2026-07-08T11:45:40,648 Created temporary directory: /tmp/pip-ephem-wheel-cache-a3qu6f1j
2026-07-08T11:45:40,650 Created temporary directory: /tmp/pip-build-tracker-pfwck8fe
2026-07-08T11:45:40,651 Initialized build tracking at /tmp/pip-build-tracker-pfwck8fe
2026-07-08T11:45:40,651 Created build tracker: /tmp/pip-build-tracker-pfwck8fe
2026-07-08T11:45:40,651 Entered build tracker: /tmp/pip-build-tracker-pfwck8fe
2026-07-08T11:45:40,652 Created temporary directory: /tmp/pip-wheel-r2tyk1a_
2026-07-08T11:45:40,655 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
2026-07-08T11:45:40,658 Created temporary directory: /tmp/pip-ephem-wheel-cache-s6yjaxu4
2026-07-08T11:45:40,679 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-08T11:45:40,683 2 location(s) to search for versions of bam-dedup:
2026-07-08T11:45:40,683 * https://pypi.org/simple/bam-dedup/
2026-07-08T11:45:40,683 * https://www.piwheels.org/simple/bam-dedup/
2026-07-08T11:45:40,684 Fetching project page and analyzing links: https://pypi.org/simple/bam-dedup/
2026-07-08T11:45:40,684 Getting page https://pypi.org/simple/bam-dedup/
2026-07-08T11:45:40,686 Found index url https://pypi.org/simple
2026-07-08T11:45:40,913 Fetched page https://pypi.org/simple/bam-dedup/ as application/vnd.pypi.simple.v1+json
2026-07-08T11:45:40,914   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
2026-07-08T11:45:40,915   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
2026-07-08T11:45:40,916 Fetching project page and analyzing links: https://www.piwheels.org/simple/bam-dedup/
2026-07-08T11:45:40,917 Getting page https://www.piwheels.org/simple/bam-dedup/
2026-07-08T11:45:40,918 Found index url https://www.piwheels.org/simple
2026-07-08T11:45:41,111 Fetched page https://www.piwheels.org/simple/bam-dedup/ as text/html
2026-07-08T11:45:41,112 Skipping link: not a file: https://www.piwheels.org/simple/bam-dedup/
2026-07-08T11:45:41,113 Skipping link: not a file: https://pypi.org/simple/bam-dedup/
2026-07-08T11:45:41,131 Given no hashes to check 1 links for project 'bam-dedup': discarding no candidates
2026-07-08T11:45:41,149 Collecting bam-dedup==0.2.0
2026-07-08T11:45:41,151   Created temporary directory: /tmp/pip-unpack-4o_0qyk1
2026-07-08T11:45:41,305   Downloading bam_dedup-0.2.0.tar.gz (492 kB)
2026-07-08T11:45:41,524   Added bam-dedup==0.2.0 from https://files.pythonhosted.org/packages/b7/1f/67c5018a28543090f7dda9ff8c92b5b267640f1db79c3e34493db5eb2e14/bam_dedup-0.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-pfwck8fe'
2026-07-08T11:45:41,529   Created temporary directory: /tmp/pip-build-env-ok5ubm31
2026-07-08T11:45:41,534   Installing build dependencies: started
2026-07-08T11:45:41,535   Running command pip subprocess to install build dependencies
2026-07-08T11:45:42,671   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2026-07-08T11:45:43,148   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
2026-07-08T11:45:43,171   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-08T11:45:44,985   Collecting setuptools>=61
2026-07-08T11:45:44,986     Obtaining dependency information for setuptools>=61 from https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata
2026-07-08T11:45:45,002     Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl.metadata (6.6 kB)
2026-07-08T11:45:45,237   Collecting wheel
2026-07-08T11:45:45,238     Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata
2026-07-08T11:45:45,253     Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
2026-07-08T11:45:47,414   Collecting Cython>=0.29
2026-07-08T11:45:47,415     Obtaining dependency information for Cython>=0.29 from https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl.metadata
2026-07-08T11:45:47,433     Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl.metadata (4.2 kB)
2026-07-08T11:45:47,615   Collecting packaging>=24.0
2026-07-08T11:45:47,616     Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata
2026-07-08T11:45:47,630     Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
2026-07-08T11:45:47,893   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-07-08T11:45:48,695   Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl (11.2 MB)
2026-07-08T11:45:48,905   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-08T11:45:48,981   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-08T11:45:49,014   Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB)
2026-07-08T11:45:49,855   Using cached https://www.piwheels.org/simple/cython/cython-3.2.8-cp311-cp311-linux_armv7l.whl (11.2 MB)
2026-07-08T11:45:50,174   Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB)
2026-07-08T11:45:50,264   Using cached https://www.piwheels.org/simple/setuptools/setuptools-83.0.0-py3-none-any.whl (1.0 MB)
2026-07-08T11:45:52,996   Installing collected packages: setuptools, packaging, Cython, wheel
2026-07-08T11:46:00,031     Creating /tmp/pip-build-env-ok5ubm31/overlay/local/bin
2026-07-08T11:46:00,033     changing mode of /tmp/pip-build-env-ok5ubm31/overlay/local/bin/cygdb to 755
2026-07-08T11:46:00,035     changing mode of /tmp/pip-build-env-ok5ubm31/overlay/local/bin/cython to 755
2026-07-08T11:46:00,037     changing mode of /tmp/pip-build-env-ok5ubm31/overlay/local/bin/cythonize to 755
2026-07-08T11:46:00,172     changing mode of /tmp/pip-build-env-ok5ubm31/overlay/local/bin/wheel to 755
2026-07-08T11:46:00,198   Successfully installed Cython-3.2.8 packaging-26.2 setuptools-83.0.0 wheel-0.47.0
2026-07-08T11:46:00,600   Installing build dependencies: finished with status 'done'
2026-07-08T11:46:00,606   Getting requirements to build wheel: started
2026-07-08T11:46:00,607   Running command Getting requirements to build wheel
2026-07-08T11:46:05,229   Compiling dedup/_fast.pyx because it depends on /tmp/pip-build-env-ok5ubm31/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd.
2026-07-08T11:46:05,229   [1/1] Cythonizing dedup/_fast.pyx
2026-07-08T11:46:05,737   Getting requirements to build wheel: finished with status 'done'
2026-07-08T11:46:05,749   Created temporary directory: /tmp/pip-modern-metadata-pf6b1lsb
2026-07-08T11:46:05,751   Preparing metadata (pyproject.toml): started
2026-07-08T11:46:05,753   Running command Preparing metadata (pyproject.toml)
2026-07-08T11:46:06,989   /tmp/pip-build-env-ok5ubm31/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-07-08T11:46:06,989   !!

2026-07-08T11:46:06,990           ********************************************************************************
2026-07-08T11:46:06,991           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-07-08T11:46:06,992           License :: OSI Approved :: MIT License

2026-07-08T11:46:06,993           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-07-08T11:46:06,993           ********************************************************************************

2026-07-08T11:46:06,994   !!
2026-07-08T11:46:06,995     self._finalize_license_expression()
2026-07-08T11:46:07,020   running dist_info
2026-07-08T11:46:07,032   creating /tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info
2026-07-08T11:46:07,033   writing /tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/PKG-INFO
2026-07-08T11:46:07,038   writing dependency_links to /tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/dependency_links.txt
2026-07-08T11:46:07,039   writing entry points to /tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/entry_points.txt
2026-07-08T11:46:07,041   writing requirements to /tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/requires.txt
2026-07-08T11:46:07,042   writing top-level names to /tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/top_level.txt
2026-07-08T11:46:07,043   writing manifest file '/tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/SOURCES.txt'
2026-07-08T11:46:07,084   reading manifest file '/tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/SOURCES.txt'
2026-07-08T11:46:07,086   reading manifest template 'MANIFEST.in'
2026-07-08T11:46:07,093   warning: no files found matching '*.pxd' under directory 'dedup'
2026-07-08T11:46:07,115   warning: no files found matching '*.bai' under directory 'tests/data'
2026-07-08T11:46:07,116   no previously-included directories found matching '*.egg-info'
2026-07-08T11:46:07,117   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-08T11:46:07,118   warning: no previously-included files matching '*.DS_Store' found anywhere in distribution
2026-07-08T11:46:07,119   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-08T11:46:07,119   warning: no previously-included files matching '*.jar' found anywhere in distribution
2026-07-08T11:46:07,120   adding license file 'LICENSE.txt'
2026-07-08T11:46:07,123   writing manifest file '/tmp/pip-modern-metadata-pf6b1lsb/bam_dedup.egg-info/SOURCES.txt'
2026-07-08T11:46:07,124   creating '/tmp/pip-modern-metadata-pf6b1lsb/bam_dedup-0.2.0.dist-info'
2026-07-08T11:46:07,314   Preparing metadata (pyproject.toml): finished with status 'done'
2026-07-08T11:46:07,319   Source in /tmp/pip-wheel-r2tyk1a_/bam-dedup_aa62d1233f9648759b611050c8dd8350 has version 0.2.0, which satisfies requirement bam-dedup==0.2.0 from https://files.pythonhosted.org/packages/b7/1f/67c5018a28543090f7dda9ff8c92b5b267640f1db79c3e34493db5eb2e14/bam_dedup-0.2.0.tar.gz
2026-07-08T11:46:07,320   Removed bam-dedup==0.2.0 from https://files.pythonhosted.org/packages/b7/1f/67c5018a28543090f7dda9ff8c92b5b267640f1db79c3e34493db5eb2e14/bam_dedup-0.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-pfwck8fe'
2026-07-08T11:46:07,325 Created temporary directory: /tmp/pip-unpack-x5wbw3sa
2026-07-08T11:46:07,326 Building wheels for collected packages: bam-dedup
2026-07-08T11:46:07,330   Created temporary directory: /tmp/pip-wheel-ju4ir7zg
2026-07-08T11:46:07,331   Destination directory: /tmp/pip-wheel-ju4ir7zg
2026-07-08T11:46:07,334   Building wheel for bam-dedup (pyproject.toml): started
2026-07-08T11:46:07,335   Running command Building wheel for bam-dedup (pyproject.toml)
2026-07-08T11:46:08,580   /tmp/pip-build-env-ok5ubm31/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-07-08T11:46:08,581   !!

2026-07-08T11:46:08,582           ********************************************************************************
2026-07-08T11:46:08,582           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-07-08T11:46:08,584           License :: OSI Approved :: MIT License

2026-07-08T11:46:08,585           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-07-08T11:46:08,585           ********************************************************************************

2026-07-08T11:46:08,586   !!
2026-07-08T11:46:08,586     self._finalize_license_expression()
2026-07-08T11:46:08,609   running bdist_wheel
2026-07-08T11:46:08,641   running build
2026-07-08T11:46:08,642   running build_py
2026-07-08T11:46:08,651   creating build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,653   copying dedup/fgbiolike.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,656   copying dedup/cli.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,658   copying dedup/__init__.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,659   copying dedup/picardlike.py -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,662   running egg_info
2026-07-08T11:46:08,673   writing bam_dedup.egg-info/PKG-INFO
2026-07-08T11:46:08,677   writing dependency_links to bam_dedup.egg-info/dependency_links.txt
2026-07-08T11:46:08,678   writing entry points to bam_dedup.egg-info/entry_points.txt
2026-07-08T11:46:08,680   writing requirements to bam_dedup.egg-info/requires.txt
2026-07-08T11:46:08,680   writing top-level names to bam_dedup.egg-info/top_level.txt
2026-07-08T11:46:08,690   reading manifest file 'bam_dedup.egg-info/SOURCES.txt'
2026-07-08T11:46:08,693   reading manifest template 'MANIFEST.in'
2026-07-08T11:46:08,699   warning: no files found matching '*.pxd' under directory 'dedup'
2026-07-08T11:46:08,720   warning: no files found matching '*.bai' under directory 'tests/data'
2026-07-08T11:46:08,722   warning: no previously-included files matching '*.so' found anywhere in distribution
2026-07-08T11:46:08,723   warning: no previously-included files matching '*.DS_Store' found anywhere in distribution
2026-07-08T11:46:08,724   warning: no previously-included files matching '__pycache__' found anywhere in distribution
2026-07-08T11:46:08,724   warning: no previously-included files matching '*.jar' found anywhere in distribution
2026-07-08T11:46:08,725   adding license file 'LICENSE.txt'
2026-07-08T11:46:08,728   writing manifest file 'bam_dedup.egg-info/SOURCES.txt'
2026-07-08T11:46:08,731   copying dedup/_fast.c -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,753   copying dedup/_fast.pyx -> build/lib.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,757   running build_ext
2026-07-08T11:46:08,763   building 'dedup._fast' extension
2026-07-08T11:46:08,764   creating build/temp.linux-armv7l-cpython-311/dedup
2026-07-08T11:46:08,766   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
2026-07-08T11:46:25,110   In function ‘__pyx_f_5dedup_5_fast__find’,
2026-07-08T11:46:25,110       inlined from ‘__pyx_pf_5dedup_5_fast_4optical_flags_graph’ at dedup/_fast.c:17729:17,
2026-07-08T11:46:25,111       inlined from ‘__pyx_pw_5dedup_5_fast_5optical_flags_graph’ at dedup/_fast.c:17214:13:
2026-07-08T11:46:25,125   dedup/_fast.c:17042:33: warning: ‘*__pyx_v_parent_464 + _875’ may be used uninitialized [-Wmaybe-uninitialized]
2026-07-08T11:46:25,126   17042 |     __pyx_t_1 = ((__pyx_v_parent[__pyx_v_a]) != __pyx_v_a);
2026-07-08T11:46:25,127         |                  ~~~~~~~~~~~~~~~^~~~~~~~~~~~
2026-07-08T11:46:28,121   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
2026-07-08T11:46:28,284   installing to build/bdist.linux-armv7l/wheel
2026-07-08T11:46:28,285   running install
2026-07-08T11:46:28,307   running install_lib
2026-07-08T11:46:28,316   creating build/bdist.linux-armv7l/wheel
2026-07-08T11:46:28,318   creating build/bdist.linux-armv7l/wheel/dedup
2026-07-08T11:46:28,319   copying build/lib.linux-armv7l-cpython-311/dedup/fgbiolike.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T11:46:28,323   copying build/lib.linux-armv7l-cpython-311/dedup/_fast.c -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T11:46:28,345   copying build/lib.linux-armv7l-cpython-311/dedup/cli.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T11:46:28,347   copying build/lib.linux-armv7l-cpython-311/dedup/__init__.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T11:46:28,349   copying build/lib.linux-armv7l-cpython-311/dedup/picardlike.py -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T11:46:28,352   copying build/lib.linux-armv7l-cpython-311/dedup/_fast.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T11:46:28,368   copying build/lib.linux-armv7l-cpython-311/dedup/_fast.pyx -> build/bdist.linux-armv7l/wheel/./dedup
2026-07-08T11:46:28,371   running install_egg_info
2026-07-08T11:46:28,385   Copying bam_dedup.egg-info to build/bdist.linux-armv7l/wheel/./bam_dedup-0.2.0-py3.11.egg-info
2026-07-08T11:46:28,400   running install_scripts
2026-07-08T11:46:28,445   creating build/bdist.linux-armv7l/wheel/bam_dedup-0.2.0.dist-info/WHEEL
2026-07-08T11:46:28,448   creating '/tmp/pip-wheel-ju4ir7zg/.tmp-ggci7ovj/bam_dedup-0.2.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-07-08T11:46:28,452   adding 'bam_dedup-0.2.0.dist-info/licenses/LICENSE.txt'
2026-07-08T11:46:28,454   adding 'dedup/__init__.py'
2026-07-08T11:46:28,552   adding 'dedup/_fast.c'
2026-07-08T11:46:28,762   adding 'dedup/_fast.cpython-311-arm-linux-gnueabihf.so'
2026-07-08T11:46:28,770   adding 'dedup/_fast.pyx'
2026-07-08T11:46:28,772   adding 'dedup/cli.py'
2026-07-08T11:46:28,775   adding 'dedup/fgbiolike.py'
2026-07-08T11:46:28,779   adding 'dedup/picardlike.py'
2026-07-08T11:46:28,781   adding 'bam_dedup-0.2.0.dist-info/METADATA'
2026-07-08T11:46:28,782   adding 'bam_dedup-0.2.0.dist-info/WHEEL'
2026-07-08T11:46:28,784   adding 'bam_dedup-0.2.0.dist-info/entry_points.txt'
2026-07-08T11:46:28,785   adding 'bam_dedup-0.2.0.dist-info/top_level.txt'
2026-07-08T11:46:28,789   adding 'bam_dedup-0.2.0.dist-info/RECORD'
2026-07-08T11:46:28,794   removing build/bdist.linux-armv7l/wheel
2026-07-08T11:46:28,955   Building wheel for bam-dedup (pyproject.toml): finished with status 'done'
2026-07-08T11:46:28,971   Created wheel for bam-dedup: filename=bam_dedup-0.2.0-cp311-cp311-linux_armv7l.whl size=581579 sha256=e4a60c54237b1ed617280b57c4946173639d407e3ea622f581f54cee3e75cce3
2026-07-08T11:46:28,972   Stored in directory: /tmp/pip-ephem-wheel-cache-s6yjaxu4/wheels/c8/e4/88/258cc64da52bf4db3819028b9abc211c14892fe7e6b1ff703b
2026-07-08T11:46:28,983 Successfully built bam-dedup
2026-07-08T11:46:28,998 Removed build tracker: '/tmp/pip-build-tracker-pfwck8fe'