2024-05-21T16:53:20,280 Created temporary directory: /tmp/pip-build-tracker-nb5p834m
2024-05-21T16:53:20,281 Initialized build tracking at /tmp/pip-build-tracker-nb5p834m
2024-05-21T16:53:20,282 Created build tracker: /tmp/pip-build-tracker-nb5p834m
2024-05-21T16:53:20,282 Entered build tracker: /tmp/pip-build-tracker-nb5p834m
2024-05-21T16:53:20,282 Created temporary directory: /tmp/pip-wheel-3bs7pg0i
2024-05-21T16:53:20,286 Created temporary directory: /tmp/pip-ephem-wheel-cache-3g0b24sm
2024-05-21T16:53:20,310 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-05-21T16:53:20,314 2 location(s) to search for versions of scbamtools:
2024-05-21T16:53:20,314 * https://pypi.org/simple/scbamtools/
2024-05-21T16:53:20,314 * https://www.piwheels.org/simple/scbamtools/
2024-05-21T16:53:20,314 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/
2024-05-21T16:53:20,315 Getting page https://pypi.org/simple/scbamtools/
2024-05-21T16:53:20,316 Found index url https://pypi.org/simple/
2024-05-21T16:53:20,368 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json
2024-05-21T16:53:20,370   Link requires a different Python (3.9.2 not in: '>=3.10'): https://files.pythonhosted.org/packages/90/98/a7355f2097b73330b58718e0c6e83ee7b93bee0d6a00a010db3eaea2fbd5/scbamtools-0.1.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10)
2024-05-21T16:53:20,371   Skipping link: 0.1 Requires-Python >=3.10: https://files.pythonhosted.org/packages/90/98/a7355f2097b73330b58718e0c6e83ee7b93bee0d6a00a010db3eaea2fbd5/scbamtools-0.1.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10)
2024-05-21T16:53:20,371   Link requires a different Python (3.9.2 not in: '>=3.10'): https://files.pythonhosted.org/packages/24/fa/fd646836da42c49f38967ac48eaf7b6e360da3f50b94a305ef06f093a6ba/scbamtools-0.2.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10)
2024-05-21T16:53:20,371   Skipping link: 0.2 Requires-Python >=3.10: https://files.pythonhosted.org/packages/24/fa/fd646836da42c49f38967ac48eaf7b6e360da3f50b94a305ef06f093a6ba/scbamtools-0.2.tar.gz (from https://pypi.org/simple/scbamtools/) (requires-python:>=3.10)
2024-05-21T16:53:20,372   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
2024-05-21T16:53:20,372   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
2024-05-21T16:53:20,373 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/
2024-05-21T16:53:20,373 Getting page https://www.piwheels.org/simple/scbamtools/
2024-05-21T16:53:20,374 Found index url https://www.piwheels.org/simple/
2024-05-21T16:53:20,483 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html
2024-05-21T16:53:20,486   Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.6-cp311-cp311-linux_armv6l.whl#sha256=9288a1e72295542d124c65f92013e3c61eedae50599500c2ac00821300907afb (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8)
2024-05-21T16:53:20,486   Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.6-cp311-cp311-linux_armv7l.whl#sha256=9288a1e72295542d124c65f92013e3c61eedae50599500c2ac00821300907afb (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8)
2024-05-21T16:53:20,486   Skipping link: No binaries permitted for scbamtools: https://www.piwheels.org/simple/scbamtools/scbamtools-0.5-cp311-cp311-linux_armv6l.whl#sha256=9eeb10371047b47673bf1fa28614f1f47c0b6089fd1cf486ed8be089efd51140 (from https://www.piwheels.org/simple/scbamtools/) (requires-python:>=3.8)
2024-05-21T16:53:20,486   Skipping link: No binaries permitted for scbamtools: https://www.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)
2024-05-21T16:53:20,487   Skipping link: No binaries permitted for scbamtools: https://www.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)
2024-05-21T16:53:20,487   Skipping link: No binaries permitted for scbamtools: https://www.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)
2024-05-21T16:53:20,487 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/
2024-05-21T16:53:20,487 Skipping link: not a file: https://pypi.org/simple/scbamtools/
2024-05-21T16:53:20,505 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates
2024-05-21T16:53:20,522 Collecting scbamtools==0.6
2024-05-21T16:53:20,524   Created temporary directory: /tmp/pip-unpack-mr2i1vme
2024-05-21T16:53:20,568   Downloading scbamtools-0.6.tar.gz (378 kB)
2024-05-21T16:53:20,771   Added scbamtools==0.6 from https://files.pythonhosted.org/packages/77/33/b3f2ccfca129f9a1135d936e8ad2030b88bef0e859bf281620d9af5d6b0c/scbamtools-0.6.tar.gz to build tracker '/tmp/pip-build-tracker-nb5p834m'
2024-05-21T16:53:20,778   Created temporary directory: /tmp/pip-build-env-oe8chrxu
2024-05-21T16:53:20,788   Installing build dependencies: started
2024-05-21T16:53:20,789   Running command pip subprocess to install build dependencies
2024-05-21T16:53:21,976   Using pip 24.0 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9)
2024-05-21T16:53:22,487   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-05-21T16:53:23,959   Collecting setuptools>=65.5.1
2024-05-21T16:53:23,975     Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB)
2024-05-21T16:53:24,230   Collecting wheel
2024-05-21T16:53:24,248     Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB)
2024-05-21T16:53:25,631   Collecting cython>=3.0.8
2024-05-21T16:53:25,674     Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp39-cp39-linux_armv7l.whl (10.7 MB)
2024-05-21T16:53:27,065   Collecting numpy
2024-05-21T16:53:27,082     Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.4-cp39-cp39-linux_armv7l.whl (5.6 MB)
2024-05-21T16:53:29,128   Installing collected packages: wheel, setuptools, numpy, cython
2024-05-21T16:53:29,354     Creating /tmp/pip-build-env-oe8chrxu/overlay/bin
2024-05-21T16:53:29,356     changing mode of /tmp/pip-build-env-oe8chrxu/overlay/bin/wheel to 755
2024-05-21T16:53:39,338     changing mode of /tmp/pip-build-env-oe8chrxu/overlay/bin/f2py to 755
2024-05-21T16:53:42,761     changing mode of /tmp/pip-build-env-oe8chrxu/overlay/bin/cygdb to 755
2024-05-21T16:53:42,763     changing mode of /tmp/pip-build-env-oe8chrxu/overlay/bin/cython to 755
2024-05-21T16:53:42,765     changing mode of /tmp/pip-build-env-oe8chrxu/overlay/bin/cythonize to 755
2024-05-21T16:53:42,787   Successfully installed cython-3.0.10 numpy-1.26.4 setuptools-70.0.0 wheel-0.43.0
2024-05-21T16:53:43,423   Installing build dependencies: finished with status 'done'
2024-05-21T16:53:43,428   Getting requirements to build wheel: started
2024-05-21T16:53:43,429   Running command Getting requirements to build wheel
2024-05-21T16:53:47,375   warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier
2024-05-21T16:53:51,693   Compiling scbamtools/cython/kmers.pyx because it depends on /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
2024-05-21T16:53:51,693   Compiling scbamtools/cython/bctree.pyx because it depends on /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd.
2024-05-21T16:53:51,694   [1/2] Cythonizing scbamtools/cython/bctree.pyx
2024-05-21T16:53:51,694   [2/2] Cythonizing scbamtools/cython/kmers.pyx
2024-05-21T16:53:51,872   /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2024-05-21T16:53:51,872     corresp(dist, value, root_dir)
2024-05-21T16:53:52,167   running egg_info
2024-05-21T16:53:52,172   writing scbamtools.egg-info/PKG-INFO
2024-05-21T16:53:52,176   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2024-05-21T16:53:52,178   writing requirements to scbamtools.egg-info/requires.txt
2024-05-21T16:53:52,179   writing top-level names to scbamtools.egg-info/top_level.txt
2024-05-21T16:53:52,204   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,204   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,204   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,204   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,205   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,205   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,205   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,205   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,205   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,205   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:52,210   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2024-05-21T16:53:52,213   reading manifest template 'MANIFEST.in'
2024-05-21T16:53:52,215   adding license file 'LICENSE'
2024-05-21T16:53:52,219   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2024-05-21T16:53:52,847   Getting requirements to build wheel: finished with status 'done'
2024-05-21T16:53:52,856   Created temporary directory: /tmp/pip-modern-metadata-h463pjs_
2024-05-21T16:53:52,859   Preparing metadata (pyproject.toml): started
2024-05-21T16:53:52,860   Running command Preparing metadata (pyproject.toml)
2024-05-21T16:53:54,519   /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2024-05-21T16:53:54,519     corresp(dist, value, root_dir)
2024-05-21T16:53:54,760   running dist_info
2024-05-21T16:53:54,766   creating /tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info
2024-05-21T16:53:54,771   writing /tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info/PKG-INFO
2024-05-21T16:53:54,775   writing dependency_links to /tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info/dependency_links.txt
2024-05-21T16:53:54,777   writing requirements to /tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info/requires.txt
2024-05-21T16:53:54,778   writing top-level names to /tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info/top_level.txt
2024-05-21T16:53:54,780   writing manifest file '/tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info/SOURCES.txt'
2024-05-21T16:53:54,801   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,801   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,801   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,801   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,801   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,801   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,801   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,802   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,802   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,802   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:54,806   reading manifest file '/tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info/SOURCES.txt'
2024-05-21T16:53:54,809   reading manifest template 'MANIFEST.in'
2024-05-21T16:53:54,812   adding license file 'LICENSE'
2024-05-21T16:53:54,815   writing manifest file '/tmp/pip-modern-metadata-h463pjs_/scbamtools.egg-info/SOURCES.txt'
2024-05-21T16:53:54,816   creating '/tmp/pip-modern-metadata-h463pjs_/scbamtools-0.6.dist-info'
2024-05-21T16:53:55,006   Preparing metadata (pyproject.toml): finished with status 'done'
2024-05-21T16:53:55,012   Source in /tmp/pip-wheel-3bs7pg0i/scbamtools_cf0942734e4f487496b2493e56104591 has version 0.6, which satisfies requirement scbamtools==0.6 from https://files.pythonhosted.org/packages/77/33/b3f2ccfca129f9a1135d936e8ad2030b88bef0e859bf281620d9af5d6b0c/scbamtools-0.6.tar.gz
2024-05-21T16:53:55,013   Removed scbamtools==0.6 from https://files.pythonhosted.org/packages/77/33/b3f2ccfca129f9a1135d936e8ad2030b88bef0e859bf281620d9af5d6b0c/scbamtools-0.6.tar.gz from build tracker '/tmp/pip-build-tracker-nb5p834m'
2024-05-21T16:53:55,019 Created temporary directory: /tmp/pip-unpack-ny0a2omy
2024-05-21T16:53:55,020 Created temporary directory: /tmp/pip-unpack-6k2lljwt
2024-05-21T16:53:55,026 Building wheels for collected packages: scbamtools
2024-05-21T16:53:55,031   Created temporary directory: /tmp/pip-wheel-2uilyy6e
2024-05-21T16:53:55,031   Destination directory: /tmp/pip-wheel-2uilyy6e
2024-05-21T16:53:55,033   Building wheel for scbamtools (pyproject.toml): started
2024-05-21T16:53:55,034   Running command Building wheel for scbamtools (pyproject.toml)
2024-05-21T16:53:56,659   /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
2024-05-21T16:53:56,659     corresp(dist, value, root_dir)
2024-05-21T16:53:56,892   running bdist_wheel
2024-05-21T16:53:56,914   running build
2024-05-21T16:53:56,914   running build_py
2024-05-21T16:53:56,920   creating build
2024-05-21T16:53:56,921   creating build/lib.linux-armv7l-cpython-39
2024-05-21T16:53:56,922   creating build/lib.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:56,923   copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:56,926   copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:56,928   copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:56,930   copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:56,933   copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:56,934   copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:56,937   creating build/lib.linux-armv7l-cpython-39/scbamtools/bin
2024-05-21T16:53:56,938   copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-39/scbamtools/bin
2024-05-21T16:53:56,940   copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-39/scbamtools/bin
2024-05-21T16:53:56,943   copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-39/scbamtools/bin
2024-05-21T16:53:56,945   copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-39/scbamtools/bin
2024-05-21T16:53:56,947   copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-39/scbamtools/bin
2024-05-21T16:53:56,950   creating build/lib.linux-armv7l-cpython-39/scbamtools/config
2024-05-21T16:53:56,950   copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-39/scbamtools/config
2024-05-21T16:53:56,952   running egg_info
2024-05-21T16:53:56,957   writing scbamtools.egg-info/PKG-INFO
2024-05-21T16:53:56,961   writing dependency_links to scbamtools.egg-info/dependency_links.txt
2024-05-21T16:53:56,962   writing requirements to scbamtools.egg-info/requires.txt
2024-05-21T16:53:56,963   writing top-level names to scbamtools.egg-info/top_level.txt
2024-05-21T16:53:56,971   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,971   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,972   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,972   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,972   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,972   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,972   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,972   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,972   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,973   dependency /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2024-05-21T16:53:56,977   reading manifest file 'scbamtools.egg-info/SOURCES.txt'
2024-05-21T16:53:56,979   reading manifest template 'MANIFEST.in'
2024-05-21T16:53:56,982   adding license file 'LICENSE'
2024-05-21T16:53:56,985   writing manifest file 'scbamtools.egg-info/SOURCES.txt'
2024-05-21T16:53:56,989   creating build/lib.linux-armv7l-cpython-39/scbamtools/cython
2024-05-21T16:53:56,990   copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-39/scbamtools/cython
2024-05-21T16:53:57,020   copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-39/scbamtools/cython
2024-05-21T16:53:57,022   copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-39/scbamtools/cython
2024-05-21T16:53:57,050   copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-39/scbamtools/cython
2024-05-21T16:53:57,052   copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-39/scbamtools/cython
2024-05-21T16:53:57,054   copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-39/scbamtools/config
2024-05-21T16:53:57,058   running build_ext
2024-05-21T16:53:57,067   building 'scbamtools.cython.kmers' extension
2024-05-21T16:53:57,068   creating build/temp.linux-armv7l-cpython-39
2024-05-21T16:53:57,068   creating build/temp.linux-armv7l-cpython-39/scbamtools
2024-05-21T16:53:57,069   creating build/temp.linux-armv7l-cpython-39/scbamtools/cython
2024-05-21T16:53:57,070   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c scbamtools/cython/kmers.c -o build/temp.linux-armv7l-cpython-39/scbamtools/cython/kmers.o
2024-05-21T16:53:57,423   In file included from /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2024-05-21T16:53:57,423                    from /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2024-05-21T16:53:57,423                    from /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
2024-05-21T16:53:57,424                    from scbamtools/cython/kmers.c:1249:
2024-05-21T16:53:57,424   /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2024-05-21T16:53:57,424      17 | #warning "Using deprecated NumPy API, disable it with " \
2024-05-21T16:53:57,424         |  ^~~~~~~
2024-05-21T16:54:21,358   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/scbamtools/cython/kmers.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/scbamtools/cython/kmers.cpython-39-arm-linux-gnueabihf.so
2024-05-21T16:54:21,512   building 'scbamtools.cython.bctree' extension
2024-05-21T16:54:21,513   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c scbamtools/cython/bctree.c -o build/temp.linux-armv7l-cpython-39/scbamtools/cython/bctree.o
2024-05-21T16:54:21,831   In file included from /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2024-05-21T16:54:21,831                    from /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2024-05-21T16:54:21,832                    from /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
2024-05-21T16:54:21,832                    from scbamtools/cython/bctree.c:1249:
2024-05-21T16:54:21,832   /tmp/pip-build-env-oe8chrxu/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
2024-05-21T16:54:21,832      17 | #warning "Using deprecated NumPy API, disable it with " \
2024-05-21T16:54:21,832         |  ^~~~~~~
2024-05-21T16:54:22,128   scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’:
2024-05-21T16:54:22,138   scbamtools/cython/bctree.c:21807:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2024-05-21T16:54:22,139   21807 |     __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]) ))));
2024-05-21T16:54:22,139         |                  ^
2024-05-21T16:54:46,116   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/scbamtools/cython/bctree.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/scbamtools/cython/bctree.cpython-39-arm-linux-gnueabihf.so
2024-05-21T16:54:46,309   installing to build/bdist.linux-armv7l/wheel
2024-05-21T16:54:46,309   running install
2024-05-21T16:54:46,334   running install_lib
2024-05-21T16:54:46,340   creating build/bdist.linux-armv7l
2024-05-21T16:54:46,341   creating build/bdist.linux-armv7l/wheel
2024-05-21T16:54:46,342   creating build/bdist.linux-armv7l/wheel/scbamtools
2024-05-21T16:54:46,344   creating build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,345   copying build/lib.linux-armv7l-cpython-39/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,347   copying build/lib.linux-armv7l-cpython-39/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,368   copying build/lib.linux-armv7l-cpython-39/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,371   copying build/lib.linux-armv7l-cpython-39/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,401   copying build/lib.linux-armv7l-cpython-39/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,404   copying build/lib.linux-armv7l-cpython-39/scbamtools/cython/bctree.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,422   copying build/lib.linux-armv7l-cpython-39/scbamtools/cython/kmers.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/scbamtools/cython
2024-05-21T16:54:46,446   copying build/lib.linux-armv7l-cpython-39/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/scbamtools
2024-05-21T16:54:46,451   copying build/lib.linux-armv7l-cpython-39/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/scbamtools
2024-05-21T16:54:46,457   copying build/lib.linux-armv7l-cpython-39/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/scbamtools
2024-05-21T16:54:46,463   creating build/bdist.linux-armv7l/wheel/scbamtools/config
2024-05-21T16:54:46,464   copying build/lib.linux-armv7l-cpython-39/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/scbamtools/config
2024-05-21T16:54:46,466   copying build/lib.linux-armv7l-cpython-39/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/scbamtools/config
2024-05-21T16:54:46,469   copying build/lib.linux-armv7l-cpython-39/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/scbamtools
2024-05-21T16:54:46,474   copying build/lib.linux-armv7l-cpython-39/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/scbamtools
2024-05-21T16:54:46,478   copying build/lib.linux-armv7l-cpython-39/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/scbamtools
2024-05-21T16:54:46,483   creating build/bdist.linux-armv7l/wheel/scbamtools/bin
2024-05-21T16:54:46,484   copying build/lib.linux-armv7l-cpython-39/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin
2024-05-21T16:54:46,488   copying build/lib.linux-armv7l-cpython-39/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin
2024-05-21T16:54:46,492   copying build/lib.linux-armv7l-cpython-39/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin
2024-05-21T16:54:46,496   copying build/lib.linux-armv7l-cpython-39/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin
2024-05-21T16:54:46,501   copying build/lib.linux-armv7l-cpython-39/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin
2024-05-21T16:54:46,505   running install_egg_info
2024-05-21T16:54:46,512   Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/scbamtools-0.6-py3.9.egg-info
2024-05-21T16:54:46,557   running install_scripts
2024-05-21T16:54:46,617   creating build/bdist.linux-armv7l/wheel/scbamtools-0.6.dist-info/WHEEL
2024-05-21T16:54:46,620   creating '/tmp/pip-wheel-2uilyy6e/.tmp-gv08c5_k/scbamtools-0.6-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-05-21T16:54:46,625   adding 'scbamtools/annotation.py'
2024-05-21T16:54:46,627   adding 'scbamtools/bctree.py'
2024-05-21T16:54:46,628   adding 'scbamtools/contrib.py'
2024-05-21T16:54:46,631   adding 'scbamtools/gene_model.py'
2024-05-21T16:54:46,635   adding 'scbamtools/quant.py'
2024-05-21T16:54:46,636   adding 'scbamtools/util.py'
2024-05-21T16:54:46,638   adding 'scbamtools/bin/BamTagHistogram.py'
2024-05-21T16:54:46,640   adding 'scbamtools/bin/ann.py'
2024-05-21T16:54:46,643   adding 'scbamtools/bin/count.py'
2024-05-21T16:54:46,645   adding 'scbamtools/bin/trim.py'
2024-05-21T16:54:46,647   adding 'scbamtools/bin/uBAM.py'
2024-05-21T16:54:46,649   adding 'scbamtools/config/__init__.py'
2024-05-21T16:54:46,650   adding 'scbamtools/config/default.yaml'
2024-05-21T16:54:46,750   adding 'scbamtools/cython/bctree.c'
2024-05-21T16:54:46,979   adding 'scbamtools/cython/bctree.cpython-39-arm-linux-gnueabihf.so'
2024-05-21T16:54:46,991   adding 'scbamtools/cython/bctree.pyx'
2024-05-21T16:54:47,093   adding 'scbamtools/cython/kmers.c'
2024-05-21T16:54:47,322   adding 'scbamtools/cython/kmers.cpython-39-arm-linux-gnueabihf.so'
2024-05-21T16:54:47,330   adding 'scbamtools/cython/kmers.pyx'
2024-05-21T16:54:47,331   adding 'scbamtools/cython/types.pxd'
2024-05-21T16:54:47,334   adding 'scbamtools-0.6.dist-info/LICENSE'
2024-05-21T16:54:47,335   adding 'scbamtools-0.6.dist-info/METADATA'
2024-05-21T16:54:47,336   adding 'scbamtools-0.6.dist-info/WHEEL'
2024-05-21T16:54:47,337   adding 'scbamtools-0.6.dist-info/top_level.txt'
2024-05-21T16:54:47,338   adding 'scbamtools-0.6.dist-info/RECORD'
2024-05-21T16:54:47,369   removing build/bdist.linux-armv7l/wheel
2024-05-21T16:54:47,574   Building wheel for scbamtools (pyproject.toml): finished with status 'done'
2024-05-21T16:54:47,620   Created wheel for scbamtools: filename=scbamtools-0.6-cp39-cp39-linux_armv7l.whl size=1210426 sha256=404de3ce08ae3d71ac8cb8a1eb1765fd44623031d1c6dddf6ac18e89cd1599d9
2024-05-21T16:54:47,621   Stored in directory: /tmp/pip-ephem-wheel-cache-3g0b24sm/wheels/36/bd/63/f7d76eb512f86120613766d650def7087ead0040be79725ebf
2024-05-21T16:54:47,634 Successfully built scbamtools
2024-05-21T16:54:47,677 Removed build tracker: '/tmp/pip-build-tracker-nb5p834m'