2024-05-21T14:47:01,997 Created temporary directory: /tmp/pip-build-tracker-x4hb9f20 2024-05-21T14:47:01,998 Initialized build tracking at /tmp/pip-build-tracker-x4hb9f20 2024-05-21T14:47:01,999 Created build tracker: /tmp/pip-build-tracker-x4hb9f20 2024-05-21T14:47:01,999 Entered build tracker: /tmp/pip-build-tracker-x4hb9f20 2024-05-21T14:47:02,000 Created temporary directory: /tmp/pip-wheel-67c2jaui 2024-05-21T14:47:02,003 Created temporary directory: /tmp/pip-ephem-wheel-cache-sxd2a3jg 2024-05-21T14:47:02,027 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-21T14:47:02,030 2 location(s) to search for versions of scbamtools: 2024-05-21T14:47:02,030 * https://pypi.org/simple/scbamtools/ 2024-05-21T14:47:02,030 * https://www.piwheels.org/simple/scbamtools/ 2024-05-21T14:47:02,031 Fetching project page and analyzing links: https://pypi.org/simple/scbamtools/ 2024-05-21T14:47:02,032 Getting page https://pypi.org/simple/scbamtools/ 2024-05-21T14:47:02,034 Found index url https://pypi.org/simple/ 2024-05-21T14:47:02,246 Fetched page https://pypi.org/simple/scbamtools/ as application/vnd.pypi.simple.v1+json 2024-05-21T14:47:02,248 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 2024-05-21T14:47:02,249 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 2024-05-21T14:47:02,250 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 2024-05-21T14:47:02,251 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 2024-05-21T14:47:02,251 Fetching project page and analyzing links: https://www.piwheels.org/simple/scbamtools/ 2024-05-21T14:47:02,252 Getting page https://www.piwheels.org/simple/scbamtools/ 2024-05-21T14:47:02,253 Found index url https://www.piwheels.org/simple/ 2024-05-21T14:47:02,440 Fetched page https://www.piwheels.org/simple/scbamtools/ as text/html 2024-05-21T14:47:02,442 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) 2024-05-21T14:47:02,443 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) 2024-05-21T14:47:02,443 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) 2024-05-21T14:47:02,444 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) 2024-05-21T14:47:02,444 Skipping link: not a file: https://www.piwheels.org/simple/scbamtools/ 2024-05-21T14:47:02,445 Skipping link: not a file: https://pypi.org/simple/scbamtools/ 2024-05-21T14:47:02,464 Given no hashes to check 1 links for project 'scbamtools': discarding no candidates 2024-05-21T14:47:02,481 Collecting scbamtools==0.6 2024-05-21T14:47:02,484 Created temporary directory: /tmp/pip-unpack-qnis748c 2024-05-21T14:47:02,864 Downloading scbamtools-0.6.tar.gz (378 kB) 2024-05-21T14:47:03,100 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-x4hb9f20' 2024-05-21T14:47:03,107 Created temporary directory: /tmp/pip-build-env-_lpafd_l 2024-05-21T14:47:03,111 Installing build dependencies: started 2024-05-21T14:47:03,112 Running command pip subprocess to install build dependencies 2024-05-21T14:47:04,281 Using pip 24.0 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2024-05-21T14:47:04,777 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-21T14:47:06,584 Collecting setuptools>=65.5.1 2024-05-21T14:47:06,611 Using cached https://www.piwheels.org/simple/setuptools/setuptools-70.0.0-py3-none-any.whl (863 kB) 2024-05-21T14:47:06,855 Collecting wheel 2024-05-21T14:47:06,871 Using cached https://www.piwheels.org/simple/wheel/wheel-0.43.0-py3-none-any.whl (65 kB) 2024-05-21T14:47:08,089 Collecting cython>=3.0.8 2024-05-21T14:47:08,110 Using cached https://www.piwheels.org/simple/cython/Cython-3.0.10-cp311-cp311-linux_armv7l.whl (11.8 MB) 2024-05-21T14:47:09,126 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) 2024-05-21T14:47:09,130 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) 2024-05-21T14:47:09,134 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) 2024-05-21T14:47:09,137 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) 2024-05-21T14:47:09,141 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) 2024-05-21T14:47:09,452 Collecting numpy 2024-05-21T14:47:09,467 Using cached https://www.piwheels.org/simple/numpy/numpy-1.26.4-cp311-cp311-linux_armv7l.whl (5.6 MB) 2024-05-21T14:47:12,461 Installing collected packages: wheel, setuptools, numpy, cython 2024-05-21T14:47:12,690 Creating /tmp/pip-build-env-_lpafd_l/overlay/local/bin 2024-05-21T14:47:12,693 changing mode of /tmp/pip-build-env-_lpafd_l/overlay/local/bin/wheel to 755 2024-05-21T14:47:23,296 changing mode of /tmp/pip-build-env-_lpafd_l/overlay/local/bin/f2py to 755 2024-05-21T14:47:26,846 changing mode of /tmp/pip-build-env-_lpafd_l/overlay/local/bin/cygdb to 755 2024-05-21T14:47:26,848 changing mode of /tmp/pip-build-env-_lpafd_l/overlay/local/bin/cython to 755 2024-05-21T14:47:26,850 changing mode of /tmp/pip-build-env-_lpafd_l/overlay/local/bin/cythonize to 755 2024-05-21T14:47:26,884 Successfully installed cython-3.0.10 numpy-1.26.4 setuptools-70.0.0 wheel-0.43.0 2024-05-21T14:47:27,543 Installing build dependencies: finished with status 'done' 2024-05-21T14:47:27,546 Getting requirements to build wheel: started 2024-05-21T14:47:27,548 Running command Getting requirements to build wheel 2024-05-21T14:47:31,150 warning: scbamtools/cython/bctree.pyx:155:15: Assigning to 'bc_info_t *' from 'const bc_info_t *' discards const qualifier 2024-05-21T14:47:35,175 Compiling scbamtools/cython/kmers.pyx because it depends on /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-05-21T14:47:35,175 Compiling scbamtools/cython/bctree.pyx because it depends on /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/Cython/Includes/libc/string.pxd. 2024-05-21T14:47:35,176 [1/2] Cythonizing scbamtools/cython/bctree.pyx 2024-05-21T14:47:35,176 [2/2] Cythonizing scbamtools/cython/kmers.pyx 2024-05-21T14:47:35,334 /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2024-05-21T14:47:35,335 corresp(dist, value, root_dir) 2024-05-21T14:47:35,586 running egg_info 2024-05-21T14:47:35,596 writing scbamtools.egg-info/PKG-INFO 2024-05-21T14:47:35,599 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2024-05-21T14:47:35,600 writing requirements to scbamtools.egg-info/requires.txt 2024-05-21T14:47:35,602 writing top-level names to scbamtools.egg-info/top_level.txt 2024-05-21T14:47:35,625 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,626 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,626 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,626 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,627 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,628 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,628 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,629 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,629 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,630 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:35,631 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2024-05-21T14:47:35,634 reading manifest template 'MANIFEST.in' 2024-05-21T14:47:35,637 adding license file 'LICENSE' 2024-05-21T14:47:35,639 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2024-05-21T14:47:36,292 Getting requirements to build wheel: finished with status 'done' 2024-05-21T14:47:36,301 Created temporary directory: /tmp/pip-modern-metadata-6pp3wugw 2024-05-21T14:47:36,304 Preparing metadata (pyproject.toml): started 2024-05-21T14:47:36,305 Running command Preparing metadata (pyproject.toml) 2024-05-21T14:47:37,890 /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2024-05-21T14:47:37,890 corresp(dist, value, root_dir) 2024-05-21T14:47:38,126 running dist_info 2024-05-21T14:47:38,132 creating /tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info 2024-05-21T14:47:38,137 writing /tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info/PKG-INFO 2024-05-21T14:47:38,141 writing dependency_links to /tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info/dependency_links.txt 2024-05-21T14:47:38,142 writing requirements to /tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info/requires.txt 2024-05-21T14:47:38,144 writing top-level names to /tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info/top_level.txt 2024-05-21T14:47:38,145 writing manifest file '/tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info/SOURCES.txt' 2024-05-21T14:47:38,164 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,165 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,166 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,166 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,167 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,167 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,168 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,168 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,169 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,169 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:38,172 reading manifest file '/tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info/SOURCES.txt' 2024-05-21T14:47:38,174 reading manifest template 'MANIFEST.in' 2024-05-21T14:47:38,176 adding license file 'LICENSE' 2024-05-21T14:47:38,179 writing manifest file '/tmp/pip-modern-metadata-6pp3wugw/scbamtools.egg-info/SOURCES.txt' 2024-05-21T14:47:38,180 creating '/tmp/pip-modern-metadata-6pp3wugw/scbamtools-0.6.dist-info' 2024-05-21T14:47:38,404 Preparing metadata (pyproject.toml): finished with status 'done' 2024-05-21T14:47:38,408 Source in /tmp/pip-wheel-67c2jaui/scbamtools_f00cbd61d0384d3c9c9111e217bfac0f has version 0.6, which satisfies requirement scbamtools==0.6 from https://files.pythonhosted.org/packages/77/33/b3f2ccfca129f9a1135d936e8ad2030b88bef0e859bf281620d9af5d6b0c/scbamtools-0.6.tar.gz 2024-05-21T14:47:38,410 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-x4hb9f20' 2024-05-21T14:47:38,415 Created temporary directory: /tmp/pip-unpack-8pp9eof0 2024-05-21T14:47:38,417 Created temporary directory: /tmp/pip-unpack-1ey3mq3c 2024-05-21T14:47:38,422 Building wheels for collected packages: scbamtools 2024-05-21T14:47:38,426 Created temporary directory: /tmp/pip-wheel-koprz299 2024-05-21T14:47:38,427 Destination directory: /tmp/pip-wheel-koprz299 2024-05-21T14:47:38,429 Building wheel for scbamtools (pyproject.toml): started 2024-05-21T14:47:38,430 Running command Building wheel for scbamtools (pyproject.toml) 2024-05-21T14:47:39,950 /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:83: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2024-05-21T14:47:39,950 corresp(dist, value, root_dir) 2024-05-21T14:47:40,170 running bdist_wheel 2024-05-21T14:47:40,191 running build 2024-05-21T14:47:40,192 running build_py 2024-05-21T14:47:40,197 creating build 2024-05-21T14:47:40,198 creating build/lib.linux-armv7l-cpython-311 2024-05-21T14:47:40,198 creating build/lib.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,200 copying scbamtools/quant.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,202 copying scbamtools/annotation.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,205 copying scbamtools/bctree.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,207 copying scbamtools/contrib.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,208 copying scbamtools/gene_model.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,211 copying scbamtools/util.py -> build/lib.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,214 creating build/lib.linux-armv7l-cpython-311/scbamtools/bin 2024-05-21T14:47:40,215 copying scbamtools/bin/trim.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2024-05-21T14:47:40,217 copying scbamtools/bin/ann.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2024-05-21T14:47:40,219 copying scbamtools/bin/uBAM.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2024-05-21T14:47:40,221 copying scbamtools/bin/count.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2024-05-21T14:47:40,223 copying scbamtools/bin/BamTagHistogram.py -> build/lib.linux-armv7l-cpython-311/scbamtools/bin 2024-05-21T14:47:40,226 creating build/lib.linux-armv7l-cpython-311/scbamtools/config 2024-05-21T14:47:40,227 copying scbamtools/config/__init__.py -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2024-05-21T14:47:40,229 running egg_info 2024-05-21T14:47:40,233 writing scbamtools.egg-info/PKG-INFO 2024-05-21T14:47:40,236 writing dependency_links to scbamtools.egg-info/dependency_links.txt 2024-05-21T14:47:40,237 writing requirements to scbamtools.egg-info/requires.txt 2024-05-21T14:47:40,238 writing top-level names to scbamtools.egg-info/top_level.txt 2024-05-21T14:47:40,245 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,246 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,246 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,247 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,247 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,248 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,249 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,249 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,250 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,250 dependency /tmp/pip-build-env-_lpafd_l/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 2024-05-21T14:47:40,251 reading manifest file 'scbamtools.egg-info/SOURCES.txt' 2024-05-21T14:47:40,253 reading manifest template 'MANIFEST.in' 2024-05-21T14:47:40,255 adding license file 'LICENSE' 2024-05-21T14:47:40,258 writing manifest file 'scbamtools.egg-info/SOURCES.txt' 2024-05-21T14:47:40,261 creating build/lib.linux-armv7l-cpython-311/scbamtools/cython 2024-05-21T14:47:40,262 copying scbamtools/cython/bctree.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2024-05-21T14:47:40,292 copying scbamtools/cython/bctree.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2024-05-21T14:47:40,294 copying scbamtools/cython/kmers.c -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2024-05-21T14:47:40,315 copying scbamtools/cython/kmers.pyx -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2024-05-21T14:47:40,318 copying scbamtools/cython/types.pxd -> build/lib.linux-armv7l-cpython-311/scbamtools/cython 2024-05-21T14:47:40,320 copying scbamtools/config/default.yaml -> build/lib.linux-armv7l-cpython-311/scbamtools/config 2024-05-21T14:47:40,325 running build_ext 2024-05-21T14:47:40,334 building 'scbamtools.cython.kmers' extension 2024-05-21T14:47:40,335 creating build/temp.linux-armv7l-cpython-311 2024-05-21T14:47:40,336 creating build/temp.linux-armv7l-cpython-311/scbamtools 2024-05-21T14:47:40,337 creating build/temp.linux-armv7l-cpython-311/scbamtools/cython 2024-05-21T14:47:40,338 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-_lpafd_l/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 2024-05-21T14:47:40,727 In file included from /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-05-21T14:47:40,728 from /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-21T14:47:40,728 from /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-21T14:47:40,729 from scbamtools/cython/kmers.c:1249: 2024-05-21T14:47:40,729 /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-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] 2024-05-21T14:47:40,730 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-21T14:47:40,731 | ^~~~~~~ 2024-05-21T14:47:41,945 scbamtools/cython/kmers.c: In function ‘__Pyx_PyInt_AndObjC’: 2024-05-21T14:47:41,969 scbamtools/cython/kmers.c:28260:36: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2024-05-21T14:47:41,969 28260 | if ((intval & PyLong_MASK) == intval) { 2024-05-21T14:47:41,970 | ^~ 2024-05-21T14:47:41,993 scbamtools/cython/kmers.c:28262:71: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2024-05-21T14:47:41,994 28262 | long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1)); 2024-05-21T14:47:41,994 | ^~~~~~~~~~ 2024-05-21T14:48:08,387 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 2024-05-21T14:48:08,524 building 'scbamtools.cython.bctree' extension 2024-05-21T14:48:08,524 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-_lpafd_l/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 2024-05-21T14:48:08,905 In file included from /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 2024-05-21T14:48:08,906 from /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2024-05-21T14:48:08,907 from /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5, 2024-05-21T14:48:08,907 from scbamtools/cython/bctree.c:1249: 2024-05-21T14:48:08,908 /tmp/pip-build-env-_lpafd_l/overlay/local/lib/python3.11/dist-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] 2024-05-21T14:48:08,909 17 | #warning "Using deprecated NumPy API, disable it with " \ 2024-05-21T14:48:08,909 | ^~~~~~~ 2024-05-21T14:48:09,344 scbamtools/cython/bctree.c: In function ‘__pyx_f_10scbamtools_6cython_6bctree_check_contains’: 2024-05-21T14:48:09,363 scbamtools/cython/bctree.c:21807:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-05-21T14:48:09,364 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]) )))); 2024-05-21T14:48:09,365 | ^ 2024-05-21T14:48:10,140 scbamtools/cython/bctree.c: In function ‘__Pyx_PyInt_AndObjC’: 2024-05-21T14:48:10,164 scbamtools/cython/bctree.c:28268:36: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 2024-05-21T14:48:10,165 28268 | if ((intval & PyLong_MASK) == intval) { 2024-05-21T14:48:10,166 | ^~ 2024-05-21T14:48:10,189 scbamtools/cython/bctree.c:28270:71: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘long unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2024-05-21T14:48:10,190 28270 | long result = intval & (likely(__Pyx_PyLong_IsPos(op1)) ? last_digit : (PyLong_MASK - last_digit + 1)); 2024-05-21T14:48:10,190 | ^~~~~~~~~~ 2024-05-21T14:48:36,569 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 2024-05-21T14:48:36,721 installing to build/bdist.linux-armv7l/wheel 2024-05-21T14:48:36,722 running install 2024-05-21T14:48:36,745 running install_lib 2024-05-21T14:48:36,751 creating build/bdist.linux-armv7l 2024-05-21T14:48:36,752 creating build/bdist.linux-armv7l/wheel 2024-05-21T14:48:36,754 creating build/bdist.linux-armv7l/wheel/scbamtools 2024-05-21T14:48:36,755 creating build/bdist.linux-armv7l/wheel/scbamtools/bin 2024-05-21T14:48:36,756 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/trim.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin 2024-05-21T14:48:36,759 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/ann.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin 2024-05-21T14:48:36,761 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/uBAM.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin 2024-05-21T14:48:36,764 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/count.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin 2024-05-21T14:48:36,766 copying build/lib.linux-armv7l-cpython-311/scbamtools/bin/BamTagHistogram.py -> build/bdist.linux-armv7l/wheel/scbamtools/bin 2024-05-21T14:48:36,768 copying build/lib.linux-armv7l-cpython-311/scbamtools/quant.py -> build/bdist.linux-armv7l/wheel/scbamtools 2024-05-21T14:48:36,771 copying build/lib.linux-armv7l-cpython-311/scbamtools/annotation.py -> build/bdist.linux-armv7l/wheel/scbamtools 2024-05-21T14:48:36,774 copying build/lib.linux-armv7l-cpython-311/scbamtools/bctree.py -> build/bdist.linux-armv7l/wheel/scbamtools 2024-05-21T14:48:36,777 creating build/bdist.linux-armv7l/wheel/scbamtools/config 2024-05-21T14:48:36,778 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/default.yaml -> build/bdist.linux-armv7l/wheel/scbamtools/config 2024-05-21T14:48:36,780 copying build/lib.linux-armv7l-cpython-311/scbamtools/config/__init__.py -> build/bdist.linux-armv7l/wheel/scbamtools/config 2024-05-21T14:48:36,782 copying build/lib.linux-armv7l-cpython-311/scbamtools/contrib.py -> build/bdist.linux-armv7l/wheel/scbamtools 2024-05-21T14:48:36,784 creating build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,785 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,806 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.c -> build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,829 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,850 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.pyx -> build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,853 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/types.pxd -> build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,855 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/kmers.pyx -> build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,857 copying build/lib.linux-armv7l-cpython-311/scbamtools/cython/bctree.c -> build/bdist.linux-armv7l/wheel/scbamtools/cython 2024-05-21T14:48:36,882 copying build/lib.linux-armv7l-cpython-311/scbamtools/gene_model.py -> build/bdist.linux-armv7l/wheel/scbamtools 2024-05-21T14:48:36,885 copying build/lib.linux-armv7l-cpython-311/scbamtools/util.py -> build/bdist.linux-armv7l/wheel/scbamtools 2024-05-21T14:48:36,887 running install_egg_info 2024-05-21T14:48:36,891 Copying scbamtools.egg-info to build/bdist.linux-armv7l/wheel/scbamtools-0.6-py3.11.egg-info 2024-05-21T14:48:36,904 running install_scripts 2024-05-21T14:48:36,950 creating build/bdist.linux-armv7l/wheel/scbamtools-0.6.dist-info/WHEEL 2024-05-21T14:48:36,953 creating '/tmp/pip-wheel-koprz299/.tmp-y4nmpt08/scbamtools-0.6-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-21T14:48:36,958 adding 'scbamtools/annotation.py' 2024-05-21T14:48:36,960 adding 'scbamtools/bctree.py' 2024-05-21T14:48:36,961 adding 'scbamtools/contrib.py' 2024-05-21T14:48:36,965 adding 'scbamtools/gene_model.py' 2024-05-21T14:48:36,968 adding 'scbamtools/quant.py' 2024-05-21T14:48:36,969 adding 'scbamtools/util.py' 2024-05-21T14:48:36,972 adding 'scbamtools/bin/BamTagHistogram.py' 2024-05-21T14:48:36,973 adding 'scbamtools/bin/ann.py' 2024-05-21T14:48:36,976 adding 'scbamtools/bin/count.py' 2024-05-21T14:48:36,977 adding 'scbamtools/bin/trim.py' 2024-05-21T14:48:36,979 adding 'scbamtools/bin/uBAM.py' 2024-05-21T14:48:36,981 adding 'scbamtools/config/__init__.py' 2024-05-21T14:48:36,982 adding 'scbamtools/config/default.yaml' 2024-05-21T14:48:37,081 adding 'scbamtools/cython/bctree.c' 2024-05-21T14:48:37,314 adding 'scbamtools/cython/bctree.cpython-311-arm-linux-gnueabihf.so' 2024-05-21T14:48:37,321 adding 'scbamtools/cython/bctree.pyx' 2024-05-21T14:48:37,419 adding 'scbamtools/cython/kmers.c' 2024-05-21T14:48:37,652 adding 'scbamtools/cython/kmers.cpython-311-arm-linux-gnueabihf.so' 2024-05-21T14:48:37,659 adding 'scbamtools/cython/kmers.pyx' 2024-05-21T14:48:37,660 adding 'scbamtools/cython/types.pxd' 2024-05-21T14:48:37,662 adding 'scbamtools-0.6.dist-info/LICENSE' 2024-05-21T14:48:37,664 adding 'scbamtools-0.6.dist-info/METADATA' 2024-05-21T14:48:37,665 adding 'scbamtools-0.6.dist-info/WHEEL' 2024-05-21T14:48:37,666 adding 'scbamtools-0.6.dist-info/top_level.txt' 2024-05-21T14:48:37,666 adding 'scbamtools-0.6.dist-info/RECORD' 2024-05-21T14:48:37,682 removing build/bdist.linux-armv7l/wheel 2024-05-21T14:48:37,887 Building wheel for scbamtools (pyproject.toml): finished with status 'done' 2024-05-21T14:48:37,922 Created wheel for scbamtools: filename=scbamtools-0.6-cp311-cp311-linux_armv7l.whl size=1265830 sha256=9288a1e72295542d124c65f92013e3c61eedae50599500c2ac00821300907afb 2024-05-21T14:48:37,923 Stored in directory: /tmp/pip-ephem-wheel-cache-sxd2a3jg/wheels/db/b6/19/fa06cc943a7552b2b4732abc471c60765bc4e49563d312927c 2024-05-21T14:48:37,934 Successfully built scbamtools 2024-05-21T14:48:37,980 Removed build tracker: '/tmp/pip-build-tracker-x4hb9f20'