist-info/METADATA'
2025-10-15T11:28:45,004   adding 'scbamtools-0.8.3.dist-info/WHEEL'
2025-10-15T11:28:45,005   adding 'scbamtools-0.8.3.dist-info/entry_points.txt'
2025-10-15T11:28:45,006   adding 'scbamtools-0.8.3.dist-info/top_level.txt'
2025-10-15T11:28:45,007   adding 'scbamtools-0.8.3.dist-info/RECORD'
2025-10-15T11:28:45,025   removing build/bdist.linux-armv7l/wheel
2025-10-15T11:28:45,214   Building wheel for scbamtools (pyproject.toml): finished with status 'done'
2025-10-15T11:28:45,243   Created wheel for scbamtools: filename=scbamtools-0.8.3-cp311-cp311-linux_armv7l.whl size=1262675 sha256=3ddd860d448ff4a31cc207ae510f4e9e192c849c0de2d148730e7084ce32a701
2025-10-15T11:28:45,244   Stored in directory: /tmp/pip-ephem-wheel-cache-lejhg_9q/wheels/12/46/d7/5c911a222602834a32d06bbee6bc06eba97ccd3e4744b4a8c2
2025-10-15T11:28:45,256 Successfully built scbamtools
2025-10-15T11:28:45,292 Removed build tracker: '/tmp/pip-build-tracker-dz40uqlk'