2026-02-09T05:44:06,703 Created temporary directory: /tmp/pip-ephem-wheel-cache-cloydg2i 2026-02-09T05:44:06,704 Created temporary directory: /tmp/pip-build-tracker-bt7yqgre 2026-02-09T05:44:06,705 Initialized build tracking at /tmp/pip-build-tracker-bt7yqgre 2026-02-09T05:44:06,705 Created build tracker: /tmp/pip-build-tracker-bt7yqgre 2026-02-09T05:44:06,706 Entered build tracker: /tmp/pip-build-tracker-bt7yqgre 2026-02-09T05:44:06,706 Created temporary directory: /tmp/pip-wheel-wxtjuxha 2026-02-09T05:44:06,709 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-09T05:44:06,712 Created temporary directory: /tmp/pip-ephem-wheel-cache-c4h_fpxr 2026-02-09T05:44:06,733 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-09T05:44:06,736 2 location(s) to search for versions of scbamtools: 2026-02-09T05:44:06,736 * https://pypi.org/simple/scbamtools/ 2026-02-09T05:44:06,736 * https://www.piwheels.org/simple/scbamtools/ 2026-02-09T05:44:06,737 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/ 2026-02-09T05:44:06,738 Getting page https://pypi.org/simple/scbamtools/ 2026-02-09T05:44:06,739 Found index url https://pypi.org/simple 2026-02-09T05:44:06,956 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json 2026-02-09T05:44:06,960 Found link https://files.pythonhosted.org/packages/90/98/a7355f2097b73330b58718e0c6e83ee7b93bee0d6a00a010db3eaea2fbd5/scbamtools-0.1.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10), version: 0.1 2026-02-09T05:44:06,961 Found link https://files.pythonhosted.org/packages/24/fa/fd646836da42c49f38967ac48eaf7b6e360da3f50b94a305ef06f093a6ba/scbamtools-0.2.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10), version: 0.2 2026-02-09T05:44:06,962 Found link https://files.pythonhosted.org/packages/60/fe/4740173cbc7a3bc2c6b041d19db568741f4e5339a3bb12951bb652467fd1/scbamtools-0.5.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.5 2026-02-09T05:44:06,963 Found link https://files.pythonhosted.org/packages/77/33/b3f2ccfca129f9a1135d936e8ad2030b88bef0e859bf281620d9af5d6b0c/scbamtools-0.6.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.6 2026-02-09T05:44:06,964 Found link https://files.pythonhosted.org/packages/ed/c4/49dabbc8f6e5a6957f3451ec60363c7f804b1bcd2ad95eed323faa9fd6ba/scbamtools-0.8.1.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.1 2026-02-09T05:44:06,965 Found link https://files.pythonhosted.org/packages/f4/e3/382060f419dfa54214c760869e2272bf621f794cfabc13183ce0430f8539/scbamtools-0.8.2.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.2 2026-02-09T05:44:06,966 Found link https://files.pythonhosted.org/packages/58/a8/a17afb0e466cf567d8c13497d0f025c286b28da8ade10f7bb4697652cdec/scbamtools-0.8.3.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.3 2026-02-09T05:44:06,967 Found link https://files.pythonhosted.org/packages/f7/c0/d98768b070c431f1c02c5d08bd1e9b5bf59e6b8e0513ef157ff6aa604673/scbamtools-0.8.5.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.5 2026-02-09T05:44:06,968 Found link https://files.pythonhosted.org/packages/15/99/167036ec2645eb2793461a74cae353ea51708aa75af11e71db641e7fa0ac/scbamtools-0.8.6.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.6 2026-02-09T05:44:06,969 Found link https://files.pythonhosted.org/packages/d9/80/be7b6ed952e6f9c6d31b49f937ff6ce6c87183c6c8da3d7367703145bdc4/scbamtools-0.8.7.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.7 2026-02-09T05:44:06,970 Skipping link: No binaries permitted for scbamtools: https://files.pythonhosted.org/packages/de/43/54c74b3821005050acbd40788206b62177e6b938bfb5c095cca50b4f64dc/scbamtools-0.8.8-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:06,971 Found link https://files.pythonhosted.org/packages/ac/ac/814920459689b676193f71f87d40fd1ce45ff7338c05c6efde95a2c2f37a/scbamtools-0.8.8.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.8), version: 0.8.8 2026-02-09T05:44:06,971 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/ 2026-02-09T05:44:06,972 Getting page https://www.piwheels.org/simple/scbamtools/ 2026-02-09T05:44:06,973 Found index url https://www.piwheels.org/simple 2026-02-09T05:44:07,132 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html 2026-02-09T05:44:07,144 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.7-cp311-cp311-linux_armv6l.whl#sha256=3bdbf53559ea976bd0e9c51f4498ab1aadc3eca1a83dfc0350255bc376186771 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,144 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.7-cp311-cp311-linux_armv7l.whl#sha256=3bdbf53559ea976bd0e9c51f4498ab1aadc3eca1a83dfc0350255bc376186771 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,145 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.7-cp39-cp39-linux_armv6l.whl#sha256=9202da888e7801139943b899b7b91645f9a5c7eb5c014bf73a2f99f3f9beb727 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,145 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.7-cp39-cp39-linux_armv7l.whl#sha256=9202da888e7801139943b899b7b91645f9a5c7eb5c014bf73a2f99f3f9beb727 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,146 Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.8.6-cp311-cp311-linux_armv6l.whl#sha256=e06d1f685481047d82616faced558ab95931ad4825326ad183cd4e3215948b53 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,147 Skipping link: No binaries permitted for scbamtools: 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https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp311-cp311-linux_armv7l.whl#sha256=9eeb10371047b47673bf1fa28614f1f47c0b6089fd1cf486ed8be089efd51140 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,164 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp39-cp39-linux_armv6l.whl#sha256=44ad821dcd492f55a691e24b59160b6016e170304ae897bde1333049698ef26b (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,165 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp39-cp39-linux_armv7l.whl#sha256=44ad821dcd492f55a691e24b59160b6016e170304ae897bde1333049698ef26b (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,165 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp313-cp313-linux_armv6l.whl#sha256=69b2f634075f82e42e3725c16b49f3d54b4c054997bbf4ffe0c013f0efe1b343 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,165 Skipping link: No binaries permitted for scbamtools: https://archive1.piwheels.org/simple/scbamtools/scbamtools-0.5-cp313-cp313-linux_armv7l.whl#sha256=69b2f634075f82e42e3725c16b49f3d54b4c054997bbf4ffe0c013f0efe1b343 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8) 2026-02-09T05:44:07,166 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/ 2026-02-09T05:44:07,166 Skipping link: not a file: https://pypi.org/simple/scbamtools/ 2026-02-09T05:44:07,186 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates 2026-02-09T05:44:07,204 Collecting scbamtools==0.8.8 2026-02-09T05:44:07,206 Created temporary directory: /tmp/pip-unpack-ns7ku6aa 2026-02-09T05:44:07,339 Downloading scbamtools-0.8.8.tar.gz (599 kB) 2026-02-09T05:44:07,759 Added scbamtools==0.8.8 from https://files.pythonhosted.org/packages/ac/ac/814920459689b676193f71f87d40fd1ce45ff7338c05c6efde95a2c2f37a/scbamtools-0.8.8.tar.gz to build tracker '/tmp/pip-build-tracker-bt7yqgre' 2026-02-09T05:44:07,766 Created temporary directory: /tmp/pip-build-env-wwhwhj8x 2026-02-09T05:44:07,771 Installing build dependencies: started 2026-02-09T05:44:07,772 Running command pip subprocess to install build dependencies 2026-02-09T05:44:08,928 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-09T05:44:09,480 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-09T05:44:09,503 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-09T05:44:11,248 Collecting setuptools>=65.5.1 2026-02-09T05:44:11,267 Using cached setuptools-82.0.0-py3-none-any.whl (1.0 MB) 2026-02-09T05:44:11,529 Collecting wheel 2026-02-09T05:44:11,534 Using cached wheel-0.46.3-py3-none-any.whl (30 kB) 2026-02-09T05:44:13,619 Collecting cython>=3.0.8 2026-02-09T05:44:14,414 Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-02-09T05:44:15,765 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-09T05:44:15,773 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-09T05:44:15,780 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-09T05:44:15,787 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-09T05:44:15,795 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2026-02-09T05:44:16,676 Collecting numpy 2026-02-09T05:44:17,118 Using cached https://www.piwheels.org/simple/numpy/numpy-2.4.1-cp311-cp311-linux_armv7l.whl (6.3 MB) 2026-02-09T05:44:17,483 Collecting packaging>=24.0 2026-02-09T05:44:17,488 Using cached packaging-26.0-py3-none-any.whl (74 kB) 2026-02-09T05:44:20,538 Installing collected packages: setuptools, packaging, numpy, cython, wheel 2026-02-09T05:44:32,437 Creating /tmp/pip-build-env-wwhwhj8x/overlay/local/bin 2026-02-09T05:44:32,439 changing mode of /tmp/pip-build-env-wwhwhj8x/overlay/local/bin/f2py to 755 2026-02-09T05:44:32,441 changing mode of /tmp/pip-build-env-wwhwhj8x/overlay/local/bin/numpy-config to 755 2026-02-09T05:44:36,374 changing mode of /tmp/pip-build-env-wwhwhj8x/overlay/local/bin/cygdb to 755 2026-02-09T05:44:36,377 changing mode of /tmp/pip-build-env-wwhwhj8x/overlay/local/bin/cython to 755 2026-02-09T05:44:36,379 changing mode of /tmp/pip-build-env-wwhwhj8x/overlay/local/bin/cythonize to 755 2026-02-09T05:44:36,503 changing mode of /tmp/pip-build-env-wwhwhj8x/overlay/local/bin/wheel to 755 2026-02-09T05:44:36,539 Successfully installed cython-3.2.4 numpy-2.4.1 packaging-26.0 setuptools-82.0.0 wheel-0.46.3 2026-02-09T05:44:37,006 Installing build dependencies: finished with status 'done' 2026-02-09T05:44:37,012 Getting requirements to build wheel: started 2026-02-09T05:44:37,014 Running command Getting requirements to build wheel 2026-02-09T05:44:41,235 warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier 2026-02-09T05:44:48,997 Compiling scbamtools/cython/kmers.pyx because it changed. 2026-02-09T05:44:48,998 Compiling scbamtools/cython/bctree.pyx because it changed. 2026-02-09T05:44:48,999 Compiling scbamtools/cython/fastquery.pyx because it changed. 2026-02-09T05:44:48,999 [1/3] Cythonizing scbamtools/cython/bctree.pyx 2026-02-09T05:44:49,000 [2/3] Cythonizing scbamtools/cython/fastquery.pyx 2026-02-09T05:44:49,001 [3/3] Cythonizing scbamtools/cython/kmers.pyx 2026-02-09T05:44:49,020 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-09T05:44:49,020 !! 2026-02-09T05:44:49,021 ******************************************************************************** 2026-02-09T05:44:49,022 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-09T05:44:49,023 License :: OSI Approved :: MIT License 2026-02-09T05:44:49,024 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:49,025 ******************************************************************************** 2026-02-09T05:44:49,026 !! 2026-02-09T05:44:49,026 self._finalize_license_expression() 2026-02-09T05:44:49,085 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-09T05:44:49,085 !! 2026-02-09T05:44:49,087 ******************************************************************************** 2026-02-09T05:44:49,087 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-09T05:44:49,089 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-09T05:44:49,089 or your builds will no longer be supported. 2026-02-09T05:44:49,090 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:49,091 ******************************************************************************** 2026-02-09T05:44:49,091 !! 2026-02-09T05:44:49,092 corresp(dist, value, root_dir) 2026-02-09T05:44:49,092 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-02-09T05:44:49,093 corresp(dist, value, root_dir) 2026-02-09T05:44:49,166 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-09T05:44:49,166 !! 2026-02-09T05:44:49,167 ******************************************************************************** 2026-02-09T05:44:49,168 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-09T05:44:49,170 License :: OSI Approved :: MIT License 2026-02-09T05:44:49,171 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:49,172 ******************************************************************************** 2026-02-09T05:44:49,173 !! 2026-02-09T05:44:49,173 dist._finalize_license_expression() 2026-02-09T05:44:49,178 running egg_info 2026-02-09T05:44:49,185 writing scbamtools.egg-info/PKG-INFO 2026-02-09T05:44:49,189 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2026-02-09T05:44:49,191 writing entry points to scbamtools.egg-info/entry_points.txt 2026-02-09T05:44:49,193 writing requirements to scbamtools.egg-info/requires.txt 2026-02-09T05:44:49,194 writing top-level names to scbamtools.egg-info/top_level.txt 2026-02-09T05:44:49,222 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,223 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,223 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,224 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,225 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,225 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,226 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,226 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,227 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,228 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,228 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,228 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,229 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,229 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,230 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:49,235 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-09T05:44:49,242 reading manifest template 'MANIFEST.in' 2026-02-09T05:44:49,245 adding license file 'LICENSE' 2026-02-09T05:44:49,250 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-09T05:44:50,081 Getting requirements to build wheel: finished with status 'done' 2026-02-09T05:44:50,084 Created temporary directory: /tmp/pip-modern-metadata-htvu5fjs 2026-02-09T05:44:50,086 Preparing metadata (pyproject.toml): started 2026-02-09T05:44:50,087 Running command Preparing metadata (pyproject.toml) 2026-02-09T05:44:51,700 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-09T05:44:51,700 !! 2026-02-09T05:44:51,702 ******************************************************************************** 2026-02-09T05:44:51,702 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-09T05:44:51,704 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-09T05:44:51,704 or your builds will no longer be supported. 2026-02-09T05:44:51,705 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:51,706 ******************************************************************************** 2026-02-09T05:44:51,707 !! 2026-02-09T05:44:51,707 corresp(dist, value, root_dir) 2026-02-09T05:44:51,708 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-02-09T05:44:51,708 corresp(dist, value, root_dir) 2026-02-09T05:44:51,774 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-09T05:44:51,774 !! 2026-02-09T05:44:51,776 ******************************************************************************** 2026-02-09T05:44:51,776 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-09T05:44:51,778 License :: OSI Approved :: MIT License 2026-02-09T05:44:51,779 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:51,779 ******************************************************************************** 2026-02-09T05:44:51,780 !! 2026-02-09T05:44:51,780 dist._finalize_license_expression() 2026-02-09T05:44:51,781 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-09T05:44:51,781 !! 2026-02-09T05:44:51,782 ******************************************************************************** 2026-02-09T05:44:51,782 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-09T05:44:51,783 License :: OSI Approved :: MIT License 2026-02-09T05:44:51,784 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:51,784 ******************************************************************************** 2026-02-09T05:44:51,785 !! 2026-02-09T05:44:51,786 self._finalize_license_expression() 2026-02-09T05:44:51,786 running dist_info 2026-02-09T05:44:51,799 creating /tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info 2026-02-09T05:44:51,799 writing /tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/PKG-INFO 2026-02-09T05:44:51,803 writing dependency_links to /tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/dependency_links.txt 2026-02-09T05:44:51,805 writing entry points to /tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/entry_points.txt 2026-02-09T05:44:51,806 writing requirements to /tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/requires.txt 2026-02-09T05:44:51,807 writing top-level names to /tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/top_level.txt 2026-02-09T05:44:51,808 writing manifest file '/tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/SOURCES.txt' 2026-02-09T05:44:51,831 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,832 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,833 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,833 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,834 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,834 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,835 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,836 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,836 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,837 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,838 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,838 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,838 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,839 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,839 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:51,840 reading manifest file '/tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/SOURCES.txt' 2026-02-09T05:44:51,841 reading manifest template 'MANIFEST.in' 2026-02-09T05:44:51,844 adding license file 'LICENSE' 2026-02-09T05:44:51,848 writing manifest file '/tmp/pip-modern-metadata-htvu5fjs/scbamtools.egg-info/SOURCES.txt' 2026-02-09T05:44:51,849 creating '/tmp/pip-modern-metadata-htvu5fjs/scbamtools-0.8.8.dist-info' 2026-02-09T05:44:52,057 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-09T05:44:52,061 Source in /tmp/pip-wheel-wxtjuxha/scbamtools_cfd693f25f374650b8c39347849522c0 has version 0.8.8, which satisfies requirement scbamtools==0.8.8 from https://files.pythonhosted.org/packages/ac/ac/814920459689b676193f71f87d40fd1ce45ff7338c05c6efde95a2c2f37a/scbamtools-0.8.8.tar.gz 2026-02-09T05:44:52,063 Removed scbamtools==0.8.8 from https://files.pythonhosted.org/packages/ac/ac/814920459689b676193f71f87d40fd1ce45ff7338c05c6efde95a2c2f37a/scbamtools-0.8.8.tar.gz from build tracker '/tmp/pip-build-tracker-bt7yqgre' 2026-02-09T05:44:52,068 Created temporary directory: /tmp/pip-unpack-ly2f1tkc 2026-02-09T05:44:52,068 Building wheels for collected packages: scbamtools 2026-02-09T05:44:52,073 Created temporary directory: /tmp/pip-wheel-g996qj1k 2026-02-09T05:44:52,073 Destination directory: /tmp/pip-wheel-g996qj1k 2026-02-09T05:44:52,075 Building wheel for scbamtools (pyproject.toml): started 2026-02-09T05:44:52,077 Running command Building wheel for scbamtools (pyproject.toml) 2026-02-09T05:44:53,644 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-02-09T05:44:53,644 !! 2026-02-09T05:44:53,646 ******************************************************************************** 2026-02-09T05:44:53,646 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-02-09T05:44:53,647 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-02-09T05:44:53,648 or your builds will no longer be supported. 2026-02-09T05:44:53,649 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:53,650 ******************************************************************************** 2026-02-09T05:44:53,651 !! 2026-02-09T05:44:53,652 corresp(dist, value, root_dir) 2026-02-09T05:44:53,652 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2026-02-09T05:44:53,653 corresp(dist, value, root_dir) 2026-02-09T05:44:53,712 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-09T05:44:53,713 !! 2026-02-09T05:44:53,713 ******************************************************************************** 2026-02-09T05:44:53,714 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-09T05:44:53,715 License :: OSI Approved :: MIT License 2026-02-09T05:44:53,715 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:53,716 ******************************************************************************** 2026-02-09T05:44:53,717 !! 2026-02-09T05:44:53,717 dist._finalize_license_expression() 2026-02-09T05:44:53,718 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-02-09T05:44:53,718 !! 2026-02-09T05:44:53,719 ******************************************************************************** 2026-02-09T05:44:53,720 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-02-09T05:44:53,720 License :: OSI Approved :: MIT License 2026-02-09T05:44:53,721 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-02-09T05:44:53,722 ******************************************************************************** 2026-02-09T05:44:53,723 !! 2026-02-09T05:44:53,724 self._finalize_license_expression() 2026-02-09T05:44:53,724 running bdist_wheel 2026-02-09T05:44:53,740 running build 2026-02-09T05:44:53,741 running build_py 2026-02-09T05:44:53,748 creating build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,750 copying scbamtools/tk.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,752 copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,754 copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,756 copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,758 copying scbamtools/pl.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,761 copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,763 copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,766 copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2026-02-09T05:44:53,769 creating build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,770 copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,773 copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,775 copying scbamtools/bin/cb_correct.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,778 copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,780 copying scbamtools/bin/pa_scanner.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,782 copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,784 copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2026-02-09T05:44:53,787 creating build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-02-09T05:44:53,788 copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-02-09T05:44:53,789 running egg_info 2026-02-09T05:44:53,801 writing scbamtools.egg-info/PKG-INFO 2026-02-09T05:44:53,804 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2026-02-09T05:44:53,805 writing entry points to scbamtools.egg-info/entry_points.txt 2026-02-09T05:44:53,806 writing requirements to scbamtools.egg-info/requires.txt 2026-02-09T05:44:53,808 writing top-level names to scbamtools.egg-info/top_level.txt 2026-02-09T05:44:53,815 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,815 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,816 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,816 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,817 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,817 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,818 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,818 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,819 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,819 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,820 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,821 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,821 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,822 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,822 dependency /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative 2026-02-09T05:44:53,824 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-09T05:44:53,828 reading manifest template 'MANIFEST.in' 2026-02-09T05:44:53,831 adding license file 'LICENSE' 2026-02-09T05:44:53,835 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2026-02-09T05:44:53,838 /tmp/pip-build-env-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'scbamtools.config.__pycache__' is absent from the `packages` configuration. 2026-02-09T05:44:53,839 !! 2026-02-09T05:44:53,840 ******************************************************************************** 2026-02-09T05:44:53,840 ############################ 2026-02-09T05:44:53,840 # Package would be ignored # 2026-02-09T05:44:53,841 ############################ 2026-02-09T05:44:53,841 Python recognizes 'scbamtools.config.__pycache__' as an importable package[^1], 2026-02-09T05:44:53,842 but it is absent from setuptools' `packages` configuration. 2026-02-09T05:44:53,842 This leads to an ambiguous overall configuration. If you want to distribute this 2026-02-09T05:44:53,843 package, please make sure that 'scbamtools.config.__pycache__' is explicitly added 2026-02-09T05:44:53,843 to the `packages` configuration field. 2026-02-09T05:44:53,844 Alternatively, you can also rely on setuptools' discovery methods 2026-02-09T05:44:53,845 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-02-09T05:44:53,845 instead of `find_packages(...)`/`find:`). 2026-02-09T05:44:53,846 You can read more about "package discovery" on setuptools documentation page: 2026-02-09T05:44:53,847 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-02-09T05:44:53,848 If you don't want 'scbamtools.config.__pycache__' to be distributed and are 2026-02-09T05:44:53,848 already explicitly excluding 'scbamtools.config.__pycache__' via 2026-02-09T05:44:53,849 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-02-09T05:44:53,849 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-02-09T05:44:53,850 combination with a more fine grained `package-data` configuration. 2026-02-09T05:44:53,851 You can read more about "package data files" on setuptools documentation page: 2026-02-09T05:44:53,853 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-02-09T05:44:53,856 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-02-09T05:44:53,856 even if it does not contain any `.py` files. 2026-02-09T05:44:53,857 On the other hand, currently there is no concept of package data 2026-02-09T05:44:53,858 directory, all directories are treated like packages. 2026-02-09T05:44:53,858 ******************************************************************************** 2026-02-09T05:44:53,859 !! 2026-02-09T05:44:53,860 check.warn(importable) 2026-02-09T05:44:53,860 creating build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,861 copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,875 copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,878 copying scbamtools/cython/cigar.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,880 copying scbamtools/cython/fastquery.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,908 copying scbamtools/cython/fastquery.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,911 copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,932 copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,934 copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,936 copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2026-02-09T05:44:53,938 creating build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-02-09T05:44:53,940 copying scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-02-09T05:44:53,942 copying scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__ 2026-02-09T05:44:53,945 running build_ext 2026-02-09T05:44:53,952 building 'scbamtools.cython.kmers' extension 2026-02-09T05:44:53,953 creating build/temp.linux-armv7l-cpython-311/scbamtools/cython 2026-02-09T05:44:53,955 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-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c scbamtools/cython/kmers.c -o build/temp.linux-armv7l-cpython-311/scbamtools/cython/kmers.o 2026-02-09T05:44:55,656 scbamtools/cython/kmers.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’: 2026-02-09T05:44:55,680 scbamtools/cython/kmers.c:27485:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2026-02-09T05:44:55,680 27485 | if ((intval & PyLong_MASK) == intval) { 2026-02-09T05:44:55,681 | ^~ 2026-02-09T05:44:55,703 scbamtools/cython/kmers.c:27487:55: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2026-02-09T05:44:55,704 27487 | long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1)); 2026-02-09T05:44:55,705 | ^~~~~~~~~~ 2026-02-09T05:45:14,828 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/scbamtools/cython/kmers.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so 2026-02-09T05:45:15,009 building 'scbamtools.cython.bctree' extension 2026-02-09T05:45:15,010 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-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c scbamtools/cython/bctree.c -o build/temp.linux-armv7l-cpython-311/scbamtools/cython/bctree.o 2026-02-09T05:45:15,727 scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’: 2026-02-09T05:45:15,745 scbamtools/cython/bctree.c:21046:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:15,746 21046 | __pyx_v_node = (&(*((struct __pyx_t_10scbamtools_6cython_6bctree_bc_info_t const *) ( /* dim=0 */ (__pyx_v_buf.data + __pyx_t_2 * __pyx_v_buf.strides[0]) )))); 2026-02-09T05:45:15,746 | ^ 2026-02-09T05:45:16,695 scbamtools/cython/bctree.c: In function ‘__Pyx_Unpacked___Pyx_PyLong_AndObjC’: 2026-02-09T05:45:16,718 scbamtools/cython/bctree.c:27497:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2026-02-09T05:45:16,719 27497 | if ((intval & PyLong_MASK) == intval) { 2026-02-09T05:45:16,720 | ^~ 2026-02-09T05:45:16,742 scbamtools/cython/bctree.c:27499:55: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2026-02-09T05:45:16,743 27499 | long result = intval & (likely(is_positive) ? last_digit : (PyLong_MASK - last_digit + 1)); 2026-02-09T05:45:16,744 | ^~~~~~~~~~ 2026-02-09T05:45:36,100 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/scbamtools/cython/bctree.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so 2026-02-09T05:45:36,232 building 'scbamtools.cython.fastquery' extension 2026-02-09T05:45:36,232 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-wwhwhj8x/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c scbamtools/cython/fastquery.c -o build/temp.linux-armv7l-cpython-311/scbamtools/cython/fastquery.o -fopenmp 2026-02-09T05:45:36,982 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_10query’: 2026-02-09T05:45:37,001 scbamtools/cython/fastquery.c:22650:89: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:37,002 22650 | __pyx_t_13 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ (__pyx_v_SL_view.data + __pyx_t_12 * __pyx_v_SL_view.strides[0]) )))), __pyx_v_nn); if (unlikely(__pyx_t_13 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 322, __pyx_L1_error) 2026-02-09T05:45:37,002 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:37,022 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-09T05:45:37,022 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-09T05:45:37,023 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-09T05:45:37,039 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_12query_idx64’: 2026-02-09T05:45:37,059 scbamtools/cython/fastquery.c:23111:89: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:37,059 23111 | __pyx_t_11 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ (__pyx_v_SL_view.data + __pyx_t_8 * __pyx_v_SL_view.strides[0]) )))), __pyx_v_nn); if (unlikely(__pyx_t_11 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 384, __pyx_L1_error) 2026-02-09T05:45:37,060 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:37,079 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-09T05:45:37,080 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-09T05:45:37,080 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-09T05:45:37,100 scbamtools/cython/fastquery.c: In function ‘__pyx_f_10scbamtools_6cython_9fastquery_make_variants_off_by_one’: 2026-02-09T05:45:37,120 scbamtools/cython/fastquery.c:24094:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-02-09T05:45:37,121 24094 | for (__pyx_t_3 = __pyx_v_start; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { 2026-02-09T05:45:37,121 | ^ 2026-02-09T05:45:37,137 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one’: 2026-02-09T05:45:37,158 scbamtools/cython/fastquery.c:24627:92: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:37,158 24627 | __pyx_t_16 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_sv, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_8)) )))), __pyx_v_nn); if (unlikely(__pyx_t_16 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 585, __pyx_L1_error) 2026-02-09T05:45:37,159 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:37,178 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-09T05:45:37,179 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-09T05:45:37,179 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-09T05:45:37,201 scbamtools/cython/fastquery.c:24723:91: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:37,202 24723 | __pyx_t_16 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_8)) )))), __pyx_v_nn); if (unlikely(__pyx_t_16 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 594, __pyx_L1_error) 2026-02-09T05:45:37,202 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:37,222 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-09T05:45:37,222 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-09T05:45:37,223 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-09T05:45:37,245 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_18query_idx64_variants_single’: 2026-02-09T05:45:37,267 scbamtools/cython/fastquery.c:25883:88: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:37,267 25883 | __pyx_t_6 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_5)) )))), __pyx_v_nn); if (unlikely(__pyx_t_6 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 800, __pyx_L1_error) 2026-02-09T05:45:37,268 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:37,287 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-09T05:45:37,288 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-09T05:45:37,289 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-09T05:45:37,314 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_20query_idx64_variants’: 2026-02-09T05:45:37,336 scbamtools/cython/fastquery.c:26559:91: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:37,337 26559 | __pyx_t_12 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_9)) )))), __pyx_v_nn); if (unlikely(__pyx_t_12 == ((uint8_t)-1) && PyErr_Occurred())) __PYX_ERR(0, 875, __pyx_L1_error) 2026-02-09T05:45:37,337 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:37,357 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-09T05:45:37,358 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-09T05:45:37,358 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-09T05:45:37,375 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp’: 2026-02-09T05:45:37,399 scbamtools/cython/fastquery.c:27171:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-09T05:45:37,400 27171 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2026-02-09T05:45:37,400 | ^ 2026-02-09T05:45:37,430 scbamtools/cython/fastquery.c:27377:119: warning: passing argument 2 of ‘__pyx_f_10scbamtools_6cython_9fastquery_find_in_list’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-09T05:45:37,431 27377 | __pyx_t_15 = __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(__pyx_v_idx_s, (&(*((uint32_t const *) ( /* dim=0 */ ((char *) (((uint32_t const *) __pyx_v_SL_view.data) + __pyx_t_12)) )))), __pyx_v_nn); if (unlikely(__pyx_t_15 == ((uint8_t)-1) && __Pyx_ErrOccurredWithGIL())) __PYX_ERR(0, 963, __pyx_L14_error) 2026-02-09T05:45:37,431 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:37,451 scbamtools/cython/fastquery.c:21940:103: note: expected ‘uint32_t *’ {aka ‘unsigned int *’} but argument is of type ‘const uint32_t *’ {aka ‘const unsigned int *’} 2026-02-09T05:45:37,451 21940 | static uint8_t __pyx_f_10scbamtools_6cython_9fastquery_find_in_list(uint32_t __pyx_v_idx_s, uint32_t *__pyx_v_slist, uint32_t __pyx_v_n) { 2026-02-09T05:45:37,452 | ~~~~~~~~~~^~~~~~~~~~~~~ 2026-02-09T05:45:37,478 scbamtools/cython/fastquery.c:27663:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-09T05:45:37,478 27663 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2026-02-09T05:45:37,479 | ^ 2026-02-09T05:45:41,006 scbamtools/cython/fastquery.c: At top level: 2026-02-09T05:45:41,028 scbamtools/cython/fastquery.c:23205:18: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_make_shifts’ defined but not used [-Wunused-function] 2026-02-09T05:45:41,028 23205 | static PyObject *__pyx_f_10scbamtools_6cython_9fastquery_make_shifts(uint64_t __pyx_v_idx, uint64_t *__pyx_v_shifts, struct __pyx_opt_args_10scbamtools_6cython_9fastquery_make_shifts *__pyx_optional_args) { 2026-02-09T05:45:41,029 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:41,048 scbamtools/cython/fastquery.c:21833:17: warning: ‘__pyx_f_10scbamtools_6cython_9fastquery_seq_to_uint32_slice’ defined but not used [-Wunused-function] 2026-02-09T05:45:41,049 21833 | static uint32_t __pyx_f_10scbamtools_6cython_9fastquery_seq_to_uint32_slice(PyObject *__pyx_v_seq, Py_ssize_t __pyx_v_start, Py_ssize_t __pyx_v_length) { 2026-02-09T05:45:41,050 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:49,834 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_22query_idx64_variants_omp.constprop’: 2026-02-09T05:45:49,858 scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_thread_id’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-09T05:45:49,859 27211 | #pragma omp parallel firstprivate(__pyx_v_idx_variants, __pyx_v_thread_id) private(__pyx_t_1, __pyx_t_10, __pyx_t_11, __pyx_t_12, __pyx_t_13, __pyx_t_14, __pyx_t_15, __pyx_t_16, __pyx_t_17, __pyx_t_18, __pyx_t_7) __Pyx_shared_in_cpython_freethreading(__pyx_parallel_freethreading_mutex) private(__pyx_filename, __pyx_lineno, __pyx_clineno) shared(__pyx_parallel_why, __pyx_parallel_exc_type, __pyx_parallel_exc_value, __pyx_parallel_exc_tb) 2026-02-09T05:45:49,859 | ^~~ 2026-02-09T05:45:49,885 scbamtools/cython/fastquery.c:26953:7: note: ‘__pyx_v_thread_id’ was declared here 2026-02-09T05:45:49,885 26953 | int __pyx_v_thread_id; 2026-02-09T05:45:49,886 | ^~~~~~~~~~~~~~~~~ 2026-02-09T05:45:49,908 scbamtools/cython/fastquery.c:27211:21: warning: ‘__pyx_v_idx_variants’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-09T05:45:49,909 27211 | #pragma omp parallel firstprivate(__pyx_v_idx_variants, __pyx_v_thread_id) private(__pyx_t_1, __pyx_t_10, __pyx_t_11, __pyx_t_12, __pyx_t_13, __pyx_t_14, __pyx_t_15, __pyx_t_16, __pyx_t_17, __pyx_t_18, __pyx_t_7) __Pyx_shared_in_cpython_freethreading(__pyx_parallel_freethreading_mutex) private(__pyx_filename, __pyx_lineno, __pyx_clineno) shared(__pyx_parallel_why, __pyx_parallel_exc_type, __pyx_parallel_exc_value, __pyx_parallel_exc_tb) 2026-02-09T05:45:49,909 | ^~~ 2026-02-09T05:45:49,935 scbamtools/cython/fastquery.c:26951:13: note: ‘__pyx_v_idx_variants’ was declared here 2026-02-09T05:45:49,935 26951 | uint64_t *__pyx_v_idx_variants; 2026-02-09T05:45:49,936 | ^~~~~~~~~~~~~~~~~~~~ 2026-02-09T05:45:58,793 scbamtools/cython/fastquery.c: In function ‘__pyx_pf_10scbamtools_6cython_9fastquery_16query_idx64_off_by_one.constprop’: 2026-02-09T05:45:58,817 scbamtools/cython/fastquery.c:24725:12: warning: ‘__pyx_v_idx_s’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-09T05:45:58,818 24725 | if (__pyx_t_10) { 2026-02-09T05:45:58,818 | ^ 2026-02-09T05:45:58,841 scbamtools/cython/fastquery.c:24339:12: note: ‘__pyx_v_idx_s’ was declared here 2026-02-09T05:45:58,842 24339 | uint32_t __pyx_v_idx_s; 2026-02-09T05:45:58,843 | ^~~~~~~~~~~~~ 2026-02-09T05:46:02,984 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/scbamtools/cython/fastquery.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so -fopenmp 2026-02-09T05:46:03,151 installing to build/bdist.linux-armv7l/wheel 2026-02-09T05:46:03,151 running install 2026-02-09T05:46:03,174 running install_lib 2026-02-09T05:46:03,183 creating build/bdist.linux-armv7l/wheel 2026-02-09T05:46:03,185 creating build/bdist.linux-armv7l/wheel/scbamtools 2026-02-09T05:46:03,187 creating build/bdist.linux-armv7l/wheel/scbamtools/cython 2026-02-09T05:46:03,188 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,206 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,230 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,233 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,236 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,265 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,267 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.c -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,298 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,321 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/cigar.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,322 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,338 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/./scbamtools/cython 2026-02-09T05:46:03,340 copying build/lib.linux-armv7l-cpython-311/scbamtools/tk.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,342 copying build/lib.linux-armv7l-cpython-311/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,344 copying build/lib.linux-armv7l-cpython-311/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,346 copying build/lib.linux-armv7l-cpython-311/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,348 copying build/lib.linux-armv7l-cpython-311/scbamtools/pl.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,351 copying build/lib.linux-armv7l-cpython-311/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,354 creating build/bdist.linux-armv7l/wheel/scbamtools/bin 2026-02-09T05:46:03,355 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-09T05:46:03,357 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-09T05:46:03,360 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/cb_correct.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-09T05:46:03,362 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-09T05:46:03,364 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/pa_scanner.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-09T05:46:03,366 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-09T05:46:03,368 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/./scbamtools/bin 2026-02-09T05:46:03,371 copying build/lib.linux-armv7l-cpython-311/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,373 copying build/lib.linux-armv7l-cpython-311/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/./scbamtools 2026-02-09T05:46:03,377 creating build/bdist.linux-armv7l/wheel/scbamtools/config 2026-02-09T05:46:03,378 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/./scbamtools/config 2026-02-09T05:46:03,380 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/./scbamtools/config 2026-02-09T05:46:03,382 creating build/bdist.linux-armv7l/wheel/scbamtools/config/__pycache__ 2026-02-09T05:46:03,383 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-311.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__ 2026-02-09T05:46:03,385 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__pycache__/__init__.cpython-310.pyc -> build/bdist.linux-armv7l/wheel/./scbamtools/config/__pycache__ 2026-02-09T05:46:03,386 running install_egg_info 2026-02-09T05:46:03,392 Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/./scbamtools-0.8.8-py3.11.egg-info 2026-02-09T05:46:03,404 running install_scripts 2026-02-09T05:46:03,449 creating build/bdist.linux-armv7l/wheel/scbamtools-0.8.8.dist-info/WHEEL 2026-02-09T05:46:03,452 creating '/tmp/pip-wheel-g996qj1k/.tmp-wcyahsfm/scbamtools-0.8.8-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-09T05:46:03,457 adding 'scbamtools/annotation.py' 2026-02-09T05:46:03,459 adding 'scbamtools/bctree.py' 2026-02-09T05:46:03,460 adding 'scbamtools/contrib.py' 2026-02-09T05:46:03,463 adding 'scbamtools/gene_model.py' 2026-02-09T05:46:03,465 adding 'scbamtools/pl.py' 2026-02-09T05:46:03,469 adding 'scbamtools/quant.py' 2026-02-09T05:46:03,470 adding 'scbamtools/tk.py' 2026-02-09T05:46:03,472 adding 'scbamtools/util.py' 2026-02-09T05:46:03,474 adding 'scbamtools/bin/BamTagHistogram.py' 2026-02-09T05:46:03,476 adding 'scbamtools/bin/ann.py' 2026-02-09T05:46:03,479 adding 'scbamtools/bin/cb_correct.py' 2026-02-09T05:46:03,481 adding 'scbamtools/bin/count.py' 2026-02-09T05:46:03,482 adding 'scbamtools/bin/pa_scanner.py' 2026-02-09T05:46:03,484 adding 'scbamtools/bin/trim.py' 2026-02-09T05:46:03,486 adding 'scbamtools/bin/uBAM.py' 2026-02-09T05:46:03,488 adding 'scbamtools/config/__init__.py' 2026-02-09T05:46:03,490 adding 'scbamtools/config/default.yaml' 2026-02-09T05:46:03,492 adding 'scbamtools/config/__pycache__/__init__.cpython-310.pyc' 2026-02-09T05:46:03,493 adding 'scbamtools/config/__pycache__/__init__.cpython-311.pyc' 2026-02-09T05:46:03,597 adding 'scbamtools/cython/bctree.c' 2026-02-09T05:46:03,822 adding 'scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so' 2026-02-09T05:46:03,829 adding 'scbamtools/cython/bctree.pyx' 2026-02-09T05:46:03,831 adding 'scbamtools/cython/cigar.pyx' 2026-02-09T05:46:03,955 adding 'scbamtools/cython/fastquery.c' 2026-02-09T05:46:04,219 adding 'scbamtools/cython/fastquery.cpython-311-arm-linux-gnueabihf.so' 2026-02-09T05:46:04,229 adding 'scbamtools/cython/fastquery.pyx' 2026-02-09T05:46:04,332 adding 'scbamtools/cython/kmers.c' 2026-02-09T05:46:04,556 adding 'scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so' 2026-02-09T05:46:04,564 adding 'scbamtools/cython/kmers.pyx' 2026-02-09T05:46:04,565 adding 'scbamtools/cython/types.pxd' 2026-02-09T05:46:04,568 adding 'scbamtools-0.8.8.dist-info/licenses/LICENSE' 2026-02-09T05:46:04,569 adding 'scbamtools-0.8.8.dist-info/METADATA' 2026-02-09T05:46:04,570 adding 'scbamtools-0.8.8.dist-info/WHEEL' 2026-02-09T05:46:04,571 adding 'scbamtools-0.8.8.dist-info/entry_points.txt' 2026-02-09T05:46:04,572 adding 'scbamtools-0.8.8.dist-info/top_level.txt' 2026-02-09T05:46:04,573 adding 'scbamtools-0.8.8.dist-info/RECORD' 2026-02-09T05:46:04,601 removing build/bdist.linux-armv7l/wheel 2026-02-09T05:46:04,794 Building wheel for scbamtools (pyproject.toml): finished with status 'done' 2026-02-09T05:46:04,834 Created wheel for scbamtools: filename=scbamtools-0.8.8-cp311-cp311-linux_armv7l.whl size=1992559 sha256=9f162ebbed5bff1a6fb14221385bbecba337cb7a373522ca0d9969f5a9cf0b53 2026-02-09T05:46:04,835 Stored in directory: /tmp/pip-ephem-wheel-cache-c4h_fpxr/wheels/b1/e4/bd/cff1232ca14eafb36963183204d751a7875dd35ff25d78744c 2026-02-09T05:46:04,847 Successfully built scbamtools 2026-02-09T05:46:04,902 Removed build tracker: '/tmp/pip-build-tracker-bt7yqgre'