2026-07-08T12:52:40,691 Created temporary directory: /tmp/pip-ephem-wheel-cache-yutp05db
2026-07-08T12:52:40,693 Created temporary directory: /tmp/pip-build-tracker-y_3upim8
2026-07-08T12:52:40,694 Initialized build tracking at /tmp/pip-build-tracker-y_3upim8
2026-07-08T12:52:40,694 Created build tracker: /tmp/pip-build-tracker-y_3upim8
2026-07-08T12:52:40,695 Entered build tracker: /tmp/pip-build-tracker-y_3upim8
2026-07-08T12:52:40,695 Created temporary directory: /tmp/pip-wheel-pgh8f8m9
2026-07-08T12:52:40,699 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
2026-07-08T12:52:40,701 Created temporary directory: /tmp/pip-ephem-wheel-cache-6i7r4t9h
2026-07-08T12:52:40,723 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-08T12:52:40,726 2 location(s) to search for versions of bam-dedup:
2026-07-08T12:52:40,726 * https://pypi.org/simple/bam-dedup/
2026-07-08T12:52:40,726 * https://www.piwheels.org/simple/bam-dedup/
2026-07-08T12:52:40,727 Fetching project page and analyzing links: https://pypi.org/simple/bam-dedup/
2026-07-08T12:52:40,728 Getting page https://pypi.org/simple/bam-dedup/
2026-07-08T12:52:40,729 Found index url https://pypi.org/simple
2026-07-08T12:52:41,056 Fetched page https://pypi.org/simple/bam-dedup/ as application/vnd.pypi.simple.v1+json
2026-07-08T12:52:41,058   Found link https://files.pythonhosted.org/packages/b7/1f/67c5018a28543090f7dda9ff8c92b5b267640f1db79c3e34493db5eb2e14/bam_dedup-0.2.0.tar.gz (from https://pypi.org/simple/bam-dedup/) (requires-python:>=3.8), version: 0.2.0
2026-07-08T12:52:41,059   Found link https://files.pythonhosted.org/packages/e8/73/6f6580b9bb436a7d26c77aff0fe0697d4e3ed4a8b31d18d2090f6c757f3f/bam_dedup-0.3.0.tar.gz (from https://pypi.org/simple/bam-dedup/) (requires-python:>=3.8), version: 0.3.0
2026-07-08T12:52:41,059 Fetching project page and analyzing links: https://www.piwheels.org/simple/bam-dedup/
2026-07-08T12:52:41,060 Getting page https://www.piwheels.org/simple/bam-dedup/
2026-07-08T12:52:41,062 Found index url https://www.piwheels.org/simple
2026-07-08T12:52:41,364 Fetched page https://www.piwheels.org/simple/bam-dedup/ as text/html
2026-07-08T12:52:41,366   Skipping link: No binaries permitted for bam-dedup: https://www.piwheels.org/simple/bam-dedup/bam_dedup-0.2.0-cp311-cp311-linux_armv6l.whl#sha256=e4a60c54237b1ed617280b57c4946173639d407e3ea622f581f54cee3e75cce3 (from https://www.piwheels.org/simple/bam-dedup/) (requires-python:>=3.8)
2026-07-08T12:52:41,367   Skipping link: No binaries permitted for bam-dedup: https://www.piwheels.org/simple/bam-dedup/bam_dedup-0.2.0-cp311-cp311-linux_armv7l.whl#sha256=e4a60c54237b1ed617280b57c4946173639d407e3ea622f581f54cee3e75cce3 (from https://www.piwheels.org/simple/bam-dedup/) (requires-python:>=3.8)
2026-07-08T12:52:41,368 Skipping link: not a file: https://www.piwheels.org/simple/bam-dedup/
2026-07-08T12:52:41,368 Skipping link: not a file: https://pypi.org/simple/bam-dedup/
2026-07-08T12:52:41,387 Given no hashes to check 1 links for project 'bam-dedup': discarding no candidates
2026-07-08T12:52:41,405 Collecting bam-dedup==0.3.0
2026-07-08T12:52:41,407   Created temporary directory: /tmp/pip-unpack-pv_tytm_
2026-07-08T12:52:41,738   Downloading bam_dedup-0.3.0.tar.gz (498 kB)
2026-07-08T12:52:42,013   Added bam-dedup==0.3.0 from https://files.pythonhosted.org/packages/e8/73/6f6580b9bb436a7d26c77aff0fe0697d4e3ed4a8b31d18d2090f6c757f3f/bam_dedup-0.3.0.tar.gz to build tracker '/tmp/pip-build-tracker-y_3upim8'
2026-07-08T12:52:42,019   Created temporary directory: /tmp/pip-build-env-cndctwhl
2026-07-08T12:52:42,023   Installing build dependencies: started
2026-07-08T12:52:42,024   Running command pip subprocess to install build dependencies
2026-07-08T12:52:43,159   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-07-08T12:52:43,569   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
2026-07-08T12:52:43,593   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-08T12:52:45,611   Collecting setuptools>=61
2026-07-08T12:52:45,612     Obtaining dependency information for setuptools>=61 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata
2026-07-08T12:52:45,627     Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB)
2026-07-08T12:52:45,863   Collecting wheel
2026-07-08T12:52:45,864     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-07-08T12:52:45,879     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-07-08T12:52:48,033   Collecting Cython>=0.29
2026-07-08T12:52:48,034     Obtaining dependency information for Cython>=0.29 from https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl.metadata
2026-07-08T12:52:48,053     Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl.metadata (4.2 kB)
2026-07-08T12:52:48,235   Collecting packaging>=24.0
2026-07-08T12:52:48,236     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-07-08T12:52:48,250     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-07-08T12:52:48,511   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-07-08T12:52:49,386   Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl (11.2 MB)
2026-07-08T12:52:49,601   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-08T12:52:49,684   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-08T12:52:49,721   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-07-08T12:52:50,539   Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl (11.2 MB)
2026-07-08T12:52:50,863   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-08T12:52:50,961   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-08T12:52:53,732   Installing collected packages: setuptools, packaging, Cython, wheel
2026-07-08T12:53:00,951     Creating /tmp/pip-build-env-cndctwhl/overlay/local/bin
2026-07-08T12:53:00,953     changing mode of /tmp/pip-build-env-cndctwhl/overlay/local/bin/cygdb to 755
2026-07-08T12:53:00,958     changing mode of /tmp/pip-build-env-cndctwhl/overlay/local/bin/cython to 755
2026-07-08T12:53:00,960     changing mode of /tmp/pip-build-env-cndctwhl/overlay/local/bin/cythonize to 755
2026-07-08T12:53:01,098     changing mode of /tmp/pip-build-env-cndctwhl/overlay/local/bin/wheel to 755
2026-07-08T12:53:01,125   Successfully installed Cython-3.2.8 packaging-26.2 setuptools-83.0.0 wheel-0.47.0
2026-07-08T12:53:01,523   Installing build dependencies: finished with status 'done'
2026-07-08T12:53:01,529   Getting requirements to build wheel: started
2026-07-08T12:53:01,531   Running command Getting requirements to build wheel
2026-07-08T12:53:06,156   Compiling dedup/_fast.pyx because it depends on /tmp/pip-build-env-cndctwhl/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd.
2026-07-08T12:53:06,156   [1/1] Cythonizing dedup/_fast.pyx
2026-07-08T12:53:06,664   Getting requirements to build wheel: finished with status 'done'
2026-07-08T12:53:06,678   Created temporary directory: /tmp/pip-modern-metadata-5rc_eysc
2026-07-08T12:53:06,681   Preparing metadata (pyproject.toml): started
2026-07-08T12:53:06,682   Running command Preparing metadata (pyproject.toml)
2026-07-08T12:53:07,908   /tmp/pip-build-env-cndctwhl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-07-08T12:53:07,908   !!

2026-07-08T12:53:07,909           ********************************************************************************
2026-07-08T12:53:07,909           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-07-08T12:53:07,910           License :: OSI Approved :: MIT License

2026-07-08T12:53:07,911           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-07-08T12:53:07,912           ********************************************************************************

2026-07-08T12:53:07,913   !!
2026-07-08T12:53:07,913     self._finalize_license_expression()
2026-07-08T12:53:07,936   running dist_info
2026-07-08T12:53:07,947   creating /tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info
2026-07-08T12:53:07,948   writing /tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/PKG-INFO
2026-07-08T12:53:07,952   writing dependency_links to /tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/dependency_links.txt
2026-07-08T12:53:07,953   writing entry points to /tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/entry_points.txt
2026-07-08T12:53:07,955   writing requirements to /tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/requires.txt
2026-07-08T12:53:07,956   writing top-level names to /tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/top_level.txt
2026-07-08T12:53:07,957   writing manifest file '/tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/SOURCES.txt'
2026-07-08T12:53:07,997   reading manifest file '/tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/SOURCES.txt'
2026-07-08T12:53:07,999   reading manifest template 'MANIFEST.in'
2026-07-08T12:53:08,004   warning: no files found matching '*.pxd' under directory 'dedup'
2026-07-08T12:53:08,024   warning: no files found matching '*.bai' under directory 'tests/data'
2026-07-08T12:53:08,025   no previously-included directories found matching '*.egg-info'
2026-07-08T12:53:08,026   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-08T12:53:08,026   warning: no previously-included files matching '*.DS_Store' found anywhere in distribution
2026-07-08T12:53:08,027   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-08T12:53:08,028   warning: no previously-included files matching '*.jar' found anywhere in distribution
2026-07-08T12:53:08,028   adding license file 'LICENSE.txt'
2026-07-08T12:53:08,031   writing manifest file '/tmp/pip-modern-metadata-5rc_eysc/bam_dedup.egg-info/SOURCES.txt'
2026-07-08T12:53:08,032   creating '/tmp/pip-modern-metadata-5rc_eysc/bam_dedup-0.3.0.dist-info'
2026-07-08T12:53:08,221   Preparing metadata (pyproject.toml): finished with status 'done'
2026-07-08T12:53:08,226   Source in /tmp/pip-wheel-pgh8f8m9/bam-dedup_4837555415f143c7b4a216ac9e72d0a5 has version 0.3.0, which satisfies requirement bam-dedup==0.3.0 from https://files.pythonhosted.org/packages/e8/73/6f6580b9bb436a7d26c77aff0fe0697d4e3ed4a8b31d18d2090f6c757f3f/bam_dedup-0.3.0.tar.gz
2026-07-08T12:53:08,227   Removed bam-dedup==0.3.0 from https://files.pythonhosted.org/packages/e8/73/6f6580b9bb436a7d26c77aff0fe0697d4e3ed4a8b31d18d2090f6c757f3f/bam_dedup-0.3.0.tar.gz from build tracker '/tmp/pip-build-tracker-y_3upim8'
2026-07-08T12:53:08,233 Created temporary directory: /tmp/pip-unpack-ghr1qo0q
2026-07-08T12:53:08,233 Building wheels for collected packages: bam-dedup
2026-07-08T12:53:08,238   Created temporary directory: /tmp/pip-wheel-xh9ge39z
2026-07-08T12:53:08,239   Destination directory: /tmp/pip-wheel-xh9ge39z
2026-07-08T12:53:08,241   Building wheel for bam-dedup (pyproject.toml): started
2026-07-08T12:53:08,242   Running command Building wheel for bam-dedup (pyproject.toml)
2026-07-08T12:53:09,464   /tmp/pip-build-env-cndctwhl/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-07-08T12:53:09,464   !!

2026-07-08T12:53:09,465           ********************************************************************************
2026-07-08T12:53:09,466           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-07-08T12:53:09,467           License :: OSI Approved :: MIT License

2026-07-08T12:53:09,468           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-07-08T12:53:09,468           ********************************************************************************

2026-07-08T12:53:09,469   !!
2026-07-08T12:53:09,469     self._finalize_license_expression()
2026-07-08T12:53:09,492   running bdist_wheel
2026-07-08T12:53:09,524   running build
2026-07-08T12:53:09,525   running build_py
2026-07-08T12:53:09,534   creating build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,537   copying dedup/cli.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,538   copying dedup/__init__.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,540   copying dedup/picardlike.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,543   copying dedup/fgbiolike.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,546   running egg_info
2026-07-08T12:53:09,556   writing bam_dedup.egg-info/PKG-INFO
2026-07-08T12:53:09,560   writing dependency_links to bam_dedup.egg-info/dependency_links.txt
2026-07-08T12:53:09,561   writing entry points to bam_dedup.egg-info/entry_points.txt
2026-07-08T12:53:09,563   writing requirements to bam_dedup.egg-info/requires.txt
2026-07-08T12:53:09,564   writing top-level names to bam_dedup.egg-info/top_level.txt
2026-07-08T12:53:09,574   reading manifest file 'bam_dedup.egg-info/SOURCES.txt'
2026-07-08T12:53:09,577   reading manifest template 'MANIFEST.in'
2026-07-08T12:53:09,582   warning: no files found matching '*.pxd' under directory 'dedup'
2026-07-08T12:53:09,602   warning: no files found matching '*.bai' under directory 'tests/data'
2026-07-08T12:53:09,603   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-08T12:53:09,604   warning: no previously-included files matching '*.DS_Store' found anywhere in distribution
2026-07-08T12:53:09,605   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-08T12:53:09,606   warning: no previously-included files matching '*.jar' found anywhere in distribution
2026-07-08T12:53:09,606   adding license file 'LICENSE.txt'
2026-07-08T12:53:09,609   writing manifest file 'bam_dedup.egg-info/SOURCES.txt'
2026-07-08T12:53:09,612   copying dedup/_fast.c -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,630   copying dedup/_fast.pyx -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,633   running build_ext
2026-07-08T12:53:09,640   building 'dedup._fast' extension
2026-07-08T12:53:09,641   creating build/temp.linux-armv7l-cpython-311/dedup
2026-07-08T12:53:09,642   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c dedup/_fast.c -o build/temp.linux-armv7l-cpython-311/dedup/_fast.o
2026-07-08T12:53:25,606   In function ‘__pyx_f_5dedup_5_fast__find’,
2026-07-08T12:53:25,607       inlined from ‘__pyx_pf_5dedup_5_fast_4optical_flags_graph’ at dedup/_fast.c:17729:17,
2026-07-08T12:53:25,608       inlined from ‘__pyx_pw_5dedup_5_fast_5optical_flags_graph’ at dedup/_fast.c:17214:13:
2026-07-08T12:53:25,622   dedup/_fast.c:17042:33: warning: ‘*__pyx_v_parent_464 + _875’ may be used uninitialized [-Wmaybe-uninitialized]
2026-07-08T12:53:25,623   17042 |     __pyx_t_1 = ((__pyx_v_parent[__pyx_v_a]) != __pyx_v_a);
2026-07-08T12:53:25,623         |                  ~~~~~~~~~~~~~~~^~~~~~~~~~~~
2026-07-08T12:53:28,554   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/dedup/_fast.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/dedup/_fast.cpython-311-arm-linux-gnueabihf.so
2026-07-08T12:53:28,709   installing to build/bdist.linux-armv7l/wheel
2026-07-08T12:53:28,710   running install
2026-07-08T12:53:28,732   running install_lib
2026-07-08T12:53:28,740   creating build/bdist.linux-armv7l/wheel
2026-07-08T12:53:28,742   creating build/bdist.linux-armv7l/wheel/dedup
2026-07-08T12:53:28,743   copying build/lib.linux-armv7l-cpython-311/dedup/_fast.pyx -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T12:53:28,746   copying build/lib.linux-armv7l-cpython-311/dedup/_fast.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T12:53:28,766   copying build/lib.linux-armv7l-cpython-311/dedup/cli.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T12:53:28,767   copying build/lib.linux-armv7l-cpython-311/dedup/__init__.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T12:53:28,769   copying build/lib.linux-armv7l-cpython-311/dedup/picardlike.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T12:53:28,772   copying build/lib.linux-armv7l-cpython-311/dedup/_fast.c -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T12:53:28,792   copying build/lib.linux-armv7l-cpython-311/dedup/fgbiolike.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T12:53:28,795   running install_egg_info
2026-07-08T12:53:28,810   Copying bam_dedup.egg-info to build/bdist.linux-armv7l/wheel/./bam_dedup-0.3.0-py3.11.egg-info
2026-07-08T12:53:28,823   running install_scripts
2026-07-08T12:53:28,868   creating build/bdist.linux-armv7l/wheel/bam_dedup-0.3.0.dist-info/WHEEL
2026-07-08T12:53:28,871   creating '/tmp/pip-wheel-xh9ge39z/.tmp-j9xiqd7o/bam_dedup-0.3.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-07-08T12:53:28,874   adding 'bam_dedup-0.3.0.dist-info/licenses/LICENSE.txt'
2026-07-08T12:53:28,876   adding 'dedup/__init__.py'
2026-07-08T12:53:28,975   adding 'dedup/_fast.c'
2026-07-08T12:53:29,187   adding 'dedup/_fast.cpython-311-arm-linux-gnueabihf.so'
2026-07-08T12:53:29,197   adding 'dedup/_fast.pyx'
2026-07-08T12:53:29,198   adding 'dedup/cli.py'
2026-07-08T12:53:29,202   adding 'dedup/fgbiolike.py'
2026-07-08T12:53:29,206   adding 'dedup/picardlike.py'
2026-07-08T12:53:29,207   adding 'bam_dedup-0.3.0.dist-info/METADATA'
2026-07-08T12:53:29,208   adding 'bam_dedup-0.3.0.dist-info/WHEEL'
2026-07-08T12:53:29,210   adding 'bam_dedup-0.3.0.dist-info/entry_points.txt'
2026-07-08T12:53:29,211   adding 'bam_dedup-0.3.0.dist-info/top_level.txt'
2026-07-08T12:53:29,211   adding 'bam_dedup-0.3.0.dist-info/RECORD'
2026-07-08T12:53:29,218   removing build/bdist.linux-armv7l/wheel
2026-07-08T12:53:29,377   Building wheel for bam-dedup (pyproject.toml): finished with status 'done'
2026-07-08T12:53:29,400   Created wheel for bam-dedup: filename=bam_dedup-0.3.0-cp311-cp311-linux_armv7l.whl size=582422 sha256=048c6c62a0981d7566783ab3bf0f8b44f3172346d29a935264a9fe9412b30902
2026-07-08T12:53:29,402   Stored in directory: /tmp/pip-ephem-wheel-cache-6i7r4t9h/wheels/41/a6/e7/57134d89ab248b082d0a1ab83a46e32c920570621745ff4331
2026-07-08T12:53:29,413 Successfully built bam-dedup
2026-07-08T12:53:29,435 Removed build tracker: '/tmp/pip-build-tracker-y_3upim8'